Academic literature on the topic 'Genetic correlation analysis'
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Journal articles on the topic "Genetic correlation analysis"
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Beck, Jeffrey J., René Pool, Margot van de Weijer, Xu Chen, Eva Krapohl, Scott D. Gordon, Marianne Nygaard, et al. "Genetic meta-analysis of twin birth weight shows high genetic correlation with singleton birth weight." Human Molecular Genetics 30, no. 19 (May 6, 2021): 1894–905. http://dx.doi.org/10.1093/hmg/ddab121.
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Abstract Birth weight (BW) is an important predictor of newborn survival and health and has associations with many adult health outcomes, including cardiometabolic disorders, autoimmune diseases and mental health. On average, twins have a lower BW than singletons as a result of a different pattern of fetal growth and shorter gestational duration. Therefore, investigations into the genetics of BW often exclude data from twins, leading to a reduction in sample size and remaining ambiguities concerning the genetic contribution to BW in twins. In this study, we carried out a genome-wide association meta-analysis of BW in 42 212 twin individuals and found a positive correlation of beta values (Pearson’s r = 0.66, 95% confidence interval [CI]: 0.47–0.77) with 150 previously reported genome-wide significant variants for singleton BW. We identified strong positive genetic correlations between BW in twins and numerous anthropometric traits, most notably with BW in singletons (genetic correlation [rg] = 0.92, 95% CI: 0.66–1.18). Genetic correlations of BW in twins with a series of health-related traits closely resembled those previously observed for BW in singletons. Polygenic scores constructed from a genome-wide association study on BW in the UK Biobank demonstrated strong predictive power in a target sample of Dutch twins and singletons. Together, our results indicate that a similar genetic architecture underlies BW in twins and singletons and that future genome-wide studies might benefit from including data from large twin registers.
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Wen, Yan, Feng Zhang, Xiancang Ma, Qianrui Fan, Wenyu Wang, Jiawen Xu, Feng Zhu, et al. "eQTLs Weighted Genetic Correlation Analysis Detected Brain Region Differences in Genetic Correlations for Complex Psychiatric Disorders." Schizophrenia Bulletin 45, no. 3 (June 15, 2018): 709–15. http://dx.doi.org/10.1093/schbul/sby080.
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Oliveira, Taniele Carvalho de, Marco Antonio Aparecido Barelli, Valvenarg Pereira da Silva, Rafhael Felipin Azevedo, Danilo de Lima Gonçalves, Paulo Ricardo Junges dos Santos, Juliana Parisotto Poletine, Carla Galbiati, and Flávio Dessaune Tardin. "Correlations between characters and path analysis in sweet sorghum (Sorghum bicolor (L.) Moench) genotypes for juice production." Australian Journal of Crop Science, no. 15(02):2021 (February 3, 2021): 290–96. http://dx.doi.org/10.21475/ajcs.21.15.02.p3083.
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Sweet sorghum presents stems with juice similar to that of sugar cane, rich in fermentable sugars, that may be used in off-season for sugar and ethanol production optimizing the sugar-ethanol sector. The objective of this work was to determine genetic correlations between characters and perform path analysis between juice volume and its components. Twenty-five sweet sorghum genotypes were evaluated in randomized blocks design with three repetitions and studied variables were: number of days to flowering; plant height; number of stems; weight of green mass; weight of dry mass; number of leaves; diameter of stems; volume of extracted juice and percentage of total soluble solids. In order to verify the existence of variability among the genotypes, data were subjected to variance analysis by F-test. Subsequently, genetic parameters were determined, as soon as genetic correlation estimator’s method, performed by t-test, to determine phenotypic correlation and bootstrap method for determining environmental and genetics correlation coefficient. Before performing path analysis a multicollinearity diagnosis was also conducted. The results of genetic correlation and path analysis point weight of green mass as the main variable influencing the juice volume, allowing these characters in indirect selection for increasing juice volume
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Skelly, Daniel A., Narayanan Raghupathy, Raymond F. Robledo, Joel H. Graber, and Elissa J. Chesler. "Reference Trait Analysis Reveals Correlations Between Gene Expression and Quantitative Traits in Disjoint Samples." Genetics 212, no. 3 (May 21, 2019): 919–29. http://dx.doi.org/10.1534/genetics.118.301865.
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Systems genetic analysis of complex traits involves the integrated analysis of genetic, genomic, and disease-related measures. However, these data are often collected separately across multiple study populations, rendering direct correlation of molecular features to complex traits impossible. Recent transcriptome-wide association studies (TWAS) have harnessed gene expression quantitative trait loci (eQTL) to associate unmeasured gene expression with a complex trait in genotyped individuals, but this approach relies primarily on strong eQTL. We propose a simple and powerful alternative strategy for correlating independently obtained sets of complex traits and molecular features. In contrast to TWAS, our approach gains precision by correlating complex traits through a common set of continuous phenotypes instead of genetic predictors, and can identify transcript–trait correlations for which the regulation is not genetic. In our approach, a set of multiple quantitative “reference” traits is measured across all individuals, while measures of the complex trait of interest and transcriptional profiles are obtained in disjoint subsamples. A conventional multivariate statistical method, canonical correlation analysis, is used to relate the reference traits and traits of interest to identify gene expression correlates. We evaluate power and sample size requirements of this methodology, as well as performance relative to other methods, via extensive simulation and analysis of a behavioral genetics experiment in 258 Diversity Outbred mice involving two independent sets of anxiety-related behaviors and hippocampal gene expression. After splitting the data set and hiding one set of anxiety-related traits in half the samples, we identified transcripts correlated with the hidden traits using the other set of anxiety-related traits and exploiting the highest canonical correlation (R = 0.69) between the trait data sets. We demonstrate that this approach outperforms TWAS in identifying associated transcripts. Together, these results demonstrate the validity, reliability, and power of reference trait analysis for identifying relations between complex traits and their molecular substrates.
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Motiar Roh, Md, A. S. M. Iqbal Hussain ., Md Saykhul Arifin ., Zerin Akhter ., and Mirza Hasanuzzaman . "Genetic Variability, Correlation and Path Analysis in Mungbean." Asian Journal of Plant Sciences 2, no. 17 (August 15, 2003): 1209–11. http://dx.doi.org/10.3923/ajps.2003.1209.1211.
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Werme, Josefin, Sophie van der Sluis, Danielle Posthuma, and Christiaan A. de Leeuw. "An integrated framework for local genetic correlation analysis." Nature Genetics 54, no. 3 (March 2022): 274–82. http://dx.doi.org/10.1038/s41588-022-01017-y.
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Ruiz del Río, N., J. M. Abelairas Gómez, F. J. Alonso García de la Rosa, J. M. Peralta Calvo, and A. de las Heras Martín. "Genetic analysis in retinoblastoma and peripheral blood correlation." Archivos de la Sociedad Española de Oftalmología (English Edition) 90, no. 12 (December 2015): 562–65. http://dx.doi.org/10.1016/j.oftale.2015.09.001.
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Mishra, Pragnyashree, A. K. Singh, and O. P. Singh. "Genetic variability, heritability, Genetic advance, correlation coefficient and path analysis in gladiolus." IOSR Journal of Agriculture and Veterinary Science 7, no. 7 (2014): 23–26. http://dx.doi.org/10.9790/2380-07722326.
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Ali, A., K. Javed, I. Zahoor, and K. M. Anjum. "Analysis of non-genetic and genetic influences underlying the growth of Kajli lambs." South African Journal of Animal Science 50, no. 4 (October 29, 2020): 613–25. http://dx.doi.org/10.4314/sajas.v50i4.13.
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Data on 2931 Kajli lambs, born from 2007 to 2018, were used to quantify environmental and genetic effects on growth performance of Kajli sheep. Traits considered for evaluation were birth weight (BWT), 120-day adjusted weight (120DWT), 180-day adjusted weight (180DWT), 270-day adjusted weight (270DWT), and 365-day adjusted weight (365DWT). Fixed effects of year of birth, season of birth, sex, birth type, and dam age on these traits were evaluated using linear procedures of SAS, 9.1. Similarly, BWT, 120DWT, 180DWT, and 270DWT were used as fixed effects mixed model analyses. Variance components, heritability and breeding values were estimated by restricted maximum likelihood. The genetic trend for each trait was obtained by regression of the estimated breeding values (EBV) on year of birth. Analyses revealed substantial influence of birth year on all traits. Sex and birth type were the significant sources of variation for BWT and 120DWT. Season of birth did not influence birth weight meaningfully, but had a significant role in the expression of 120DWT, 180DWT, and 270DWT. Heritability estimates were generally low (0.003 ± 0.018 to 0.099 ± 0.067) for all traits. With the exception of the genetic correlation of 180DWT and 365DWT, the genetic correlations between trait were strong and positive. Only 365DWT had a positive genetic trend. Although the heritability estimates for almost all weight traits were low, high and positive genetic correlations between BWT and other weight traits suggest that selection based on BWT would result in the improvement of other weight traits as a correlated response.Keywords: bodyweight, breeding value, genetic correlation, sheep
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Sharma, R. K., and K. Prasad. "Genetic divergence, correlation and path coefficient analysis in okra." Indian Journal of Agricultural Research 49, no. 1 (2015): 77. http://dx.doi.org/10.5958/0976-058x.2015.00011.6.
Full textDissertations / Theses on the topic "Genetic correlation analysis"
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Habib, Farhat Abbas. "Genotype-phenotype correlation using phylogenetic trees." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187297400.
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Albertsdóttir, Elsa. "Genetic analysis of competition traits in Icelandic horses /." Uppsala : Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/10360486.pdf.
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El, Nagar Ayman Gamal Fawzy. "Genetic analysis of longevity in specialized lines of rabbits." Doctoral thesis, Universitat Politècnica de València, 2015. http://hdl.handle.net/10251/52390.
