Journal articles on the topic 'Plant population genetics Statistical methods'
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1
Hoeschele, I., P. Uimari, F. E. Grignola, Q. Zhang, and K. M. Gage. "Advances in Statistical Methods to Map Quantitative Trait Loci in Outbred Populations." Genetics 147, no. 3 (November 1, 1997): 1445–57. http://dx.doi.org/10.1093/genetics/147.3.1445.
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Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for genetic parameter estimation in outbred populations but allow the determination of test statistic distributions via simulation or data permutation; however, further inferences including confidence intervals of QTL location require the use of Monte Carlo or bootstrap sampling techniques. A method which is intermediate in computational requirements is residual maximum likelihood (REML) with a covariance matrix of random QTL effects conditional on information from multiple linked markers. Testing for the number of QTLs on a chromosome is difficult in a classical framework. The computationally most demanding methods are maximum likelihood and Bayesian analysis, which take account of the distribution of multilocus marker-QTL genotypes on a pedigree and permit investigators to fit different models of variation at the QTL. The Bayesian analysis includes the number of QTLS on a chromosome as an unknown.
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Mitchell-Olds, T., and J. Bergelson. "Statistical genetics of an annual plant, Impatiens capensis. I. Genetic basis of quantitative variation." Genetics 124, no. 2 (February 1, 1990): 407–15. http://dx.doi.org/10.1093/genetics/124.2.407.
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Abstract Analysis of quantitative genetics in natural populations has been hindered by computational and methodological problems in statistical analysis. We developed and validated a jackknife procedure to test for existence of broad sense heritabilities and dominance or maternal effects influencing quantitative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and/or maternal effects, while later characters exhibited predominantly environmental variation. Monte Carlo simulations demonstrate that these jackknife tests of variance components are extremely robust to heterogeneous error variances. Statistical methods from human genetics provide evidence for either a major locus influencing germination date, or genes that affect phenotypic variability per se. We urge explicit consideration of statistical behavior of estimation and testing procedures for proper biological interpretation of statistical results.
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Ward, Sarah M., and Marie Jasieniuk. "Review: Sampling Weedy and Invasive Plant Populations for Genetic Diversity Analysis." Weed Science 57, no. 6 (December 2009): 593–602. http://dx.doi.org/10.1614/ws-09-082.1.
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Recent advances in molecular methods and statistical analyses provide weed scientists with powerful tools for examining the genetic structure of weedy plant populations. The value of these studies depends on effective sampling protocols; however, there is little consensus on how to sample plant populations for genetic diversity analyses. In this review, we draw on published literature that incorporates sampling theory and spatial statistics in population genetic analyses to identify key factors to consider when designing a sampling strategy. We discuss how sampling design is affected by research objectives, biology of the study species, population structure, marker choice, and the genetic parameters to be investigated, and we offer suggestions on defining sampling units and developing sampling protocols.
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EPPERSON, B. K., Z. HUANG, and T. Q. LI. "Measures of spatial structure in samples of genotypes for multiallelic loci." Genetical Research 73, no. 3 (June 1999): 251–61. http://dx.doi.org/10.1017/s001667239900378x.
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Various spatial autocorrelation statistics have been widely used both in theoretical population genetics and to study the spatial distribution of diploid genotypes in many plant and animal populations. However, previous simulation studies have considered only diallelic loci. In this paper, we use a large number of space–time simulations to characterize for the first time the parametric and statistical values of Moran's I-statistics for converted individual genotypes as well as for join- count statistics. A wide range of levels of dispersal and numbers of alleles and allele frequencies are modelled and the results reveal the different general effects of each of these factors on these statistics. We also examine the range of appropriate sampling designs and sizes for which predicted values can be interpolated for specific sampling schemes for any given population genetic field survey. Numbers of alleles and allele frequencies each affect some statistics but not others. The results indicate generally low standard deviations. The results also develop precise and efficient methods of estimating gene dispersal, based on the various autocorrelation measures of standing spatial patterns of genetic variation within populations. The results also extend these methods to loci with multiple alleles, typical of those studied through modern molecular methods.
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Zhan, J., C. C. Mundt, and B. A. McDonald. "Estimation of Rates of Recombination and Migration in Populations of Plant Pathogens—A Reply." Phytopathology® 90, no. 4 (April 2000): 324–26. http://dx.doi.org/10.1094/phyto.2000.90.4.324.
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We find that the maximum likelihood method proposed by J. K. M. Brown has deficiencies that limit its usefulness for actual data sets. We propose two alternative statistical methods based on maximum likelihood that could be used to quantify rates of recombination and immigration in fungal populations. We also show that minor modification of our original method, which was based upon posterior probabilities, leads to a result that is identical to one of the maximum likelihood methods. Our previous estimates of the relative contributions of sexual reproduction, asexual reproduction, and immigration to the genetic structure of a Mycosphaerella graminicola population did not change significantly following reanalysis of our data with these new methods.
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STEFANINI, FEDERICO MATTIA, and ALESSANDRO CAMUSSI. "Information in molecular profile components evaluated by a Genetic Classifier System: a case study in Picea abies Karst." Genetical Research 70, no. 3 (December 1997): 205–13. http://dx.doi.org/10.1017/s001667239700298x.
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Individual records from the coding of molecular polymorphism (molecular profiles) are particularly useful for the identification of clones or cultivars, in pedigree analysis, in the estimation of genetic distances and relatedness, and as a tool in genome mapping and population genetics. A parametric statistical analysis of molecular profile components can be infeasible because of the huge number of observed markers, the presence of missing values and the high number of parameters required to evaluate the importance of interactions among markers. Moreover, new powerful molecular techniques make possible the analysis of numerous markers at one time; therefore parametric statistical methods could result in troublesome models with more parameters than data. The field of computer-based techniques offers new strategies to cope with the complexity of molecular profiles. We suggest the use of a Genetic Classifier System to evaluate the importance of profile components. The procedure is based on a Genetic Algorithm approach, a numerical technique that simulates some features of the natural selection process to solve problems. A set of isozyme data from a Norway spruce population is analysed in order to assess their ability to predict the individual plant response to the presence of abiotic stresses. The results, obtained by three different computer simulations, show that this computer-based approach is particularly effective for ranking profile components according to their relevance. Genetic Classifier Systems could also be used as a preliminary step to reduce the complexity of molecular data sets.
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Sokolovic, Dejan, Zoran Lugic, Jasmina Radovic, Tomislav Zivanovic, Snezana Babic, Aleksandar Simic, and Radojka Maletic. "Evaluation of morphological traits, dry matter yield and quality of Lolium perenne L. autochthonous populations from Serbia through multivariate analysis." Genetika 43, no. 1 (2011): 129–40. http://dx.doi.org/10.2298/gensr1101129s.