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[EN] The global objective of the present thesis was to study the functional longevity defined as length of productive life (LPL) in five Spanish specialized lines of rabbit (A, V, H and LP). Chapter 3, aimed to check the genetic heterogeneity for longevity between the five lines estimating the additive variance and the corresponding effective heritabilities. As well as to test the genetic importance of time-dependent factors such as positive palpation order (OPP), physiological status (PS) and number of kits born alive (NBA) on the genetics of longevity. This point has been assessed using four different Cox proportional hazard models; the first one (Model 1) included all the previous factors in addition to the year-season effect, the inbreeding coefficient effect and finally the animal effect as random factor. The remaining three models were the same as Model 1 but excluding OPP (Model 2), or PS (Model 3), or NBA (Model 4). The complete data set comprised 15,670 does with records 35.6 % having censoring data, and the full pedigree file involved 19,405 animals. The heritability estimates for longevity in the five lines were low and ranged from 0.02±0.01 to 0.14±0.09, and consequently, it is not recommended to include this trait as selection criteria in rabbit breeding programs. Despite of the large variation of the heritability estimates, the corresponding HPD95% always overlapped and consequently the hypothesis of all lines having the same heritability cannot be discarded. Comparing the additive variance estimates of the four models, it was observed that by correcting for PS 51, 39, 38, 83 and 75% of the additive variance in lines A, V, H, LP and R, respectively, was removed. The risk of death or culling decreases as OPP advanced. Non-pregnant-non-lactating females are those under the higher risk. The does which had zero NBA had the highest risk, apart for this special figure (zero NBA) the risk decreased as NBA increased. Chapter 4 intended to estimate the genetic and environmental correlations between longevity and two prolificacy traits (number of kits born alive (NBA) and number of kits alive at weaning (NW)). Furthermore, to estimate the genetic and environmental correlations between longevity and the percentage of days that the doe spent in the different physiological statuses with respect to its entire productive life. The complete pedigree file comprised 19,405 animals. The datasets included records on 15,670 does which had 58,329 kindlings and 57,927 weanings. In general the genetic correlations between NBA and NW, and the hazard were low to very low, and the only line for which it can be said these genetic correlation to be different from zero was the LP line. Regarding the correlations between longevity and the percentage of days the doe spent in each physiological status, there were evidences of non-negligible genetic correlations between the two traits. Chapter 5 purposed to compare the five lines at their foundation and at fixed time periods during their selection programs. The first comparison was done at the origin of the lines, involving the complete data set, and using a genetic model (CM) including the additive values of the animals, so the effect of selection was considered. For the second comparison the same model as the first comparison was used, but excluding the additive effects from the model of analysis (IM), and involving only the data corresponding to each period, so the differences between the lines included the additive values of the animals. The lines V, H and LP showed at foundation a substantial superiority over line A. The line R had higher risk of death or culling with relevant differences when compared to V, H and LP lines. The maximum relative risks were observed between the lines LP and R (0.239), and between LP and A (0.317). For the comparisons at fixed times, the pattern of the differences between the A line and the others was similar to those observed at foundation.[ES] El objetivo global de la presente tesis fue estudiar la longevidad funcional en cinco líneas españolas de conejos (A, V, H y LP), el carácter se definió como la longitud de la vida productiva. En el Capítulo 3, dirigido a comprobar la heterogeneidad genética de la longevidad entre las 5 líneas, se estimaron las varianzas aditivas y sus correspondientes heredabilidades efectivas. Y además se evaluó la importancia del orden de la palpación positiva (OPP), el estado fisiológico (PS) y el número de gazapos nacidos vivos (NBA) sobre el determinismo genético de la longevidad. Para ello se utilizaron 4 modelos de Cox de riesgos proporcionales; el primer modelo (Modelo 1) incluyó todos los factores anteriores, además del efecto del año-estación, el efecto de la consanguinidad y, finalmente, el valor aditivo de los animales como efecto aleatorio. Los otros tres modelos fueron igual que el Modelo 1 pero excluyendo OPP (Modelo 2), o PS (Modelo 3), o NBA (Modelo 4). Los datos de longevidad estaban referidos a 15,670 conejas y tuvieron una tasa de censura de 35.6%. La genealogía completa involucró a 19,405 animales. Las estimas de heredabilidad efectiva para la longevidad en las 5 líneas fueron bajas y variaron de 0.02±0.01 a 0.14±0.09. A pesar de la gran variación de las estimas puntuales de heredabilidad, los correspondientes intervalos HPD95% siempre se solaparon y por lo tanto la hipótesis de que todas las líneas tengan la misma heredabilidad no pudo descartase. Se observó que la exclusión de PS incrementó la varianza aditiva aproximadamente, en un 51, 39, 38, 83 y 75% en las líneas A, V, H, LP y R, respectivamente. El riesgo de muerte o eliminación disminuía a medida que avanzaba el OPP, observándose el riesgo más alto durante los primeros dos partos, partos en los que las conejas todavía están creciendo lo que sería un factor de riesgo importante. El nivel No-Gestante-No-Lactante de PS tuvo el mayor riesgo. Este nivel se interpreta como indicador de baja fertilidad y/o problemas de salud de la coneja. Las conejas que tenían cero NBA tuvieron el mayor riesgo de muerte o eliminación, aunque para el resto de niveles de NBA se apreció una disminución del riesgo a medida que aumenta la prolificidad. En el capítulo 4, se estimaron las correlaciones genéticas y ambientales entre la longevidad y dos caracteres de prolificidad [número de gazapos nacidos vivos (NBA) y el número de destetados (NW)]. El fichero de datos incluyó 58,329 partos y 57,927 destetes. También se estimaron las correlaciones entre longevidad y el porcentaje de días que la coneja pasó en los diferentes estados fisiológicos con respecto a la totalidad de su vida productiva. La única línea para la que se puede decir que la correlación genética entre NBA o NW y el riesgo fue significativamente diferente de cero fue la línea LP. Hubo evidencias de correlaciones genéticas no despreciables entre la longevidad y el porcentaje de días que la hembra pasó en cada estado fisiológico los dos caracteres. En el capítulo 5 se compararon las longevidades medias de las 5 líneas en su fundación y en períodos de tiempo determinados. La comparación de las líneas en el origen, utilizó todos los datos y un modelo genético (CM) que incluía los valores aditivos de los animales. Para la comparación en tiempos fijos se utilizó el mismo modelo, pero excluyendo los efectos aditivos del modelo de análisis (IM), utilizando sólo los datos correspondientes a cada período, por lo que las diferencias entre las líneas incluían los cambios debidos a la selección. Las líneas V, H y LP mostraron una superioridad sustancial sobre las líneas A y R. Los riesgos relativos máximos se observaron entre las líneas LP y R (0.239), y entre LP y A (0.317). Con respecto a las comparaciones en tiempos fijos, el patrón de las diferencias entre la línea de A y las otras líneas fue similar a los observados en la fundación.
[CAT] L'objectiu global de la present tesi va ser estudiar la longevitat funcional en cinc línies espanyoles de conills (A, V, H i LP), el caràcter es va definir com la longitud de la vida productiva. Al Capítol 3, dirigit a comprovar l'heterogeneïtat genètica de la longevitat entre les 5 línies, es van estimar les variàncies additives i les seues corresponents heretabilitats efectives. A més a més, es va avaluar la importància de factors dependents del temps, com l'orde de la palpació positiva (OPP) , l'estat fisiològic (PS) i el nombre de llorigons nascuts vius (NBA) sobre el determinisme genètic de la longevitat. Per a això es van utilitzar 4 models de Cox de riscos proporcionals; el primer model (Model 1) va incloure tots els factors anteriorment assenyalats, a més de l'efecte de l'any-estació, l'efecte de la consanguinitat i, finalment, el valor additiu dels animals com a efecte aleatori. Els altres tres models van ser igual que el Model 1 però excloent l'OPP (Model 2) , o PS (Model 3) , o NBA (Model 4) . Les dades de longevitat estaven referides a 15,670 conilles i van tindre una taxa de censura de 35.6%. La genealogia completa va involucrar a 19,405 animals. Les estimes d'heretabilitat efectiva (Model 1) per a la longevitat en les 5 línies van ser baixes i van variar de 0.02±0.01 a 0.14±0.09. A pesar de la gran variació de les estimes puntuals d'heretabilitat, els corresponents intervals HPD95% sempre es van solapar i per tant la hipòtesi que totes les línies tinguen la mateixa heretabilitat no va poder descartar-se. Es va observar que l'exclusió de PS va incrementar la variància additiva, aproximadament, en un 51, 39, 38, 83 i 75% en les línies A, V, H, LP i R, respectivament. El risc de mort o eliminació disminuïa a mesura que avançava l'OPP, observant-se el risc més alt durant els primers dos parts, en què les conilles encara estan creixent el que seria un factor de risc important. El nivell No-Gestant-No-Lactant de PS va tindre el major risc en comparació amb els altres nivells. Les conilles que tenien zero NBA van tindre el major risc de mort o eliminació, encara que per a la resta de nivells de NBA es va apreciar una disminució del risc a mesura que augmentà la prolificitat. Al Capítol 4, es van estimar les correlacions genètiques i ambientals entre la longevitat i dos caràcters de prolificitat [nombre de llorigons nascuts vius (NBA) i el nombre de deslletats (NW)]. El fitxer de dades va incloure 58,329 parts i 57,927 deslletaments. L'única línia per a la que es pot dir que la correlació genètica entre NBA o NW i el risc va ser significativament diferent de zero va ser la línia LP. Evidències de correlacions genètiques no menyspreables entre longevitat i els percentatge de dies que la femella va passar en cada estat fisiològic. Al Capítol 5 es compararen les longevitats mitges de les 5 línies en la seua fundació i en períodes de temps determinats. Per a la comparació de les línies a l'origen, es van utilitzar totes les dades i un model genètic (CM) que incloïa els valors additius dels animals, per la qual cosa es va considerar l'efecte de la selecció a partir de la fundació. En la comparació en temps fixos se va utilitzar el mateix model que en l'anterior, però excloent els efectes additius del model d'anàlisi (IM), utilitzant només les dades corresponents a cada període, per la qual cosa les diferències entre les línies incloïen els canvis deguts a la selecció. Les línies V, H i LP van mostrar una superioritat substancial sobre les línies A i R. Els riscos relatius màxims es van observar entre les línies LP i R (0.239), i entre LP i A (0.317). Respecte a les comparacions en temps fixos, el patró de les diferències entre la línia de A i les altres línies va ser semblant als observats en la fundació.
El Nagar, AGF. (2015). Genetic analysis of longevity in specialized lines of rabbits [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52390
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Li, Fang Owens Kevin G. "Development of a genetic algorithm-correlation analysis (GA/CA) program for classification of chemical compounds using mass spectral data /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2803.
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Beyene, Yoseph Aydagn. "Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays L.) using molecular markers and morphological traits : implication for breeding and conservation." Thesis, University of Pretoria, 2005. http://hdl.handle.net/2263/30529.
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Knowledge of the genetic variation of crop collections is essential for their efficient use in plant breeding programs. The Ethiopian Highland Maize Germplasm Collection Mission was launched throughout the highlands of Ethiopia in 1998 and 287 traditional maize accessions were collected from farmers’ fields. To date, no information was available on the morphological and genetic diversity in this important collection. Various molecular marker techniques and quantitative genetics approaches were applied to accurately unravel the extent of phenotypic and genetic diversity, to study patterns of morphological and molecular variation and to determine association of molecular markers with quantitative trait variation, with the view of designing a sound breeding program and management strategy for maize in the highlands of Ethiopia. The morphological study confirmed that traditional Ethiopian highland maize accessions contain large amounts of variation for agro-morphological traits. The broad trait diversity observed among the accessions suggested ample opportunities for the genetic improvement of the crop through selection directly from the accessions and/ or the development of inbred lines for a future hybrid program. Selection practices followed by local farmers are mostly consistent within agroecology and gave rise to morphologically distinct maize accessions in different agroecologies. This underscores the importance of considering farmers’ knowledge of diversity in the collection and evaluation of local accessions. The results of amplified fragment length polymorphism (AFLP) and microsatellite or simple sequence repeat (SSR) marker analyses showed that bulking leaf samples from 15 individual plants per out-bred accession is an effective means of producing representative profiles of individual plants, thereby reducing the cost of DNA extraction and subsequent marker analysis of open-pollinated varieties. Cluster analyses based on AFLP and SSR data showed that most of the accessions collected from the Northern agroecology were genetically distinct from the Western and Southern accessions suggesting that differentiation for adaptive traits for drought conditions may have occurred in the Northern accessions. However, there was very little genetic differentiation between the Western and Southern accessions suggesting gene flow between the two agroecologies and recent introduction of similar improved varieties in these agroecoogies . In both marker systems, high mean genetic diversity was observed among the traditional Ethiopian highland maize accessions. This is possibly due to (i) the continuous introduction of maize from abroad by different organizations; (ii) genetic variation generated through farmers management practices; and (iii) the presence of different environmental conditions in the highlands of Ethiopia to which local landraces may have been adapted. The correlation between the morphological dissimilarity matrix and the matrices of genetic dissimilarity based on SSR and AFLP markers were 0.43 and 0.39, respectively (p = 0.001 in both cases). The correlation between SSR and AFLP dissimilarity matrices was 0.67 (p = 0.001). These significant correlations indicate that the three independent sets of data likely reflect the same pattern of genetic diversity, and validate the use of the data to calculate the different diversity statistics for Ethiopian highland maize accessions. From this study, three groups of maize accessions with distinctive genetic profiles and morphological traits were identified that will be useful for future collection, conservation and breeding programs of maize for the highlands of Ethiopia. A pilot association study using SSR markers and quantitative trait variation indicated that molecular markers could be useful to identify genetic factors controlling earliness, tallness, grain yield and associated traits, which could be exploited by various breeding schemes. The analytical tools outlined in this dissertation can be a useful tool in managing genetic variation of open-pollinated crops and will aid in the conservation of unique genetic diversity. Production stability and global food security are linked to the conservation and exploitation of worldwide genetic resources and this research attempts to add to that body of knowledge. Copyright 2005, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Beyene, YA 2005, Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays l.) using molecular markers and morphological traits : implication for breeding and conservation, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-02212006-112610 / >Thesis (PhD (Genetics))--University of Pretoria, 2005.
Genetics
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Wang, Liang. "Innovative damage assessment of steel truss bridges using modal strain energy correlation." Thesis, Queensland University of Technology, 2012. https://eprints.qut.edu.au/53177/1/Liang_Wang_Thesis.pdf.
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As a part of vital infrastructure and transportation network, bridge structures must function safely at all times. Bridges are designed to have a long life span. At any point in time, however, some bridges are aged. The ageing of bridge structures, given the rapidly growing demand of heavy and fast inter-city passages and continuous increase of freight transportation, would require diligence on bridge owners to ensure that the infrastructure is healthy at reasonable cost. In recent decades, a new technique, structural health monitoring (SHM), has emerged to meet this challenge. In this new engineering discipline, structural modal identification and damage detection have formed a vital component. Witnessed by an increasing number of publications is that the change in vibration characteristics is widely and deeply investigated to assess structural damage. Although a number of publications have addressed the feasibility of various methods through experimental verifications, few of them have focused on steel truss bridges. Finding a feasible vibration-based damage indicator for steel truss bridges and solving the difficulties in practical modal identification to support damage detection motivated this research project.
This research was to derive an innovative method to assess structural damage in steel truss bridges. First, it proposed a new damage indicator that relies on optimising the correlation between theoretical and measured modal strain energy. The optimisation is powered by a newly proposed multilayer genetic algorithm. In addition, a selection criterion for damage-sensitive modes has been studied to achieve more efficient and accurate damage detection results. Second, in order to support the proposed damage indicator, the research studied the applications of two state-of-the-art modal identification techniques by considering some practical difficulties: the limited instrumentation, the influence of environmental noise, the difficulties in finite element model updating, and the data selection problem in the output-only modal identification methods.
The numerical (by a planer truss model) and experimental (by a laboratory through truss bridge) verifications have proved the effectiveness and feasibility of the proposed damage detection scheme. The modal strain energy-based indicator was found to be sensitive to the damage in steel truss bridges with incomplete measurement. It has shown the damage indicator's potential in practical applications of steel truss bridges. Lastly, the achievement and limitation of this study, and lessons learnt from the modal analysis have been summarised.
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Alarcón, Sergio Arciniegas. "Imputação de dados em experimentos com interação genótipo por ambiente: uma aplicação a dados de algodão." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/11/11134/tde-11032009-150202/.
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Os experimentos multiambientes são um tipo especial dos experimentos bifatoriais, muito usados em melhoramento genético de plantas, nos quais algumas cultivares são avaliadas em diferentes locais. Geralmente nesses estudos se encontra uma resposta diferencial das cultivares em cada local que é chamada de interação genótipo x ambiente ou G x E, que é bem explicada por modelos de efeitos aditivos e interação multiplicativa (AMMI). Frequentemente os experimentos G x E podem ser desbalanceados e um ou vários genótipos não serem testados em alguns locais. Às vezes para o pesquisador recomendar os ambientes pode ser de interesse obter estimativas daquelas combinações genótipo ambiente que não foram testadas e tais estimativas podem ser calculadas explorando a informação inerente a aquelas combinações que foram atualmente obtidas. Além do interesse do pesquisador por essas estimativas, os da- dos ausentes podem causar alguma modificação na estimação tradicional dos parâmetros nos modelos AMMI, pois para estimar os parâmetros é necessário um processo sequencial fazendo uma análise de variância com uma posterior decomposição por valor singular da matriz de residuais, a qual não pode ser calculada se existir uma matriz de interação com dados faltantes. Para resolver esses problemas Bergamo (2007) e Bergamo et al. (2008) propuseram uma nova técnica através do uso de imputação múltipla livre de distribuição (IMLD) e é por essa razão que se decidiu avaliar o recente desenvolvimento comparando-o com algumas metodologias de imputação que têm sido usadas com sucesso nos experimentos G x E com dados ausentes como os mínimos quadrados alternados ALS(0), ALS(1) (CALINSKI et al., 1992) e estimativas robustas r-AMMI1 e r-AMMI2 (DENIS; BARIL, 1992). Assim, foi de- senvolvido um estudo de simulação baseado em uma matriz de dados reais genótipos (15) ambientes (27) do ensaio estadual de algodoeiro herbáceo 2000/01 (FARIAS, 2005), fazendo retiradas aleatórias de 10%, 20% e 30%, imputando os dados e comparando os métodos através da raiz quadrada da diferença preditiva média (RMSPD), a estatística de similari- dade de Procrustes e o coe
ciente de correlação não paramétrico de Spearman. Também foi feita uma análise sobre a escolha de componentes multiplicativos de um modelo AMMI quando se têm matrizes completadas (observados + imputados). Os resultados do estudo de simulação mostraram que segundo a distribuição da RMSPD padronizada, o método r- AMMI1 é o melhor, superando o IMLD. Entretanto, utilizando a estatística de Procrustes se encontrou que completando matrizes com ALS(0) se obtém a maior similaridade com relação à matriz de dados originais, também foi mostrado que os cinco métodos considerados têm uma alta correlação entre as imputações e os correspondentes dados reais. Finalmente, recomenda-se utilizar a imputação de dados para a estimação dos parâmetros de um modelo AMMI sob ocorrência de dados ausentes, mas para determinar o número de componentes multiplicativos é preferível tomar a decisão somente sobre a informação observada.The multienvironment trials are a special type of the two-factor experiments, widely used in genetic improvement of plants, where some cultivars are assessed in diferent locations. Generally, in these studies there is a di¤erential response of cultivars in each location that is called genotype environment interaction, or G x E, which is well explained by the additive main e¤ects and multiplicative interaction models (AMMI). Often the experiments GE may be unbalanced and one or several genotypes were not tested in some locations. Sometimes for the environments recommendations, the researcher may be interested in obtain estimates of those combinations G x E that were not tested and such estimates can be calcu- lated using the information of those combinations that were actually obtained. Additionally to the interest of the researchers in these estimates, the missing data may cause some pro- blems in the classical estimation of parameters in the AMMI models, because the parameter estimation need of a sequential process doing an analysis of variance followed by a singular value decomposition, which can not be calculated if there is a matrix of interaction with missing data. To solve these problems Bergamo (2007) and Bergamo et al. (2008) proposed a new technique using the distribution free multiple imputation (IMLD), and for this reason was decided to evaluate the recent development through the comparison with some methods of imputation that have been used successfully in experiments GE with missing data like the AMMI estimates based on alternating least squares ALS(0), ALS(1) (CALINSKI et al. 1992) and AMMI estimates with robust sub-model r-AMMI1 and r-AMMI2 (DENIS; BARIL, 1992). Thus, was developed a simulation study based on a matrix of true data genotypes (15) environments (27) of the upland cotton variety trials (ensaio estadual de algodoeiro her- báceo) 2000/01 (FARIAS, 2005), doing missed random (10%, 20%, 30%), imputing the data and comparing the methods through the root mean square predictive di¤erence (RMSPD) of the true value, the Procrustes statistic and the Spearman´s ranks correlation coe¢ cient. Also was made an analysis on the choice of the multiplicative components of an AMMI model after imputation on the complete data sets (observed + imputed). The results of the simulation study has shown that according to the distribution of RMSPD standardized, the r-AMMI1 method is better than the IMLD. However, using the Procrustes statistic was found that imputing data matrix with ALS(0), is obtained the greatest similarity related to the true data matrix. The ve methods considered show high correlation between the true and the imputed missing values. Finally, is recommended using the imputation data for the estimation of the parameters of an AMMI model under the presence of missing data, but for choosing the number of multiplicative terms is preferable take the decision only on the observed information.