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Due to specific climatic conditions, perennial ryegrass breeding in Serbia is focused on resistance or tolerance to abiotic stress factors, especially to drought and high temperatures. These traits should be associated with high dry matter yield and quality. Therefore, most frequently used initial material is autochthonous populations and ecotypes adapted to local agro-ecological conditions, but knowledge about their variability of important traits for breeding is missing. Pre-selection evaluation of ten populations of perennial ryegrass originating from Serbia is presented in this paper. Twenty five traits were investigated during the two-year period and processed using analysis of variance and multivariate statistical methods (cluster and principal components analysis). The goal was to determine diversity and genetic distances of investigated populations by phenotyping and to define traits considerably affecting the variability and discrimination of populations. On cluster diagram two groups of population are observed, but geographic origin of populations (lowland, hilly, mountainous habitat) was not influence to clustering of collection. Factor analysis has clarified that first seven principal components (PC) described almost 95%. The traits which show high correlation coefficients with first principal component were plant height in first cut, leaf length and width, DM of generative tillers, spike and spikelet length and 1000 seed weight, and with second principal component time of heading, terminal internode length, DM of vegetative tillers, spikelet number and FSU. It can be concluded that variability between populations was high and that differences of population were mainly affected by most important traits for breeding, such as components of dry matter production and some seed yield components.
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Tokhtar, Valeriy K., Yulia K. Vinogradova, Alexander A. Notov, Аndrey Yu Kurskoy, and Elena S. Danilova. "Main directions of the study of plant invasions in Russia." Environmental & Socio-economic Studies 9, no. 4 (December 1, 2021): 45–56. http://dx.doi.org/10.2478/environ-2021-0024.
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Abstract This article is focused on the analysis of major approaches to plant invasion research used by Russian researchers. They fall within three main groups: 1. Conventional approaches to floristic analysis based on the Russian scientific tradition of floristic research, 2. Approaches focused on the study of the fraction of invasive flora, making blacklists and regional Black books, 3. New comprehensive approaches based on a synthesis of methods used in botany, geo-information technology and population genetics. Multivariate statistical methods allow for the visualization of various data, including those on alien species group structures in various regions. They make it possible to identify boundaries of ecological niches occupied by plants in respect to climate-and-environmental or ecological variables. An assessment of current statistical interdependence between alien plant characteristics and scores of factors limiting their dissemination facilitates the making of predictive models of plant invasion. Examples of multivariate statistical methods used in invasion biology were analyzed, along with different approaches to the study of the variability of alien species. Alien and invasive fractions of the flora of the Trans-Siberian Railway were analyzed not by administrative units but by natural biomes. This approach allowed us to assess the correlation between the number of invasive species with different natural-climatic and floristic characteristics of biomes. The publication of "Black Books" of various administrative subjects of Russia according to a unified methodology allowed us to make an inventory of invasive species over the vast territory of the country. The experience gained by Russian researchers may be further used for developing universal approaches to plant invasion research.
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Lucic, Aleksandar, Vasilije Isajev, Ljubinko Rakonjac, Milan Mataruga, Vojka Babic, Danijela Ristic, and Snezana Mladenovic-Drinic. "Application of various statistical methods to analyze genetic diversity of Austrian (Pinus nigra Arn.) and Scots pine (Pinus sylvestris L.) based on protein markers." Genetika 43, no. 3 (2011): 477–86. http://dx.doi.org/10.2298/gensr1103477l.
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This paper presents the results of studies on protein polymorphism in seeds of Scots pine (Pinus sylvestris L.) and Austrian pine (Pinus nigra Arn.) as the most important economic species of the genus Pinus in Serbia. Polymorphism of protein markers was determined in selected genotypes originating from seven populations (Scots pine) and six populations (Austrian pine). Analysis of protein markers was performed using two statistical methods, NTSYS and correspondence analysis. Both methods give the same arrangement of the analyzed populations, whereby, because of a different view of genetic distances, they can and should be combined, enabling easier and more precise understanding of mutual relationships of the observation units.
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Lu, Zhiqiang, Yongshuai Sun, Ying Li, Yongzhi Yang, Gaini Wang, and Jianquan Liu. "Species delimitation and hybridization history of a hazel species complex." Annals of Botany 127, no. 7 (February 10, 2021): 875–86. http://dx.doi.org/10.1093/aob/mcab015.
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Abstract Background and Aims Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis–Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. Methods A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. Key Results Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. Conclusions Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.
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Dang, Zhenyu, Jixuan Yang, Lin Wang, Qin Tao, Fengjun Zhang, Yuxin Zhang, and Zewei Luo. "Sampling Variation of RAD-Seq Data from Diploid and Tetraploid Potato (Solanum tuberosum L.)." Plants 10, no. 2 (February 7, 2021): 319. http://dx.doi.org/10.3390/plants10020319.
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The new sequencing technology enables identification of genome-wide sequence-based variants at a population level and a competitively low cost. The sequence variant-based molecular markers have motivated enormous interest in population and quantitative genetic analyses. Generation of the sequence data involves a sophisticated experimental process embedded with rich non-biological variation. Statistically, the sequencing process indeed involves sampling DNA fragments from an individual sequence. Adequate knowledge of sampling variation of the sequence data generation is one of the key statistical properties for any downstream analysis of the data and for implementing statistically appropriate methods. This paper reports a thorough investigation on modeling the sampling variation of the sequence data from the optimized RAD-seq (Restriction sit associated DNA sequencing) experiments with two parents and their offspring of diploid and autotetraploid potato (Solanum tuberosum L.). The analysis shows significant dispersion in sampling variation of the sequence data over that expected under multinomial distribution as widely assumed in the literature and provides statistical methods for modeling the variation and calculating the model parameters, which may be easily implemented in real sequence datasets. The optimized design of RAD-seq experiments enabled effective control of presentation of undesirable chloroplast DNA and RNA genes in the sequence data generated.
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Paoletti, Claudia, Massimo Pigliucci, and Mauro Serafini. "Microenvironmental correlates of phenotypic variation in Capsella bursa-pastoris (Cruciferae)." Canadian Journal of Botany 69, no. 8 (August 1, 1991): 1637–41. http://dx.doi.org/10.1139/b91-207.
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The majority of papers dealing with environmental correlates of phenotypic variability are concerned with macrogeographical structuring of the investigated species. However, a possible major component of phenotypic differentiation in some taxa is small-scale variability in the microenvironment. The statistical methods usually employed for such studies seems to be restricted to a few standardized sets of procedure, often assuming linearity and additivity of effects among variates. In this paper we studied small-scale geographical differentiation of phenotypes of Capsella bursa-pastoris (Cruciferae), a species characterized by an apparent extreme degree of phenetic specialization that could be due to fixation of alternative alleles in small local demes. We use nonparametric multivariate procedures to test the relationships between phenotypic principal components, geographic distance, and a number of microenvironmental parameters. A concept recently applied to population genetics, that of biological boundaries, is used here in relation to phenetic variation to assess its association with geographical mapping of the populations studied. Key words: Capsella, Mantel test, phenotypic boundaries, biotic parameters, principal components analysis.