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Saborío, Montero Alejandro. "Study of the Host Genetic Control over the Ruminal Microbiota and their Relationships with Methane Emissions in Dairy Cattle." Doctoral thesis, Universitat Politècnica de València, 2022. http://hdl.handle.net/10251/172633.
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Tesis por compendio[ES] El análisis del control genético del hospedador sobre su microbiota ha sido señalado recientemente como un tema prometedor en diferentes campos de estudio. La relación entre el holobionte hospedador-microbioma y los fenotipos en el ganado lechero podría conducir a nuevos conocimientos en los programas de selección genética. Dentro de esta tesis doctoral, se realizó la estimación y análisis a través de diferentes enfoques estadísticos con el objetivo de desentrañar el control genético del hospedador sobre la microbiota en ganado lechero. Además, se analizó el rasgo de concentración de metano como un fenotipo potencial para ser incluido en el programa de mejora de ganado lechero español. Mayor abundancia relativa de la mayoría de los eucariotas (principalmente protozoos ciliados y hongos) y algunas arqueas (Methanobrevibacter spp. Methanothermus spp. y Methanosphaera spp.) fueron factores de riesgo para ser clasificadas en la categoría alta. Se propuso un conjunto de modelos de ecuaciones estructurales (SEM) de tipo recursivo dentro de un marco de Cadenas de Markov Monte Carlo (MCMC) para analizar conjuntamente la relación hospedador-metagenoma-fenotipo. Se estableció un modelo bivariado no-recursivo como punto de referencia. La heredabilidad de CH4 se estimó en 0,12 ± 0,01 en ambos modelos, recursivo y no recursivo. Asimismo, las estimaciones de heredabilidad para la abundancia relativa de los taxones se superpusieron entre los modelos y variaron entre 0.08 y 0.48. Las correlaciones genéticas entre la composición microbiana y el CH4 variaron de -0,76 a 0,65 en el modelo bivariado no recursivo y de -0,68 a 0,69 en el modelo recursivo. Doce matrices de relación de microbiota (K) fueron construidas a partir de diferentes métricas de distancia del microbioma, con el objetivo de comparar su desempeño dentro de un marco de estimación de componentes de varianza para CH4 y toda la microbiota. Análisis de simulación (n = 1000) y datos reales fueron desarrollados considerando cuatro modelos posibles: un modelo genómico aditivo (GBLUP), un modelo de microbioma (MBLUP), un modelo de efectos genéticos y microbioma (HBLUP) y un modelo de efectos de interacción genético, microbioma y genético × microbioma (HiBLUP). Un nuevo término "Holobiabilidad" fue definido para referirse a la proporción de la varianza atribuible a los efectos del holobionte hospedador-microbioma. Las estimaciones a partir de datos reales usando HiBLUP variaron dependiendo de la K utilizada y estuvieron entre 0.15-0.17, 0.15-0.21 y 0.42-0.59 para heredabilidad, microbiabilidad y holobiabilidad, respectivamente. El conjunto de datos de microbioma fue agregado a través de análisis de componentes principales (PCA), en pocos componentes principales (PCs) que fueron utilizados como aproximaciones del metagenoma central. Parte de la variabilidad condensada en estos PC está controlada por el genoma de la vaca, con estimaciones de heredabilidad para el primer PC (PC1) de ~ 0,30 en todos los niveles taxonómicos, con una gran probabilidad (> 83%) de que la distribución posterior sea > 0,20 y con un intervalo de mayor densidad posterior al 95% (95% HPD) no conteniendo cero. La mayoría de las estimaciones de correlación genética entre PC1 y metano fueron grandes (>0,70) en todos los niveles taxonómicos, con la mayor parte de la distribución posterior (> 82%) siendo > 0,50 y con su 95% HPD no conteniendo cero. Estos resultados sugieren que todo el metagenoma del rumen regula recursivamente las emisiones de metano en las vacas lecheras, y que tanto el CH4 como las composiciones de la microbiota están parcialmente controladas por el genotipo del hospedador. Las variables agregadas (PC) propuestas podrían ser usadas en programas de mejora de animales para reducir las emisiones de metano en las generaciones futuras.
[CA] L'anàlisi del control genètic de l'hoste sobre la seva microbiota s'ha assenyalat recentment com un tema prometedor en diferents camps d'estudi. La relació entre el holobiont hoste-microbioma i els fenotips en bovins de llet podria conduir a nous coneixements en els programes de cria. Dins d'aquest doctorat es van realitzar tesis, estimacions i anàlisis mitjançant diferents enfocaments estadístics amb l'objectiu de desentranyar el control genètic de l'hoste sobre la microbiota en bestiar lleter. A més, es va analitzar el tret de concentració de metà com a fenotip potencial a incloure en el programa espanyol de cria de bestiar lleter. La major abundància relativa de la majoria dels eucariotes (principalment protozous i fongs ciliats) i algunes arquees (Methanobrevibacter spp. Methanothermus spp i Methanosphera spp.) Van ser factors de risc per classificar-se en les categories altes. Es va proposar un conjunt de models d'equacions estructurals (SEM) de tipus recursiu dins d'un marc de cadena Markov Monte Carlo (MCMC) per analitzar conjuntament la relació hoste-metagenoma-fenotip. Es van establir models no recursius com a referència. L'heretabilitat del CH4 es va estimar en 0,12 ± 0,01 en ambdós models, recursius i no recursius. De la mateixa manera, les estimacions d'heretabilitat de l'abundància relativa dels tàxons es van superposar entre models i van oscil·lar entre 0,08 i 0,48. Les correlacions genètiques entre la composició microbiana i el CH4 van oscil·lar entre -0,76 i 0,65 en els models bivariables no recursius i de -0,68 a 0,69 en els models recursius. Dotze matrius de relació de microbiota (K) de diferents mètriques de distància de microbiomes, amb l'objectiu de comparar el seu rendiment dins d'un marc d'estimació de components de variància per CH4 i anàlisi de microbiomes sencers en simulació (n = 1000, 25 rèpliques) i es van realitzar dades reals , considerant quatre possibles models: un model genòmic additiu (GBLUP), un model de microbioma (MBLUP), un model d'efectes genètics i microbiomes (HBLUP) i un model d'efectes d'interacció genètics, microbiomes i genètics × microbiomes (HiBLUP). Es va definir un nou terme "Holobiabilitat" per referir-se a la proporció de la variància fenotípica atribuïble als efectes holobiont del microbioma host. Les estimacions de dades reals mitjançant HiBLUP van variar en funció de la K utilitzada i van oscil·lar entre 0,15-0,17, 0,15-0,21 i 0,42-0,59 per heretabilitat, microbiabilitat i holobiabilitat, respectivament. El conjunt de dades de microbiomes es va agregar mitjançant l'anàlisi de components principals (PCA) en pocs components principals (PC) que es van utilitzar com a proxies del metagenoma principal. Part de la variabilitat condensada en aquestes PC està controlada pel genoma de la vaca, amb estimacions d'heretabilitat per a la primera PC (PC1) de ~ 0,30 a tots els nivells taxonòmics, amb una gran probabilitat (> 83%) de la distribució posterior> 0,20 i amb un 95% més alt interval de densitat posterior (95% HPD) que no conté zero. La majoria de les estimacions de correlació genètica entre PC1 i metà eren grans (>0,70) en tots els nivells taxonòmics, amb una gran part de la distribució posterior (> 82%)> 0,50 i amb un 95% de HPD que no contenia zero. Aquests resultats suggereixen que tot el metagenoma del rumen regula recursivament les emissions de metà en vaques lleteres i que tant el CH4 com les composicions de microbiota estan parcialment controlades pel genotip de l'hoste. Les variables agregades proposades (PC) es podrien utilitzar en programes de cria d'animals per reduir les emissions de metà en les generacions futures.
[EN] The analysis of the host genetic control over its microbiota has recently been pointed out as a promising theme in different fields of study. The relationship between the host-microbiome holobiont and phenotypes in dairy cattle could lead to new insights in breeding programs. Within this Ph.D. thesis, estimation and analysis through different statistical approaches were performed aiming to unravel the host genetic control over the microbiota in dairy cattle. Besides, methane concentration trait was analyzed as a potential phenotype to be included in the Spanish dairy cattle breeding program. Higher relative abundance of most eukaryotes (mainly ciliate protozoa and fungi) and some archaea (Methanobrevibacter spp. Methanothermus spp and Methanosphera spp.) were risk factors for being classified in the high categories. a set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed to jointly analyze the host-metagenome-phenotype relationship. Non-recursive models were set as benchmark. Heritability of CH4 was estimated at 0.12 ± 0.01 in both, the recursive and non-recursive, models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from -0.76 to 0.65 in the non-recursive bivariate models and from -0.68 to 0.69 in the recursive models. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the 7 genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. Twelve microbiota relationship matrices (K) from different microbiome distance metrics were built, aiming to compare its performance within a variance component estimation framework for CH4 and whole microbiome analysis on simulation (n = 1000, 25 replicates) and real data were performed, considering four possible models: an additive genomic model (GBLUP), a microbiome model (MBLUP), a genetic and microbiome effects model (HBLUP) and a genetic, microbiome and genetic × microbiome interaction effects model (HiBLUP). A new term "Holobiability" was defined to refer to the proportion of the phenotypic variance attributable to the host-microbiome holobiont effects. Estimates from real data using HiBLUP varied depending on the K used and ranged between 0.15-0.17, 0.15-0.21 and 0.42-0.59 for heritability, microbiability and holobiability, respectively. The microbiome dataset was aggregated through Principal Component Analysis (PCA) into few principal components (PCs) that were used as proxies of the core metagenome. Part of the variability condensed in these PCs is controlled by the cow genome, with heritability estimates for the first PC (PC1) of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being > 0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (>0.70) at all taxonomic levels, with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. These results suggest that rumen's whole metagenome recursively regulate methane emissions in dairy cows, and that both CH4 and the microbiota compositions are partially controlled by the host genotype. The purposed aggregated variables (PCs) could be used in animal breeding programs to reduce methane emissions in future generations.
This research was financed by RTA2015-00022-C03-02 (METALGEN) project from the national plan of research, development and innovation 2013-2020 and the Department of Economic Development and Competitiveness (Madrid, Spain). We thank the regional Holstein Associations and farmers collaborating in the project. Computational support from the High-Performance Computing Centre in Galicia (Spain) is acknowledged. Alejandro Saborío-Montero acknowledges the scholarship from Universidad de Costa Rica for his doctorate studies which partially conducted to the progress of this study.
Saborío Montero, A. (2021). Study of the Host Genetic Control over the Ruminal Microbiota and their Relationships with Methane Emissions in Dairy Cattle [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172633
TESIS
Compendio
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Garcia, Marisol Peña. "Análise dos modelos AMMI bivariados." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/11/11134/tde-11022009-080418/.
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E comum encontrar nos ensaios experimentais a analise de dois fatores, cada um com diferente numero de níveis, eles proporcionam uma tabela de dados de dupla entrada. Geralmente a analise destes dados e feita através da analise de variância - ANOVA, cumprindo algumas pressuposições básicas do modelo, mas ha outros estudos nos quais e de grande importância a interação, como e o caso dos estudos de melhoramento genético, em que o objetivo e selecionar genótipos com ótimos desempenhos em diferentes ambientes. A pouca eficiência na analise da interação dos genótipos com os ambientes (GE) da ANOVA pode representar um problema aos melhoristas, que devem tirar proveito dessa interação para os seus estudos. Os modelos aditivos com interação multiplicativa - AMMI, traz vantagens na seleção de genótipos quando comparados com métodos convencionais, pois proporcionam uma melhor analise da interação (GE), alem de permitir combinar componentes aditivos e multiplicativos em um mesmo modelo; estes modelos tem demonstrado ser eficientes na analise quando se tem apenas uma variável resposta, mas quando há mais de uma, ainda n~ao existe um procedimento geral para realizar a analise. O presente trabalho propõe uma metodologia de analise quando se têm modelos AMMI bivariados, realizando analises individuais das variáveis respostas seguidas de uma analise de procrustes, que permite fazer comparações dos resultados obtidos nas analises individuais e finalmente uma confirmação destes resultados através da analise multivariada de variância - MANOVA. Os resultados obtidos permitem concluir que a analises AMMI e procrustes proporcionam uma boa alternativa de analise para os modelos AMMI bivariados.Is frequently nd in the studies the two way factor analysis, each factor with dierent number of levels, they conform a two way table of data, generally the analysis of the data is made with the analysis of variance - ANOVA, satisfying some assumptions, but there are some studies in which is very important the interaction, like the case of the improvement studies, where the objetive is select genotypes with optimum performance in dierents environments. The poor eciency in the genotypes and environment interaction (GE) analysis of the ANOVA can represents a problem for the researchers, that need to take advantage of the interaction. The additive main eects and multiplicative interactions model - AMMI, give advantages in the selection of genotypes when is compare with traditional methods, because give a better interaction (GE) analysis, also permit combine additive and multiplicative components in the same model, these models have demonstrated be ecient in the analysis with just one response variable but when there is more than one there is not a clear procedure to do the analysis. This work presents a analysis methodology for the bivariate AMMI models, doing individuals analysis in the response variables follow by the procrustes, which permit compare the results of the individuals analysis, and nally a conrmation of theses results with the multivariate analysis of variance - MANOVA. From the results can be concluded that the AMMI and the procrustes analysis give a good alternative for the bivariate AMMI models analysis.
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Leite, Carla Daniela Suguimoto [UNESP]. "Efeitos genéticos e ambientais sobre o intervalo desmame-cio em fêmeas suínas." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/92600.
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A seleção baseada em características reprodutivas tem sido muito empregada em programas de melhoramento genético de suíno. Assim, objetivaram-se avaliar os efeitos ambientais e genéticos que influenciam o intervalo desmame-cio (IDC) e verificar sua influência no número de nascidos total (TL), nascidos vivos (NV) e mortos (NM) em fêmeas suínas. Para análise dos efeitos ambientais, utilizaram-se 8.104 dados da 1ª a 6ª ordem de parição, e, para as estimativas dos parâmetros genéticos, apenas as informações do 1º ao 3º IDC, o que resultou em 6.548 observações, que foram analisadas pelo método REML, utilizando-se modelos uni e multicaracterística. Para este último, considerou-se cada IDC (1º, 2º e 3º) como uma característica distinta. Avaliaram-se, também, as correlações genéticas entre o IDC, TL, NM e idade ao primeiro parto (IPP). Para os fatores ambientais, o modelo incluiu como efeitos fixos rebanho, linhagem, ano (AP) e estação (EP) de parto, e as covariáveis idade da porca ao parto (IDPP), TL e duração da lactação (DL). A DL, na forma linear, e a IDPP, na forma quadrática, influenciaram o IDC. Rebanho, AP e EP foram fontes de variação significativas, enquanto TL e linhagem não o foram. Não foi observada influência do IDC sobre TL, NV, nem sobre NM. A herdabilidade estimada para o IDC pelo modelo de repetibilidade foi baixa. As correlações genéticas entre os IDC (1º, 2º e 3º) foram de moderada a baixa magnitude, evidenciando que o modelo multicaracterística é mais indicado para as estimativas de parâmetro genético nessa população. As correlações genéticas entre IDC, TL e NM, assim como IDC e IPP foram favoráveis à seleção.
Selection for reproductive traits has been largely used in swine breeding programs. The aims of this study were to evaluate environmental and genetic effects that affect the weaning-to-estrus interval (WEI) in sows and to assess their influence on litter size (LS), number of live born (LP) and dead born piglets (DP). Data consisting of 8,104 WEI from the 1st to 6th farrowing recorded in two herds were used for environmental analysis, but for estimating the genetic parameters only data from the 1st to 3rd farrowing were used, totalling 6,548 records. Genetic analysis was performed using the REML method with single and multitrait models, where each WEI was considered as a different trait. Genetic correlations among WEI, LS, DP and age at first farrowing (AFF) were also estimated using a multitrait model. For the environmental analysis, the model included as fixed effects the herd, line, and year (YF) and season (SF) of farrowing, and as covariates the sow’s age at farrowing (SAF), LS, and lactation length (LL). The effects were linear for LL and quadratic for SAF. The herd, YF and SF were important sources of variation, whereas LS and line were not significant. There were no effects of WEI on the litter traits (LS, LP and DP). The heritability estimated for WEI was low, and genetic correlations among its different intervals were of moderate to low magnitude, evidencing that a multitrait model was more indicated for estimating the genetic parameters for this trait in this population. The genetic correlations between WEI and LS, DP and AFF would be favourable in a selection.
Books on the topic "Genetic correlation analysis"
1
Coimbra, João. Torre de Babel e Monte Sinai: modelos de exegese do Antigo Testamento. Brazil Publishing, 2022. http://dx.doi.org/10.31012/978-65-5861-755-6.
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“Tower of Babel and Mount Sinai: Old Testament models of biblical exegesis” is an in-depth study in Genesis 11: 1-9 and Exodus 20: 1-6. An excellent tool for those who want to know and practice the principles of Bible interpretation. The exegesis model follows three fundamental principles: literary analysis, contextual analysis and theological analysis. In literary analysis we work with the delimitation, translation of the text, comparison of versions, the structure and literary genre. In the contextual analysis we emphasize the oral tradition, the literary context of Genesis and an analysis of the socio-historical context. Three approaches were made, regarding the literary formation process, about the environment in which the text was generated and regarding the socio-historical context. In the theological analysis, the study of the correlation of the text, the analysis of the theological content and the practical context for life were carried out. In the first part, we try to answer: To what extent can one accept the text of Genesis 11.1-9 literally? How to harmonize the text with the evident phases in the process of natural language, oral and written tradition? The origin of the languages occurs at the event recorded in Genesis 11? Can the biblical event of the “Tower of Babel” be indicated as the basis for the branching out of multiple languages? Can one defend a linguistic monogenism without considering religion as an included source? Among others. In the second part, the objective is to explain the origin and the importance of monotheism for Christianity based on the exegetical research of Exodus 20.1-6. The main issue is related to the literary, historical and theological relevance to the Christian faith.
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Del Giudice, Marco. Evolutionary Psychopathology. Oxford University Press, 2018. http://dx.doi.org/10.1093/med-psych/9780190246846.001.0001.
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This book presents a unified approach to evolutionary psychopathology, and advances an integrative framework for the analysis and classification of mental disorders based on the concepts of life history theory. The framework does not aim to replace existing evolutionary models of specific disorders—which are reviewed and critically discussed in the book—but to connect them in a broader perspective and explain the large-scale patterns of risk and comorbidity that characterize psychopathology. The life history framework permits a seamless integration of mental disorders with normative individual differences in personality and cognition, and offers new conceptual tools for the analysis of developmental, genetic, and neurobiological data. The concepts synthesized in the book are used to derive a new taxonomy of mental disorders, the fast-slow-defense (FSD) model. The FSD model is the first classification system explicitly based on evolutionary concepts, a biologically grounded alternative to transdiagnostic models based on empirical correlations between symptoms. The book reviews a wide range of common mental disorders, discusses their classification in the FSD model, and identifies functional subtypes within existing diagnostic categories.