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Friesen, G. M. A., S. R. Smith, D. J. Cattani, and A. T. Phan. "Characterizing genetically diverse blue grama [Bouteloua gracilis (Willd. ex Kunth) Lag. ex Griffiths] seed sources." Botany 98, no. 11 (November 2020): 661–71. http://dx.doi.org/10.1139/cjb-2020-0029.
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The need for regionally adapted native grass seed sources for the northern Great Plains has resulted in the commercial release of a range of plant materials, including ecovars™ 1 . Ecovars™ are multisite composite populations developed to combine broad genetic diversity from a geographic region. The objective of this study was to determine whether morphological data could be used to distinguish between genetically diverse blue grama [Bouteloua gracilis (Willd. ex Kunth) Lag. ex Griffiths] seed sources through classical statistical methods. Entries included a Manitoba (MB) ecovar™, a USDA–NRCS released cultivar ‘Bad River’, and ecotypes from Wyoming and Minnesota. Vegetative and reproductive measurements and ratings were taken from a spaced-plant nursery during 2000–2001 in Carman, Manitoba, Canada. The results were analyzed using statistical techniques including: ANOVA, least significant difference, canonical discriminant analysis (CDA), and coefficients of variation. These techniques distinguished four genetically diverse seed sources from each other through CDA. As hypothesized, there was greater within-population genetic diversity for the MB ecovar™ and Wyoming and Minnesota ecotypes, compared with ‘Bad River’. Our results indicate that genetically diverse blue grama seed sources can be distinguished, based on phenotypic measurements.
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Jankovic, Vesna, Savo Vuckovic, Vojislav Mihailovic, Vera Popovic, Ljubisa Zivanovic, Divna Simic, Ana Vujosevic, and Petar Stevanovic. "Assessment of some parameters productivity and quality of populations Phleum pratense L. grown in conditions of Serbia." Genetika 50, no. 1 (2018): 1–10. http://dx.doi.org/10.2298/gensr1801001j.
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Phleum pratense (L.) is the important forage grass species in Serbia. The study was conducted on 20 autochthonous population of Phleum pratense (L.), originating from Western Serbia. Plant height, protein content and crude cellulose content had a high direct impact on yield. Populations of PP16, PP20, PP2 and PP9 had the significantly higher yield of the raw matter compared to all the tested population and the highest values for the other evaluated parameters, also. The average yield of crude biomass was positive statistically highly significantly correlated with plant height (r=0.87**), and positively significantly correlated with a content of crude proteins and positive non significant correlated with crude cellulose (r=0.42 ns). Based on obtained values and by the appropriate choice of selection methods, we conclude that we have excellent genotypes, PP16, PP20, PP2 and PP9 for a successful selection process in order to obtain new high yielding varieties of Phleum pratense.
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McEwin, Rudi A., Michelle L. Hebart, Helena Oakey, Rick Tearle, Joe Grose, Greg Popplewell, and Wayne S. Pitchford. "Comparison of Methods to Select Candidates for High-Density Genotyping; Practical Observations in a Cattle Breeding Program." Agriculture 12, no. 2 (February 15, 2022): 276. http://dx.doi.org/10.3390/agriculture12020276.
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Imputation can be used to obtain a large number of high-density genotypes at the cost of procuring low-density panels. Accurate imputation requires a well-formed reference population of high-density genotypes to enable statistical inference. Five methods were compared using commercial Wagyu genotype data to identify individuals to produce a “well-formed” reference population. Two methods utilised a relationship matrix (MCG and MCA), two of which utilised a haplotype block library (AHAP2 and IWS), and the last selected high influential sires with greater than 10 progeny (PROG). The efficacy of the methods was assessed based on the total proportion of genetic variance accounted for and the number of haplotypes captured, as well as practical considerations in implementing these methods. Concordance was high between the MCG and MCA and between AHAP2 and IWS but was low between these groupings. PROG-selected animals were most similar to MCA. MCG accounted for the greatest proportion of genetic variance in the population (35%, while the other methods accounted for approximately 30%) and the greatest number of unique haplotypes when a frequency threshold was applied. MCG was also relatively simple to implement, although modifications need to be made to account for DNA availability when running over a whole population. Of the methods compared, MCG is the recommended starting point for an ongoing sequencing project.
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Montesinos-López, Osval A., Arron H. Carter, David Alejandro Bernal-Sandoval, Bernabe Cano-Paez, Abelardo Montesinos-López, and José Crossa. "A Comparison between Three Tuning Strategies for Gaussian Kernels in the Context of Univariate Genomic Prediction." Genes 13, no. 12 (December 3, 2022): 2282. http://dx.doi.org/10.3390/genes13122282.
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Genomic prediction is revolutionizing plant breeding since candidate genotypes can be selected without the need to measure their trait in the field. When a reference population contains both phenotypic and genotypic information, it is trained by a statistical machine learning method that is subsequently used for making predictions of breeding or phenotypic values of candidate genotypes that were only genotyped. Nevertheless, the successful implementation of the genomic selection (GS) methodology depends on many factors. One key factor is the type of statistical machine learning method used since some are unable to capture nonlinear patterns available in the data. While kernel methods are powerful statistical machine learning algorithms that capture complex nonlinear patterns in the data, their successful implementation strongly depends on the careful tuning process of the involved hyperparameters. As such, in this paper we compare three methods of tuning (manual tuning, grid search, and Bayesian optimization) for the Gaussian kernel under a Bayesian best linear unbiased predictor model. We used six real datasets of wheat (Triticum aestivum L.) to compare the three strategies of tuning. We found that if we want to obtain the major benefits of using Gaussian kernels, it is very important to perform a careful tuning process. The best prediction performance was observed when the tuning process was performed with grid search and Bayesian optimization. However, we did not observe relevant differences between the grid search and Bayesian optimization approach. The observed gains in terms of prediction performance were between 2.1% and 27.8% across the six datasets under study.
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Oliveira, Gabriela França, Ana Carolina Campana Nascimento, Moysés Nascimento, Isabela de Castro Sant'Anna, Juan Vicente Romero, Camila Ferreira Azevedo, Leonardo Lopes Bhering, and Eveline Teixeira Caixeta Moura. "Quantile regression in genomic selection for oligogenic traits in autogamous plants: A simulation study." PLOS ONE 16, no. 1 (January 5, 2021): e0243666. http://dx.doi.org/10.1371/journal.pone.0243666.
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This study assessed the efficiency of Genomic selection (GS) or genome‐wide selection (GWS), based on Regularized Quantile Regression (RQR), in the selection of genotypes to breed autogamous plant populations with oligogenic traits. To this end, simulated data of an F2 population were used, with traits with different heritability levels (0.10, 0.20 and 0.40), controlled by four genes. The generations were advanced (up to F6) at two selection intensities (10% and 20%). The genomic genetic value was computed by RQR for different quantiles (0.10, 0.50 and 0.90), and by the traditional GWS methods, specifically RR-BLUP and BLASSO. A second objective was to find the statistical methodology that allows the fastest fixation of favorable alleles. In general, the results of the RQR model were better than or equal to those of traditional GWS methodologies, achieving the fixation of favorable alleles in most of the evaluated scenarios. At a heritability level of 0.40 and a selection intensity of 10%, RQR (0.50) was the only methodology that fixed the alleles quickly, i.e., in the fourth generation. Thus, it was concluded that the application of RQR in plant breeding, to simulated autogamous plant populations with oligogenic traits, could reduce time and consequently costs, due to the reduction of selfing generations to fix alleles in the evaluated scenarios.
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Mahdi, Tajalifar, and Rasooli Mohammad. "Importance of BLUP method in plant breeding." Journal of Plant Science and Phytopathology 6, no. 2 (May 31, 2022): 040–42. http://dx.doi.org/10.29328/journal.jpsp.1001072.
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Introduction: The most desirable linear neutral prediction (BLUP) is a standard method for estimating the random effects of a hybrid model. This approach was originally developed in animal breeding to estimate breeding values and is now widely used in many fields of research. The main practical advantages of using REML/BLUP are: It allows the comparison of individuals or species over time (generation, year) and space (location, block). Possibility of simultaneous correction of environmental effects, estimation of variance components, and prediction of genetic values. The best BLUP prediction method, which estimates the averages with high accuracy, especially in mixed models, is also used to evaluate multi-environment experimental data (MET). Blup is one method is statistical. Pedigree-based blup method. Materials and methods: The BLUP method achieves this goal by combining phenotypic data and information on pedigree relationships through an index, known as family index selection. This index, which is estimated based on the coefficient of intra-class correlation, exploits the relationships of individuals within a family compared to other families in the population. Results: The results: show that BLUP has good prediction accuracy compared to other methods. Pedigree-based BLUP method can increase selection yield in production-related traits in P. zonale or shelf life of D. caryophyllus L.
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Karmanovskaya, Natalia V. "Reindeer Population as an Indicator of Sustainable Development of the Arctic Territory." International Journal of Agricultural Extension 9, no. 4 (August 18, 2021): 21–28. http://dx.doi.org/10.33687/ijae.009.00.3718.
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The objectives of this study are to carry out genetic monitoring of domestic reindeer of Nenets breed raised on the territory of Taimyr; establishment of the genetic bank of domestic reindeer of Nenets breed; as well as a comparative analysis with populations of the Nenets breed from other breeding regions (Nenets and Yamalo-Nenets Autonomous Okrug, Murmansk Oblast and the Komi Republic) using DNA markers. The microsatellites were used in the studies as DNA markers of genetic diversity. Genotyping was carried out by the methods of the Laboratory of molecular selection basis of L.K. Ernst Federal Research Center for Animal Husbandry. Statistical data processing was performed using the GenAlEx 6.5, SplitsTree 4.14.5 software, as well as the software packages “diveRsity”, “pophelper”, and “adegenet” for the R computing environment. As a result of the study, it was found that the population of reindeer of Taimyr breed in the village of Tukhard is characterised by the minimum level of polymorphism and genetic diversity, as indicated by the minimum values of all population genetic indicators. The authors assume that the patterns that have been identified are primarily the result of breeding programmes on the samples presented in this study (such studies have not been conducted before). The results of the PCA analysis and the phylogenetic dendrogram of genetic relationships, built on the basis of the matrix of Jost's D pairwise genetic distances using the NeighborNet, revealed a similar genetic structure of Taimyr populations, which, most likely, could be due to the close geographical localisation of the studied individuals. The authors come to the conclusion that a low level of both allelic and genetic diversity in the future may negatively affect the adaptation of animals to environmental conditions.
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Siah, Ali, Myriam Bomble, Benoit Tisserant, Thierry Cadalen, Maxime Holvoet, Jean-Louis Hilbert, Patrice Halama, and Philippe Reignault. "Genetic Structure of Zymoseptoria tritici in Northern France at Region, Field, Plant, and Leaf Layer Scales." Phytopathology® 108, no. 9 (September 2018): 1114–23. http://dx.doi.org/10.1094/phyto-09-17-0322-r.
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Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant, and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values of ≥0.44 and haplotype frequencies of ≥94%) were found at all the examined scales. Such rates of diversity are likely due to an active sexual recombination in the investigated areas, as revealed by equal proportions of the two mating types scored in all sampled populations. Interestingly, a rare occurrence of clones among lesions from a same leaf, as well as among leaves from different plant leaf layers (e.g., upper versus lower leaves), was highlighted, indicating that ascospores contribute much more than expected to Z. tritici epidemics, compared with pycnidiospores. Population structure and analyses of molecular variance revealed significant genetic differentiation at the regional scale (GST = 0.23) and, as expected, not at the other more local scales (GST ≤ 0.01). Further analyses using Bayesian and unweighted neighbor-joining statistical methods detected six genetic clusters within the regional population, overall distributed according to the locations from which the isolates were sampled. Neither clear directional relative migration linked to the geographical distribution of the locations, nor isolation by distance, were observed. Separate evolutionary trajectories caused by selection and adaptations to habitat heterogeneity could be the main forces shaping such structuration. This study provides new insights into the epidemiology and the genetic structure of Z. tritici at small local and, for the first time, at single plant and leaf layer scales. Such findings would be helpful in implementing effective control strategies.
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Naroui Rad, Mohammad, and Gholamali Keikha. "First evaluation of melon (Cucumis melo. L) landraces under high tunnel condition in Sistan." Genetika 53, no. 1 (2021): 121–30. http://dx.doi.org/10.2298/gensr2101121n.
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In order to evaluate a number of agro-morphological characteristics in 10 melon population, an experiment based on randomized complete block design with three replications was carried out in two years (2017-2018) at high tunnel condition at Zahak Agriculture Research Station. The relationships among the related traits evaluated using by statistical methods. The combined analysis of variance revealed highly significant differences among landraces in evaluated traits. A highly and significant correlation was observed between fruit width and yield (0.81**). Mean comparison using Duncan?s multiple rang test revealed that maximum yield belonged to landrace Zardeivanaki with 29160 kg/ha. Factor analysis was used for understanding the data structure and trait relations. The factor analysis showed that five factors explained 84% of the total variation among the traits. Therefore, the selection may be done according to the first component and it was helpful for a good breeding program for development of high yielding genotypes also landraces Dargazi, Zardeivanaki and Sabzsooski were placed very closely indicating that the responses of these landraces to be similar to high tunnel cultivation condition.
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Kloepper, Joseph W., and Chantal J. Beauchamp. "A review of issues related to measuring colonization of plant roots by bacteria." Canadian Journal of Microbiology 38, no. 12 (December 1, 1992): 1219–32. http://dx.doi.org/10.1139/m92-202.