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Zucker, Robert A., and Sandra A. Brown, eds. The Oxford Handbook of Adolescent Substance Abuse. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199735662.001.0001.
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This Handbook explores the origins, development, and course of substance use as it emerges and unfolds in adolescence. Given the large causal network involved in adolescent substance use and abuse as well as its powerful impact, both at the time of use and in terms of the long term outcomes and complications of use, the domains covered by this volume range from infancy to adulthood, and from molecular genetics to social policy. The book is organized into eight sections, beginning with a review of the conceptual framework. It explains why a developmental framework is essential in understanding the adolescent period and goes on to discuss the epidemiology of substance use and abuse. It then examines the similarities and differences among the different drugs of abuse, namely: nicotine, alcohol, marijuana, prescription drugs, and other illicit drugs. The remaining sections deal with etiology and course in the context of adolescent development; the correlation between developmental tasks and adolescent substance abuse; clinical symptomatology and comorbidity; and the different assessment and intervention methods that have been developed to address the problem of adolescent alcohol and other drug abuse. These interventions include targeted prevention approaches, family-based treatments, twelve-step approaches, and inpatient and outpatient models. The book concludes with a chapter that analyzes the multi-level structure of public policy for the prevention of alcohol, tobacco, and drug problems among the youth.
Book chapters on the topic "Genetic correlation analysis"
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Ahmad Dar, Mayasar, and Deepmala Sharma. "Revisiting the Genomics and Genetic Codes Using Walsh-Hadamard Spectrum Analysis." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 106–13. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_11.
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AbstractWalsh-Hadamard spectrum is widely used in the field of science and technology like classification of cancer cells, image processing, speech processing, signal and image compression etc. In this paper, a genomic analysis using Walsh-Hadamard spectrum and cross-correlation has been done. Transformation of genetic code using Walsh-Hadamard spectrum has been given. We redefine the Walsh-Hadamard spectrum in genomics and analyse the origin of mRNA features by using this spectra. Finally, using Walsh-Hadamard spectrum the overall energy of the mRNA sequence has been evaluated.
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Deych, Elena, Robert Culverhouse, and William D. Shannon. "Microarray Dimension Reduction Based on Maximizing Mantel Correlation Coefficients Using a Genetic Algorithm Search Strategy." In Studies in Classification, Data Analysis, and Knowledge Organization, 49–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-10745-0_5.
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Bhagya Lakshmi, Nandipati, Nagaraju Devarakonda, Zdzislaw Polkowski, and Anusha Papasani. "A Quick Dynamic Attribute Subset Method for High Dimensional Data Using Correlation-Guided Cluster Analysis and Genetic Algorithm." In Advances in Intelligent Systems and Computing, 395–408. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-0475-2_35.
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Simm, Geoff, Geoff Pollott, Raphael Mrode, Ross Houston, and Karen Marshall. "Analysing genetic variation in farm animals." In Genetic improvement of farmed animals, 178–92. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789241723.0178.
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Abstract In this chapter, topics focused on how to quantify the extent to which genes affect measured traits and how to use this information in breeding programmes. Highlights include: estimating heritability; estimating non-additive parameters, correlations, and genotype by environment interactions, molecular genetics and trait variations; and calculating inbreeding using SNP markers.
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Du, Lei, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Heng Huang, Mark Inlow, Jason H. Moore, Andrew J. Saykin, Li Shen, and [Authorinst]for the Alzheimer’s Dis Initiative. "GN-SCCA: GraphNet Based Sparse Canonical Correlation Analysis for Brain Imaging Genetics." In Brain Informatics and Health, 275–84. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-23344-4_27.
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Forseth, Ry R., and Frank C. Schroeder. "Correlating Secondary Metabolite Production with Genetic Changes Using Differential Analysis of 2D NMR Spectra." In Fungal Secondary Metabolism, 207–19. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-122-6_15.
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Loosen, Simon, Matthias Meinke, and Wolfgang Schröder. "Numerical Analysis of the Turbulent Wake for a Generic Space Launcher with a Dual-Bell Nozzle." In Notes on Numerical Fluid Mechanics and Multidisciplinary Design, 163–77. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-53847-7_10.
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Abstract The turbulent wake of an axisymmetric generic space launcher equipped with a dual-bell nozzle is simulated at transonic ($$Ma_\infty = 0.8$$ and $$Re_D = 4.3\cdot 10^5$$) and supersonic ($$Ma_\infty = 3$$ and $$Re_D = 1.2\cdot 10^6$$) freestream conditions, to investigate the influence of the dual-bell nozzle jet onto the wake flow and vice versa. In addition, flow control by means of four in circumferential direction equally distributed jets injecting air encountering the backflow in the recirculation region is utilized to determine if the coherence of the wake and consequently, the buffet loads can be reduced by flow control. The simulations are performed using a zonal RANS/LES approach. The time-resolved flow field data are analyzed by classical spectral analysis, two-point correlation analysis, and dynamic mode decomposition (DMD). At supersonic freestream conditions, the nozzle counter pressure is reduced by the expansion of the outer flow around the nozzle lip leading to a decreased transition nozzle pressure ratio. In the transonic configuration a spatio-temporal mode with an eigenvalue matching the characteristic buffet frequency of $$Sr_D=0.2$$ is extracted by the spectral and DMD analysis. The spatial shape of the detected mode describes an antisymmetric wave-like undulating motion of the shear layer inducing the low frequency dynamic buffet loads. By flow control this antisymmetric coherent motion is weakened leading to a reduction of the buffet loads on the nozzle fairing.
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Hötte, Felix, Oliver Günther, Christoph von Sethe, Matthias Haupt, Peter Scholz, and Michael Rohdenburg. "Lifetime Experiments of Regeneratively Cooled Rocket Combustion Chambers and PIV Measurements in a High Aspect Ratio Cooling Duct." In Notes on Numerical Fluid Mechanics and Multidisciplinary Design, 279–93. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-53847-7_18.
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Abstract This paper aims at experimental investigations of the life limiting mechanisms of regeneratively cooled rocket combustion chambers, especially the so called doghouse effect. In this paper the set up of a cyclic thermo-mechanical fatigue experiment and its results are shown. This experiment has an actively cooled fatigue specimen that is mounted downstream of a subscale GOX-GCH$$_{\text {4}}$$ combustion chamber with rectangular cross section. The specimen is loaded cyclically and inspected after each cycle. The effects of roughness, the use of thermal barrier coatings, the length of the hot gas phase, the oxygen/fuel ratio and the hot gas pressure are shown. In a second experiment the flow in a generic high aspect ratio cooling duct is measured with the Particle Image Velocimetry (PIV) to characterize the basic flow. The main focus of the analysis is on the different recording and processing parameters of the PIV method. Based on this analysis a laser pulse interval and the window size for auto correlation is chosen. Also the repeatability of the measurements is demonstrated. These results are the starting point for future measurements on the roughness effect on heat transfer and pressure loss in a high aspect ratio cooling duct.
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Pandey, H. K., S. K. Srivastava, and Prashant Pandey. "Petro-Geochemical Analysis and Their Correlation for Genesis of Fluoride Contamination in Groundwater of District Sonbhadra, U.P., India." In Springer Hydrogeology, 61–79. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-4552-3_5.
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Nordberg, Ana. "Biobank and Biomedical Research: Responsibilities of Controllers and Processors Under the EU General Data Protection Regulation." In GDPR and Biobanking, 61–89. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-49388-2_5.
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AbstractBiobanks are essential infrastructures in current health and biomedical research. Advanced scientific research increasingly relies on processing and correlating large amounts of genetic, clinical and behavioural data. These data are particularly sensitive in nature and the risk of privacy invasion and misuse is high. The EU General Data Protection Regulation (GDPR) developed and increased harmonisation, resulting in a framework in which the specific duties and obligations of entities processing personal data—controllers and processors—were defined. Biobanks, in the exercise of their functions, assume the role of controllers and/or processors and as such need to comply with a number of complex rules. This chapter analyses these rules in the light of Article 89 GDPR, which creates safeguards and derogations relating to ‘processing for archiving purposes in the public interest, scientific or historical research purposes or statistical purposes’. It identifies key compliance challenges faced by biobanks as data controllers and processors, such as determining whether the GDPR is applicable and its intersection with other regulations; when a biobank should be considered controller and processor; and what are the main duties of biobanks as data controllers and processors and options for compliance.
Conference papers on the topic "Genetic correlation analysis"
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Liefooghe, Arnaud, and Bilel Derbel. "A Correlation Analysis of Set Quality Indicator Values in Multiobjective Optimization." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908812.2908906.
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Liu, Yang, Xiaojun Bai, and Xiaofeng Kang. "Analysis and Study of the Correlation of Genetic Loci." In 2016 6th International Conference on Mechatronics, Computer and Education Informationization (MCEI 2016). Paris, France: Atlantis Press, 2016. http://dx.doi.org/10.2991/mcei-16.2016.237.
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Sun, Shaofei, Hongxin Zhang, Weijun Cheng, Liang Dong, Yang Wang, and Xiaotong Cui. "An Improved Correlation Electromagnetic Analysis Based On Genetic Algorithm Optimization." In 2019 International Workshop on Electromagnetics: Applications and Student Innovation Competition (iWEM). IEEE, 2019. http://dx.doi.org/10.1109/iwem.2019.8887920.
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Bhuva, Meha, Richard Sandford, and William Griffiths. "O01 Genetic analysis and phenotypic correlation in ductal plate malformation." In Abstracts of the British Association for the Study of the Liver Annual Meeting, 22–24 November 2021. BMJ Publishing Group Ltd and British Society of Gastroenterology, 2021. http://dx.doi.org/10.1136/gutjnl-2021-basl.1.
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Boutte, David, and Jingyu Liu. "Sparse canonical correlation analysis applied to fMRI and genetic data fusion." In 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2010. http://dx.doi.org/10.1109/bibm.2010.5706603.