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Root colonization by introduced bacteria is an important step in the interaction of beneficial bacteria with the host plant. Investigators attempting to measure root colonization by bacteria must face several issues. A clear concept or definition of root colonization should be stated in each research summary, as several different definitions have been proposed. We consider true root colonists to be those bacteria that colonize roots in competitive conditions, i.e., natural field soils. Different methods of processing root samples are required if one is measuring external root colonization alone, internal colonization alone, or both. Given that most beneficial bacterial strains currently under investigation as root colonists are members of taxa naturally found in soils, a marking system is required to differentiate the introduced strain from members of the indigenous rhizosphere community. Spontaneous antibiotic resistance, immunological approaches, and foreign DNA sequences are among the marking systems that have been used and each has some possible advantages and disadvantages. More research is needed in the development and comparison of marking systems. The design of experiments to measure root colonization should take into account several statistical issues. One must decide what constitutes the sample unit for each replication of a given treatment, e.g., whole root systems or root segments. Consideration should also be given to how best to express the estimated population of root colonists (e.g., cfu/g fresh or dry weight root, cfu/cm root, or cfu/surface area root). Statistical analysis by standard analysis of variance tests should be used whenever possible to separate treatment means of colonization levels; however, one must determine that the underlying assumptions of these tests are correct for each experiment. Finally, in quantification of populations on roots, one will almost certainly encounter replications with no bacteria, i.e., zeros. There are several options for how to calculate treatment means when one or more replications is a zero, and the implications of these options are discussed. Key words: bioluminescence, genetic markers, plant growth-promoting rhizobacteria, rhizosphere bacteria, root, colonization.
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Özel, Halil, Sezgin Ayan, and Vasilije Isajev. "Inter population variability of frost-resistance in provenances of scot pines (Pinusylvestris L.R. hamata Steven) in Turkey." Genetika 48, no. 2 (2016): 653–63. http://dx.doi.org/10.2298/gensr1602653o.
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Frost-resistance variability of Scotch pine (Pinus sylvestris L. var. hamata Steven) seedlings grown in nurseries conditions, originated from 10 provenances, have been analyzed. The provenances from Black Sea region, Central Anatolian region and Eastern Anatolian region in Turkey have been used in selection of seed zones. The results of frost-resistance tests indicated a strong relationship of implemented freezing degrees with injury degrees of Scotch pine needles and photosynthetic productivities. On the other hand, another significant relationship has been determined between chlorophyll fluorescence and ion leakage methods (r=-0.801). This result shows that those two methods can be safely used in determining the damages due to low temperatures. In frost resistance tests, Scotch pine seedlings from different provenances have been frozen at -10, -20, -30 and -40?C. According to the Duncan test results, it has been determined that damage increased as temperature decreased. The damage level at -10?C implementation is 3.5% which can be tolerated by plants. But when the temperature has been decreased to -20?C, the level of damage has increased to 51.25%. As a result of photosynthetic analyses in this phase, it has been determined that there is a statistically significant relationship between provenances and temperature levels. Under the light of those findings, they have determined that the photosynthetic productivity has significantly decreased at temperatures between -20?C and -40?C. This situation conforms to injury index values determined in this study. As a result of injury index and photosynthetic productivity tests used for determining the damage after frost-resistance tests, it has been determined that the provenances of Amasya-Kunduz, Bolu-Alada?, D?zce-Y???lca, Samsun-Vezirk?pr? and Eski?ehir-?atac?k are more sensitive to frost than other provenances.
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Kan, Mustafa, Arzu Kan, Ömer Sözen, Ufuk Karadavut, and Mehmet Yağmur. "Evaluation of the farms producing dry bean landraces by capital approach in the Middle Kızılırmak Valley of Turkey." Plant Genetic Resources: Characterization and Utilization 17, no. 5 (May 6, 2019): 391–400. http://dx.doi.org/10.1017/s1479262119000169.
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AbstractThis study was conducted to determine the opinions of the farmers producing dry bean landraces (DBL) at the regional level of Turkey (eight provinces). In total, 140 questionnaire forms were filled by DBL producers. The population and then the sample size were determined according to 2016-year-preliminary-study. The capital structures of the farms according to the production types were evaluated using the Five-Capital-Model approach, and differences were tested by parametric and non-parametric statistical methods. The study showed that 37.86% of the DBL producers produce as the home-garden-type while 62.14% of them as the field-type, which is larger than 0.1 ha. While home-garden-type producers majorly produce for their own family needs, commercial ideas and concerns are at the forefront for field-type producers. While field-type producers have higher values in terms of five capitals, home-garden-type producers move within a more traditional way of production. More than half of the producers indicate that they will continue to produce DBL; this ratio is higher in home-garden-type producers. This indication of approximately 25% of both types of producers wherein their children will continue to produce DBL, there is a need for more human labour, efficiency and profitability concerns, production mostly by the elderly population increasing the risk of future depletion in DBL-genetic resources. This calls for more efforts to increase the awareness among the young population on the importance and protection of genetic resources and to make special policies for the protection of genetic resources by policy makers and develop models based on genetic resources.
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LIU, YUEFU, and ZHAO-BANG ZENG. "A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines." Genetical Research 75, no. 3 (June 2000): 345–55. http://dx.doi.org/10.1017/s0016672300004493.
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Most current statistical methods developed for mapping quantitative trait loci (QTL) based on inbred line designs apply to crosses from two inbred lines. Analysis of QTL in these crosses is restricted by the parental genetic differences between lines. Crosses from multiple inbred lines or multiple families are common in plant and animal breeding programmes, and can be used to increase the efficiency of a QTL mapping study. A general statistical method using mixture model procedures and the EM algorithm is developed for mapping QTL from various cross designs of multiple inbred lines. The general procedure features three cross design matrices, W, that define the contribution of parental lines to a particular cross and a genetic design matrix, D, that specifies the genetic model used in multiple line crosses. By appropriately specifying W matrices, the statistical method can be applied to various cross designs, such as diallel, factorial, cyclic, parallel or arbitrary-pattern cross designs with two or multiple parental lines. Also, with appropriate specification for the D matrix, the method can be used to analyse different kinds of cross populations, such as F2 backcross, four-way cross and mixed crosses (e.g. combining backcross and F2). Simulation studies were conducted to explore the properties of the method, and confirmed its applicability to diverse experimental designs.
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Czyczyło-Mysza, Cyganek, Dziurka, Quarrie, Skrzypek, Marcińska, Myśków, et al. "Genetic Parameters and QTLs for Total Phenolic Content and Yield of Wheat Mapping Population of CSDH Lines under Drought Stress." International Journal of Molecular Sciences 20, no. 23 (December 1, 2019): 6064. http://dx.doi.org/10.3390/ijms20236064.
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A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse. Genetic parameters, such as additive and epistatic effects, affecting total phenolic content, were estimated for eight year-by-drought combinations. Twenty-one markers showed a significant additive effect on total phenolic content in all eight year-by-drought combinations. These markers were located on chromosomes: 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, and 4D. A region on 4AL with a stable QTL controlling the phenolic content, confirmed by various statistical methods is particularly noteworthy. In all years and treatments, three markers significantly linked to QTLs have been identified for both phenols and yield. Thirteen markers were coincident with candidate genes. Our results indicated the importance of both additive and epistatic gene effects on total phenolic content in eight year-by-drought combinations.
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Miluchová, Martina, Michal Gábor, and Juraj Candrák. "The Effect of the Genotypes of the CSN2 Gene on Test-Day Milk Yields in the Slovak Holstein Cow." Agriculture 13, no. 1 (January 7, 2023): 154. http://dx.doi.org/10.3390/agriculture13010154.
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The aim of this study was to analyze the polymorphisms of the beta-casein gene and describe the association between the beta-casein genotypes and milk production in high milk-production Slovak Holstein cattle herds. Genomic DNA was isolated from the hair root samples of 1478 cows using a commercial column kit. The detection of the specific alleles A1 and A2 of the CSN2 gene was carried out using three molecular-genetics methods, including the TaqMan allelic discrimination assay, ACRS-PCR and SBE primer extension technology. The results of the molecular-genetic analysis were used for calculating the genetic structure in the analyzed population. All three genotypes, including A1A1 (5.28%), A1A2 (37.08%) and A2A2 (57.64%), were detected. The frequency of the allele A1 was 23.82% and the allele A2 was 76.18%. The statistical analysis and data preparation were performed using the SAS 9.2 Enterprise Guide 4.2 software. A general linear model (GLM) and the least squares means adjusted for multiple comparisons were used. A significant positive effect of the beta-casein genotype A2A2 on protein in kilograms and partially for the protein content in Holstein cows was found. Only the highest the least squares means for the fat percentage was found for the genotype A1A1 compared to the genotype A2A2. This can be considered a slightly negative trend.
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Govindaraj, M., M. Vetriventhan, and M. Srinivasan. "Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives." Genetics Research International 2015 (March 19, 2015): 1–14. http://dx.doi.org/10.1155/2015/431487.
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The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.
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Taylor, Shawn D. "Estimating flowering transition dates from status-based phenological observations: a test of methods." PeerJ 7 (September 24, 2019): e7720. http://dx.doi.org/10.7717/peerj.7720.
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The scale of phenological research has expanded due to the digitization of herbarium specimens and volunteer based contributions. These data are status-based, representing the presence or absence of a specific phenophase. Modelling the progress of plant dormancy to growth and reproduction and back to dormancy requires estimating the transition dates from these status-based observations. There are several methods available for this ranging from statistical moments using the day of year to newly introduced methods using concepts from other fields. Comparing the proficiency of different estimators is difficult since true transition dates are rarely known. Here I use a recently released dataset of in-situ flowering observations of the perennial forb Echinacea angustifolia. In this dataset, due to high sampling frequency and unique physiology, the transition dates of onset, peak, and end of flowering are known to within 3 days. I used a Monte Carlo analysis to test eight different estimators across two scales using a range of sample sizes and proportion of flowering presence observations. I evaluated the estimators accuracy in predicting the onset, peak, and end of flowering at the population level, and predicting onset and end of flowering for individual plants. Overall, a method using a Weibull distribution performed the best for population level onset and end estimates, but other estimators may be more appropriate when there is a large amount of absence observations relative to presence observations. For individual estimates a method using the midway point between the first flower presence and most prior flower absence, within 7 days, is the best option as long as the restriction does not limit the final sample size. Otherwise, the Weibull method is adequate for individual estimates as well. These methods allow practitioners to effectively utilize the large amount of status-based phenological observations currently available.
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Radušiene, Jolita, and Odeta Gudaityte. "Distribution of proazulenes in Achillea millefolium s.l. wild populations in relation to phytosociological dependence and morphological characters." Plant Genetic Resources 3, no. 2 (August 2005): 136–43. http://dx.doi.org/10.1079/pgr200568.
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Millefolii herba is one of the oldest and most important drugs in Lithuania, used both in folk and official medicine. The raw material is usually gathered from spontaneous populations. It would be reasonable to develop methods to identify the populations which produce high plant biomass and accumulate high levels of proazulenes. The quantitative variation of proazulenes and their relationships with phytosociological dependence and morphological characters of Achillea millefolium from wild populations has been examined. The vegetation records were made at 140 growing sites of A. millefolium. The species was found in 29 types of community representing different growing habitats. The resources of milfoils prevailed in dry grasslands of Arrhenatheretalia communities and ruderal habitats of Dauco-Meliliotion. The data on productivity and morphological characters were subjected to multivariate statistical analysis. A hierarchical cluster analysis indicated that higher productivity of A. millefolium populations was associated with their dependence on ruderal and segetal communities. The testing of A. millefolium plants revealed high variation for proazulenes in different communities. The proazulene-containing plants have been identified in 38% of all analysed cases. In the highest segetal and wasteland communities of Agropyretalia repentis, Sisybietalia, Digitario-Setarion, Aperion spicae-venti, Senecion fluviatilis only proazulene-free plants were found. Results of the ANOVA showed the proazulene-containing and proazulene-free plants significantly differed (P<0.05) for width of leaves and number of nodes. The presence of nodes in high number and narrow leaves in high proazulene-containing plants distinctly marked them from the proazulene-free plants. The study raised the possibility that selection based on the two morphological marker traits (node number and leaf width) and proazulene distribution in the populations would be effective for rapid identification of highly productive population(s) of pharmaceutical importance.
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Sarma, I., D. B. Phookan, L. Saikia, A. Sarma, R. Borgohain, P. Kalita, N. Sarma Barua, and J. Saikia. "Heritable variation and trait relatedness in smooth gourd (Luffa cylindrica L.) genetic resources of Assam." Journal of Environmental Biology 43, no. 6 (November 15, 2022): 779–85. http://dx.doi.org/10.22438/jeb/43/6/mrn-3099.
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Aim: The North-Eastern Region (NER) of India is endowed with enormous variability in genetic resources of smooth gourd. The present investigation was carried out to assess the hereditary variation and determine the trait relatedness in a collection of smooth gourd germplasm. Methodology: The experiment was conducted in a Randomized Complete Block Design with thirty-three smooth gourd germplasm consisting of thirty germplasm collected from Assam, two collected from Nagaland while another (Pusa Sneha) collected from IARI, New Delhi. Genetic variability parameters were estimated using standard statistical methodology. Results: The percent estimates of both genotypic coefficient of variability (31.36) and phenotypic coefficient of variability (31.83) were found to be the largest in respect of primary branches per plant. Higher estimates of both heritability in broad sense (>60%) and genetic advance as per cent of mean (>20%) were observed for the traits. Marketable fruit yield per plant had highly significant positive correlation with the number of primary branches, internodes, female flowers and fruits per plant and the weight of fruit. At genotypic level, path analysis revealed large direct effects of fruits per plant and fruit weight on marketable fruit yield. Interpretation: High h2 coupled with high GAM observed for the characters substantiates that inheritance of these characters could largely be due to genes with additive effects. Simple selection methods such as mass selection without progeny testing would be efficient for improving the population with respect to such characters. Selecting plants having higher mean values for genetically correlated traits would enhance the marketable fruit yield. Key words: Correlation, Heritability, Smooth gourd, Variability
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Oliveira, Darllan JLSF de, Maria Eduarda F. Otoboni, Bruno E. Pavan, Maria Isabel Andrade, and Pablo F. Vargas. "Genetic divergence of sweet potato genotypes based on morpho-agronomic traits." Horticultura Brasileira 39, no. 2 (April 2021): 229–35. http://dx.doi.org/10.1590/s0102-0536-20210215.