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Ching-Roa, Vincent Ralph D., Songfeng Han, Jingxuan Ren, Gabriel A. Ramirez, Seung Hyun Kim, and Regine Choe. "Diffuse Correlation Tomography Geometry Optimization with Genetic Algorithm Using Singular Value Analysis." In Clinical and Translational Biophotonics. Washington, D.C.: OSA, 2018. http://dx.doi.org/10.1364/translational.2018.jw3a.22.
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Lin, Dongdong, Jigang Zhang, Jingyao Li, Vince Calhoun, and Yu-Ping Wang. "Identifying genetic connections with brain functions in schizophrenia using group sparse canonical correlation analysis." In 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI 2013). IEEE, 2013. http://dx.doi.org/10.1109/isbi.2013.6556466.
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Mingon Kang, Baoju Zhang, Xiaoyong Wu, Chunyu Liu, and Jean Gao. "Sparse generalized canonical correlation analysis for biological model integration: A genetic study of psychiatric disorders." In 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2013. http://dx.doi.org/10.1109/embc.2013.6609794.
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Pacheco-Vega, Arturo, Mihir Sen, K. T. Yang, and Rodney L. McClain. "Correlations of Fin-Tube Heat Exchanger Performance Data Using Genetic Algorithms, Simulated Annealing and Interval Methods." In ASME 2001 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/imece2001/htd-24296.
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Abstract We consider the prediction of the performance of an air-water fin-tube compact heat exchanger using correlations of the power-law type. Measurements of the in-tube and over-tube mass flow rates, inlet temperatures and heat transfer rates, with water as the in-tube fluid and air as the over-tube fluid, are used to show that a regression analysis for the best-fit correlation of a prescribed form does not provide a unique answer in the heat rate predictions and that a global, rather than a local, search for the best correlation should be conducted. To this end, we propose the application of three different global optimization techniques to find the constants in a prescribed correlating function which can then be used to predict the performance of this heat exchanger under different operating conditions. Comparisons of the different results are then made to determine the relative advantages and disadvantages among the methods in terms of efficiency, accuracy and certainty of the results. Every method is found to have advantages over the others, and the results demonstrate that all three techniques are able to predict well the performance of this heat exchanger.
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Sha, Jiahang, Jingxuan Bao, Kefei Liu, Shu Yang, Zixuan Wen, Yuhan Cui, Junhao Wen, et al. "Preference Matrix Guided Sparse Canonical Correlation Analysis for Genetic Study of Quantitative Traits in Alzheimer’s Disease." In 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2022. http://dx.doi.org/10.1109/bibm55620.2022.9995342.
Full textReports on the topic "Genetic correlation analysis"
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Zhang, Hongbin B., David J. Bonfil, and Shahal Abbo. Genomics Tools for Legume Agronomic Gene Mapping and Cloning, and Genome Analysis: Chickpea as a Model. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7586464.bard.
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The goals of this project were to develop essential genomic tools for modern chickpea genetics and genomics research, map the genes and quantitative traits of importance to chickpea production and generate DNA markers that are well-suited for enhanced chickpea germplasm analysis and breeding. To achieve these research goals, we proposed the following research objectives in this period of the project: 1) Develop an ordered BAC library with an average insert size of 150 - 200 kb (USA); 2) Develop 300 simple sequence repeat (SSR) markers with an aid of the BAC library (USA); 3) Develop SSR marker tags for Ascochyta response, flowering date and grain weight (USA); 4) Develop a molecular genetic map consisting of at least 200 SSR markers (Israel and USA); 5) Map genes and QTLs most important to chickpea production in the U.S. and Israel: Ascochyta response, flowering and seed set date, grain weight, and grain yield under extreme dryland conditions (Israel); and 6) Determine the genetic correlation between the above four traits (Israel). Chickpea is the third most important pulse crop in the world and ranks the first in the Middle East. Chickpea seeds are a good source of plant protein (12.4-31.5%) and carbohydrates (52.4-70.9%). Although it has been demonstrated in other major crops that the modern genetics and genomics research is essential to enhance our capacity for crop genetic improvement and breeding, little work was pursued in these research areas for chickpea. It was absent in resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. For instance, there were no large-insert BAC and BIBAC libraries, no sufficient and user- friendly DNA markers, and no intraspecific genetic map. Grain sizes, flowering time and Ascochyta response are three main constraints to chickpea production in drylands. Combination of large seeds, early flowering time and Ascochyta blight resistance is desirable and of significance for further genetic improvement of chickpea. However, it was unknown how many genes and/or loci contribute to each of the traits and what correlations occur among them, making breeders difficult to combine these desirable traits. In this period of the project, we developed the resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. In particular, we constructed the proposed large-insert BAC library and an additional plant-transformation-competent BIBAC library from an Israeli advanced chickpea cultivar, Hadas. The BAC library contains 30,720 clones and has an average insert size of 151 kb, equivalent to 6.3 x chickpea haploid genomes. The BIBAC library contains 18,432 clones and has an average insert size of 135 kb, equivalent to 3.4 x chickpea haploid genomes. The combined libraries contain 49,152 clones, equivalent to 10.7 x chickpea haploid genomes. We identified all SSR loci-containing clones from the chickpea BAC library, generated sequences for 536 SSR loci from a part of the SSR-containing BACs and developed 310 new SSR markers. From the new SSR markers and selected existing SSR markers, we developed a SSR marker-based molecular genetic map of the chickpea genome. The BAC and BIBAC libraries, SSR markers and the molecular genetic map have provided essential resources and tools for modern genetic and genomic analyses of the chickpea genome. Using the SSR markers and genetic map, we mapped the genes and loci for flowering time and Ascochyta responses; one major QTL and a few minor QTLs have been identified for Ascochyta response and one major QTL has been identified for flowering time. The genetic correlations between flowering time, grain weight and Ascochyta response have been established. These results have provided essential tools and knowledge for effective manipulation and enhanced breeding of the traits in chickpea.
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Lers, Amnon, Majid R. Foolad, and Haya Friedman. genetic basis for postharvest chilling tolerance in tomato fruit. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600014.bard.
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ABSTRACT Postharvest losses of fresh produce are estimated globally to be around 30%. Reducing these losses is considered a major solution to ensure global food security. Storage at low temperatures is an efficient practice to prolong postharvest performance of crops with minimal negative impact on produce quality or human health and the environment. However, many fresh produce commodities are susceptible to chilling temperatures, and the application of cold storage is limited as it would cause physiological chilling injury (CI) leading to reduced produce quality. Further, the primary CI becomes a preferred site for pathogens leading to decay and massive produce losses. Thus, chilling sensitive crops should be stored at higher minimal temperatures, which curtails their marketing life and in some cases necessitates the use of other storage strategies. Development of new knowledge about the biological basis for chilling tolerance in fruits and vegetables should allow development of both new varieties more tolerant to cold, and more efficient postharvest storage treatments and storage conditions. In order to improve the agricultural performance of modern crop varieties, including tomato, there is great potential in introgression of marker-defined genomic regions from wild species onto the background of elite breeding lines. To exploit this potential for improving tomato fruit chilling tolerance during postharvest storage, we have used in this research a recombinant inbred line (RIL) population derived from a cross between the red-fruited tomato wild species SolanumpimpinellifoliumL. accession LA2093 and an advanced Solanum lycopersicumL. tomato breeding line NCEBR-1, developed in the laboratory of the US co-PI. The original specific objectives were: 1) Screening of RIL population resulting from the cross NCEBR1 X LA2093 for fruit chilling response during postharvest storage and estimation of its heritability; 2) Perform a transcriptopmic and bioinformatics analysis for the two parental lines following exposure to chilling storage. During the course of the project, we learned that we could measure greater differences in chilling responses among specific RILs compared to that observed between the two parental lines, and thus we decided not to perform transcriptomic analysis and instead invest our efforts more on characterization of the RILs. Performing the transcriptomic analysis for several RILs, which significantly differ in their chilling tolerance/sensitivity, at a later stage could result with more significant insights. The RIL population, (172 lines), was used in field experiment in which fruits were examined for chilling sensitivity by determining CI severity. Following the field experiments, including 4 harvest days and CI measurements, two extreme tails of the response distribution, each consisting of 11 RILs exhibiting either high sensitivity or tolerance to chilling stress, were identified and were further examined for chilling response in greenhouse experiments. Across the RILs, we found significant (P < 0.01) correlation between field and greenhouse grown plants in fruit CI. Two groups of 5 RILs, whose fruits exhibited reproducible chilling tolerant/sensitive phenotypes in both field and greenhouse experiments, were selected for further analyses. Numerous genetic, physiological, biochemical and molecular variations were investigated in response to postharvest chilling stress in the selected RILs. We confirmed the differential response of the parental lines of the RIL population to chilling stress, and examined the extent of variation in the RIL population in response to chilling treatment. We determined parameters which would be useful for further characterization of chilling response in the RIL population. These included chlorophyll fluorescence Fv/Fm, water loss, total non-enzymatic potential of antioxidant activity, ascorbate and proline content, and expression of LeCBF1 gene, known to be associated with cold acclimation. These parameters could be used in continuation studies for the identification and genetic mapping of loci contributing to chilling tolerance in this population, and identifying genetic markers associated with chilling tolerance in tomato. Once genetic markers associated with chilling tolerance are identified, the trait could be transferred to different genetic background via marker-assisted selection (MAS) and breeding. The collaborative research established in this program has resulted in new information and insights in this area of research and the collaboration will be continued to obtain further insights into the genetic, molecular biology and physiology of postharvest chilling tolerance in tomato fruit. The US Co-PI, developed the RIL population that was used for screening and measurement of the relevant chilling stress responses and conducted statistical analyses of the data. Because we were not able to grow the RIL population under field conditions in two successive generations, we could not estimate heritability of response to chilling temperatures. However, we plan to continue the research, grow the RIL progeny in the field again, and determine heritability of chilling tolerance in a near future. The IS and US investigators interacted regularly and plan to continue and expand on this study, since combing the expertise of the Co-PI in genetics and breeding with that of the PI in postharvest physiology and molecular biology will have great impact on this line of research, given the significant findings of this one-year feasibility project.
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Aharoni, Asaph, Zhangjun Fei, Efraim Lewinsohn, Arthur Schaffer, and Yaakov Tadmor. System Approach to Understanding the Metabolic Diversity in Melon. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7593400.bard.