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ABSTRACT Sweet potato is a vegetable of great importance in human consumption, due to its high nutritional value. It presents high phenotypic variation, with different forms of roots, leaves and vines. Given the above, we aimed to study the genetic divergence of sweet potato genotypes based on morpho-agronomic traits. The experiment was conducted in an experimental area of Unesp, Ilha Solteira Campus, located in Selvíria-MS. The experimental design used was randomized blocks with two replicates, including 200 genotypes and ‘Beauregard’ as a biofortified control. Shoot morphological traits of the genotypes were evaluated at 110 days and root morphological traits were evaluated at 127 days after planting. We used the obtained data to perform descriptive analysis, in percentage of phenotypic classes. In order to study genetic divergence, multivariate analysis was performed, grouping was done using Tocher’s and Ward’s methods. We also analyzed relative contribution of each trait for genetic divergence. Statistical analyzes were performed using Genes software and SAS. Wide genetic variability could be verified in the population studied in this experiment, being possible to obtain genetic gains in recombination between genotypes. Grouping using Tocher’s method was more effective for discriminating dissimilarity between genotypes. The low relative importance of leaf size, internode diameter and secondary peel color makes further evaluation of these traits unnecessary, reducing labor costs, cost and execution time.
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Galuszynski, Nicholas C., and Alastair J. Potts. "Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush." PeerJ 8 (September 2, 2020): e9818. http://dx.doi.org/10.7717/peerj.9818.
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Background The current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.
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Spyrides-Cunha, Maria Helena, Clarice G. B. Demétrio, and Luis E. A. Camargo. "Proportional odds model applied to mapping of disease resistance genes in plants." Genetics and Molecular Biology 23, no. 1 (March 2000): 223–27. http://dx.doi.org/10.1590/s1415-47572000000100039.
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Molecular markers have been used extensively to map quantitative trait loci (QTL) controlling disease resistance in plants. Mapping is usually done by establishing a statistical association between molecular marker genotypes and quantitative variations in disease resistance. However, most statistical approaches require a continuous distribution of the response variable, a requirement not always met since evaluation of disease resistance is often done using visual ratings based on an ordinal scale of disease severity. This paper discusses the application of the proportional odds model to the mapping of disease resistance genes in plants amenable to expression as ordinal data. The model was used to map two resistance QTL of maize to Puccinia sorghi. The microsatellite markers bngl166 and bngl669, located on chromosomes 2 and 8, respectively, were used to genotype F2 individuals from a segregating population. Genotypes at each marker locus were then compared by assessing disease severity in F3 plants derived from the selfing of each genotyped F2 plant based on an ordinal scale severity. The residual deviance and the chi-square score statistic indicated a good fit of the model to the data and the odds had a constant proportionality at each threshold. Single-marker analyses detected significant differences among marker genotypes at both marker loci, indicating that these markers were linked to disease resistance QTL. The inclusion of the interaction term after single-marker analysis provided strong evidence of an epistatic interaction between the two QTL. These results indicate that the proportional odds model can be used as an alternative to traditional methods in cases where the response variable consists of an ordinal scale, thus eliminating the problems of heterocedasticity, non-linearity, and the non-normality of residuals often associated with this type of data.
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Amalova, Akerke, Kanat Yermekbayev, Simon Griffiths, Saule Abugalieva, Adylkhan Babkenov, Elena Fedorenko, Aigul Abugalieva, and Yerlan Turuspekov. "Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva × Paragon mapping population harvested in three regions of Kazakhstan." PeerJ 10 (November 9, 2022): e14324. http://dx.doi.org/10.7717/peerj.14324.
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Background Although genome-wide association studies (GWAS) are an increasingly informative tool in the mining of new quantitative trait loci (QTLs), a classical biparental mapping approach is still a powerful, widely used method to search the unique genetic factors associated with important agronomic traits in bread wheat. Methods In this study, a newly constructed mapping population of Pamyati Azieva (Russian Federation) × Paragon (UK), consisting of 94 recombinant inbred lines (RILs), was tested in three different regions of Kazakhstan with the purpose of QTL identification for key agronomic traits. The RILs were tested in 11 environments of two northern breeding stations (Petropavlovsk, North Kazakhstan region, and Shortandy, Aqmola region) and one southeastern station (Almalybak, Almaty region). The following eight agronomic traits were studied: heading days, seed maturation days, plant height, spike length, number of productive spikes, number of kernels per spike, thousand kernel weight, and yield per square meter. The 94 RILs of the PAxP cross were genotyped using Illumina’s iSelect 20K single nucleotide polymorphism (SNP) array and resulted in the identification of 4595 polymorphic SNP markers. Results The application of the QTL Cartographer statistical package allowed the identification of 53 stable QTLs for the studied traits. A survey of published studies related to common wheat QTL identification suggested that 28 of those 53 QTLs were presumably novel genetic factors. The SNP markers for the identified QTLs of the analyzed agronomic traits of common wheat can be efficiently applied in ongoing breeding activities in the wheat breeding community using a marker-assisted selection approach.
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Fernández, Jose D., Daniel Lobo, Gema M. Martn, René Doursat, and Francisco J. Vico. "Emergent Diversity in an Open-Ended Evolving Virtual Community." Artificial Life 18, no. 2 (April 2012): 199–222. http://dx.doi.org/10.1162/artl_a_00059.
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Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires species' characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.
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Baktemur, Gökhan, Hatıra Taşkın, and Saadet Büyükalaca. "Comparison of Different Methods for Separation of Haploid Embryo Induced through Irradiated Pollen and Their Economic Analysis in Melon (Cucumis melovar.inodorus)." Scientific World Journal 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/529502.
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Irradiated pollen technique is the most successful haploidization technique withinCucurbitaceae. After harvesting of fruits pollinated with irradiated pollen, classical method called as “inspecting the seeds one by one” is used to find haploid embryos in the seeds. In this study, different methods were used to extract the embryos more easily, quickly, economically, and effectively. “Inspecting the seeds one by one” was used as control treatment. Other four methods tested were “sowing seeds direct nutrient media,” “inspecting seeds in the light source,” “floating seeds on liquid media,” and “floating seeds on liquid media after surface sterilization.” Y2 and Y3 melon genotypes selected from the third backcross population of Yuva were used as plant material. Results of this study show that there is no statistically significant difference among methods “inspecting the seeds one by one,” “sowing seeds direct CP nutrient media,” and “inspecting seeds in the light source,” although the average number of embryos per fruit is slightly different. No embryo production was obtained from liquid culture because of infection. When considered together with labor costs and time required for embryo rescue, the best methods were “sowing seeds directly in the CP nutrient media“ and ”inspecting seeds in the light source.”