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Fruit quality is determined by numerous genetic factors that affect taste, aroma, color, texture, nutritional value and shelf life. To unravel the genetic components involved in the metabolic pathways behind these traits, the major goal of the project was to identify novel genes that are involved in, or that regulate, these pathways using correlation analysis between genotype, metabolite and gene expression data. The original and specific research objectives were: (1) Collection of replicated fruit from a population of 96 RI lines derived from parents distinguished by great diversity in fruit development and quality phenotypes, (2) Phenotypic and metabolic profiling of mature fruit from all 96 RI lines and their parents, (3) 454 pyrosequencing of cDNA representing mRNA of mature fruit from each line to facilitate gene expression analysis based on relative EST abundance, (4) Development of a database modeled after an existing database developed for tomato introgression lines (ILs) to facilitate online data analysis by members of this project and by researchers around the world. The main functions of the database will be to store and present metabolite and gene expression data so that correlations can be drawn between variation in target traits or metabolites across the RI population members and variation in gene expression to identify candidate genes which may impact phenotypic and chemical traits of interest, (5) Selection of RI lines for segregation and/or hybridization (crosses) analysis to ascertain whether or not genes associated with traits through gene expression/metabolite correlation analysis are indeed contributors to said traits. The overall research strategy was to utilize an available recombinant inbred population of melon (Cucumis melo L.) derived from phenotypically diverse parents and for which over 800 molecular markers have been mapped for the association of metabolic trait and gene expression QTLs. Transcriptomic data were obtained by high throughput sequencing using the Illumina platform instead of the originally planned 454 platform. The change was due to the fast advancement and proven advantages of the Illumina platform, as explained in the first annual scientific report. Metabolic data were collected using both targeted (sugars, organic acids, carotenoids) and non-targeted metabolomics analysis methodologies. Genes whose expression patterns were associated with variation of particular metabolites or fruit quality traits represent candidates for the molecular mechanisms that underlie them. Candidate genes that may encode enzymes catalyzingbiosynthetic steps in the production of volatile compounds of interest, downstream catabolic processes of aromatic amino acids and regulatory genes were selected and are in the process of functional analyses. Several of these are genes represent unanticipated effectors of compound accumulation that could not be identified using traditional approaches. According to the original plan, the Cucurbit Genomics Network (http://www.icugi.org/), developed through an earlier BARD project (IS-3333-02), was expanded to serve as a public portal for the extensive metabolomics and transcriptomic data resulting from the current project. Importantly, this database was also expanded to include genomic and metabolomic resources of all the cucurbit crops, including genomes of cucumber and watermelon, EST collections, genetic maps, metabolite data and additional information. In addition, the database provides tools enabling researchers to identify genes, the expression patterns of which correlate with traits of interest. The project has significantly expanded the existing EST resource for melon and provides new molecular tools for marker-assisted selection. This information will be opened to the public by the end of 2013, upon the first publication describing the transcriptomic and metabolomics resources developed through the project. In addition, well-characterized RI lines are available to enable targeted breeding for genes of interest. Segregation of the RI lines for specific metabolites of interest has been shown, demonstrating the utility in these lines and our new molecular and metabolic data as a basis for selection targeting specific flavor, quality, nutritional and/or defensive compounds. To summarize, all the specific goals of the project have been achieved and in many cases exceeded. Large scale trascriptomic and metabolomic resources have been developed for melon and will soon become available to the community. The usefulness of these has been validated. A number of novel genes involved in fruit ripening have been selected and are currently being functionally analyzed. We thus fully addressed our obligations to the project. In our view, however, the potential value of the project outcomes as ultimately manifested may be far greater than originally anticipated. The resources developed and expanded under this project, and the tools created for using them will enable us, and others, to continue to employ resulting data and discoveries in future studies with benefits both in basic and applied agricultural - scientific research.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.
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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Fallik, Elazar, Robert Joly, Ilan Paran, and Matthew A. Jenks. Study of the Physiological, Molecular and Genetic Factors Associated with Postharvest Water Loss in Pepper Fruit. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593392.bard.
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The fruit of pepper (Capsicum annuum) commonly wilts (or shrivels) during postharvest storage due to rapid water loss, a condition that greatly reduces its shelf life and market value. The fact that pepper fruit are hollow, and thus have limited water content, only exacerbates this problem in pepper. The collaborators on this project completed research whose findings provided new insight into the genetic, physiological, and biochemical basis for water loss from the fruits of pepper (Capsicum annuum and related Capsicum species). Well-defined genetic populations of pepper were used in this study, the first being a series of backcross F₁ and segregating F₂, F₃, and F₄ populations derived from two original parents selected for having dramatic differences in fruit water loss rate (very high and very low water loss). The secondly population utilized in these studies was a collection of 50 accessions representing world diversity in both species and cultivar types. We found that an unexpectedly large amount of variation was present in both fruit wax and cutin composition in these collections. In addition, our studies revealed significant correlations between the chemical composition of both the fruit cuticular waxes and cutin monomers with fruit water loss rate. Among the most significant were that high alkane content in fruit waxes conferred low fruit water loss rates and low permeability in fruit cuticles. In contrast, high amounts of terpenoids (plus steroidal compounds) were associated with very high fruit water loss and cuticle permeability. These results are consistent with our models that the simple straight chain alkanes pack closely together in the cuticle membrane and obstruct water diffusion, whereas lipids with more complex 3-dimensional structure (such as terpenoids) do not pack so closely, and thus increase the diffusion pathways. The backcross segregating populations were used to map quantitative trait loci (QTLs) associated with water loss (using DART markers, Diversity Arrays Technology LTD). These studies resulted in identification of two linked QTLs on pepper’s chromosome 10. Although the exact genetic or physiological basis for these QTLs function in water loss is unknown, the genotypic contribution in studies of near-isogenic lines selected from these backcross populations reveals a strong association between certain wax compounds, the free fatty acids and iso-alkanes. There was also a lesser association between the water loss QTLs with both fruit firmness and total soluble sugars. Results of these analyses have revealed especially strong genetic linkages between fruit water loss, cuticle composition, and two QTLs on chromosome 10. These findings lead us to further speculate that genes located at or near these QTLs have a strong influence on cuticle lipids that impact water loss rate (and possibly, whether directly or indirectly, other traits like fruit firmness and sugar content). The QTL markers identified in these studies will be valuable in the breeding programs of scientists seeking to select for low water loss, long lasting fruits, of pepper, and likely the fruits of related commodities. Further work with these newly developed genetic resources should ultimately lead to the discovery of the genes controlling these fruit characteristics, allowing for the use of transgenic breeding approaches toward the improvement of fruit postharvest shelf life.
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Abbo, Shahal, Hongbin Zhang, Clarice Coyne, Amir Sherman, Dan Shtienberg, and George J. Vandemark. Winter chickpea; towards a new winter pulse for the semiarid Pacific Northwest and wider adaptation in the Mediterranean basin. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7597909.bard.
Full textAbstract:
Original objectives: [a] Screen an array of chickpea and wild annual Cicer germplasm for winter survival. [b] Genetic analysis of winter hardiness in domesticated x wild chickpea crosses. [c] Genetic analysis of vernalization response in domesticated x wild chickpea crosses. [d] Digital expression analysis of a core selection of breeding and germplasm lines of chickpea that differ in winter hardiness and vernalization. [e] Identification of the genes involved in the chickpea winter hardiness and vernalization and construction of gene network controlling these traits. [f] Assessing the phenotypic and genetic correlations between winter hardiness, vernalization response and Ascochyta blight response in chickpea. The complexity of the vernalization response and the inefficiency of our selection experiments (below) required quitting the work on ascochyta response in the framework of this project. Background to the subject: Since its introduction to the Palouse region of WA and Idaho, and the northern Great Plains, chickpea has been a spring rotation legume due to lack of winter hardiness. The short growing season of spring chickpea limits its grain yield and leaves relatively little stubble residue for combating soil erosion. In Israel, chilling temperatures limit pod setting in early springs and narrow the effective reproductive time window of the crop. Winter hardiness and vernalization response of chickpea alleles were lost due to a series of evolutionary bottlenecks; however, such alleles are prevalent in its wild progenitor’s genepool. Major conclusions, solutions, achievements: It appears that both vernalization response and winter hardiness are polygenic traits in the wild-domesticated chickpea genepool. The main conclusion from the fieldwork in Israel is that selection of domesticated winter hardy and vernalization responsive types should be conducted in late flowering and late maturity backgrounds to minimize interference by daylength and temperature response alleles (see our Plant Breeding paper on the subject). The main conclusion from the US winter-hardiness studies is that excellent lines have been identified for germplasm release and continued genetic study. Several of the lines have good seed size and growth habit that will be useful for introgressing winter-hardiness into current chickpea cultivars to develop releases for autumn sowing. We sequenced the transcriptomes and profiled the expression of genes in 87 samples. Differential expression analysis identified a total of 2,452 differentially expressed genes (DEGs) between vernalized plants and control plants, of which 287 were shared between two or more Cicer species studied. We cloned 498 genes controlling vernalization, named CVRN genes. Each of the CVRN genes contributes to flowering date advance (FDA) by 3.85% - 10.71%, but 413 (83%) other genes had negative effects on FDA, while only 83 (17%) had positive effects on FDA, when the plant is exposed to cold temperature. The cloned CVRN genes provide new toolkits and knowledge to develop chickpea cultivars that are suitable for autumn-sowing. Scientific & agricultural implications: Unlike the winter cereals (barley, wheat) or pea, in which a single allelic change may induce a switch from winter to spring habit, we were unable to find any evidence for such major gene action in chickpea. In agricultural terms this means that an alternative strategy must be employed in order to isolate late flowering – ascochyta resistant (winter types) domesticated forms to enable autumn sowing of chickpea in the US Great Plains. An environment was identified in U.S. (eastern Washington) where autumn-sown chickpea production is possible using the levels of winter-hardiness discovered once backcrossed into advanced cultivated material with acceptable agronomic traits. The cloned CVRN genes and identified gene networks significantly advance our understanding of molecular mechanisms underlying plant vernalization in general, and chickpea in particular, and provide a new toolkit for switching chickpea from a spring-sowing to autumn-sowing crop.