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Hallmann, J., J. W. Kloepper, and R. Rodríguez-Kábana. "Application of the Scholander pressure bomb to studies on endophytic bacteria of plants." Canadian Journal of Microbiology 43, no. 5 (May 1, 1997): 411–16. http://dx.doi.org/10.1139/m97-058.
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The Scholander pressure bomb system, which expresses vascular plant sap, was compared with the trituration method, in which roots are surface disinfested and triturated, for recovery of endophytic bacteria. The two methods were compared for recovery of indigenous and introduced endophytes from roots of several plant genera. The pressure bomb method was acceptable for routine recovery of endophytes from cotton (Gossypium hirsutum), soybean (Glycine max), and bean (Phaseolus vulgaris), but owing to tissue collapse under pressure, the method did not work reliably for cucumber (Cucumis sativa) or tomato (Lycopersicon esculentum) seedlings. High bacterial densities on the root surface, experimentally obtained by dipping cotton roots into a suspension of Enterobacter asburiae JM22 immediately prior to processing, did not affect the population densities of recovered indigenous endophytic bacteria by the pressure bomb technique but resulted in increased bacterial densities for the trituration method. Internal populations of JM22 following application as a seed treatment were statistically equivalent with the trituration and pressure bomb techniques. Analysis of taxonomic diversity of a group of indigenous endophytes recovered with the trituration and pressure bomb techniques indicated some differences between the two groups. The total number of bacterial genera and species recovered was greater using the pressure bomb method. Gram-positive species, such as Bacillus spp., were more frequently isolated with the trituration method than with the pressure bomb method. Agrobacterium radiobacter and less common species were more often isolated using the pressure bomb technique. Pseudomonas spp. and Phyllobacterium spp. were recovered with equal frequencies using both techniques. These results suggest that the two techniques sample two different internal habitats available for colonization by endophytic bacteria, i.e., the trituration method recovering mainly endophytes residing in the root cortex and the pressure bomb method detecting vascular colonists. A combination of both methods is recommended for understanding the full pattern of internal plant colonization by endophytic bacteria.Key words: endophytic bacteria, Scholander pressure bomb, isolation method, cotton.
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Khan, Umar Jamal, Uzma Mumtaz, Muhammad Amjad Chaudhary, and Murad Habib. "Injection Sclerotherapy in Encysted Hydrocele in Paediatric Population." Pakistan Journal of Medical and Health Sciences 16, no. 5 (May 30, 2022): 1538–39. http://dx.doi.org/10.53350/pjmhs221651538.
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Objective: To determine the role of Sclerotherapy for treating encysted hydrocele in the paediatric population. Study Design: Prospective Study Place and Duration of Study: Department of Paediatric Surgery, Children Hospital Pakistan Institute of Medical Sciences, Islamabad for six months (1st November,2021 to 30th April,2022) Patients and Methods: This study on the captioned topic involved 39 patients aging 2 to 12 years who attended the outpatient department with the complaints of scrotal swelling. In order to rule out non-communicationg hydroceles, these patients were examined clinically and scrotal ultrasound was advised to all the patients which was carried out by them accordingly. In this study, the single team performed the above said procedure on Operation theatre days regularly. The incidence of complications was also monitored with each follow up visits on 1st, 3rd and 6th weeks after the procedure. Results: Study was conducted on 39 children having mean age 4.77 ± 2.860. Pre and post volumes of hydrocele fluid were satistically significant (p≤0.05) with average of 9.00 and 3.269 respectively. Complication rates were decreasing at every follow-up and these were not statisticaly significant (p≥0.05), recurrence complication was significant (p≤0.05). Conclusion: Sclerotherapy has been found to be a positive alternate approach, which is simpler to perform, less time consuming and involving lower complication rate. Keywords: Encysted Hydrocele, Paediatric Population, Sclerotherapy
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Li, Yahui, Jing Wu, and Gehong Zhu. "Efficacy Analysis of Comprehensive Nursing in the Care of Ovarian Carcinoma Treated with Paclitaxel Combined with Nedaplatin." Computational and Mathematical Methods in Medicine 2022 (September 6, 2022): 1–6. http://dx.doi.org/10.1155/2022/9398823.
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Objective. To determine the effectiveness of comprehensive nursing in the care of ovarian carcinoma (OC) patients treated with paclitaxel (PTX) plus nedaplatin (NDP). Methods. The research population comprised 180 advanced OC patients who received treatment in the Shaanxi Cancer Hospital between November 2018 and November 2021. The enrolled cases were assigned to two groups based on different nursing plans: an observation group (OG) with 100 cases treated with comprehensive nursing and a control group (CG) with 80 cases intervened by conventional nursing. Intergroup comparisons were performed to identify statistical significance in terms of the following parameters: serum NGF, TK1, and CA15-3 levels; VAS, SAS, and SDS scores; nursing compliance; incidence of adverse reactions; and nursing satisfaction. Results. Compared with CG, OG showed the following: (1) lower posttreatment NGF, TK1, and CA15-3 levels; (2) lower scores of SAS and SDS; (3) higher nursing compliance; and (4) lower incidence of adverse reactions and higher nursing satisfaction after nursing. Conclusions. Comprehensive nursing far outperformed conventional nursing in the care of advanced OC patients treated with PTX plus NDP, which is worth popularizing.
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Kuznetsov, V. M. "Comparison of methods for evaluating genetic differentiation of populations by microsatellite markers." Agricultural Science Euro-North-East 21, no. 2 (April 22, 2020): 169–82. http://dx.doi.org/10.30766/2072-9081.2020.21.2.169-182.
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Comparative studies of eight methods for evaluation of genetic differences by microsatellite (STR) markers (11 loci) DNA were carried out using the example of seven breed samples (N = 84) of dairy cattle. The range of indicators of genetic diversity of samples was as follows: the number of alleles per locus 3.5-6.2, the number of effective alleles per locus – 2.4-4.3, the Shannon index – 0.95-1.56, the observed and expected heterozygosity – 0.56-0.97 and 0.53-0.75. Evaluation summary of genetic differentiation by group A methods (FST, GST, and GST(NEI)) were 13.4, 10.3, and 11.8% (pperm < 0.001); the differences between the estimates were statistically insignificant. Estimates by group B methods (G'ST(HED), G''ST(HED), DEST) were 36.4, 37.5 and 29.2% (pperm < 0.001); differences between the estimates were also statistically insignificant. Estimates obtained by group B methods were statistically significantly higher than those obtained by group A methods by almost 3 times. Methods of groups A, B, and C (GDN and uGDN) were used to calculate paired genetic distances in the samples. Despite significant dif-ferences in estimates, the Mantel test showed a high degree of correspondence of the genetic distance matrices (RM≥0.97; pperm < 0.001), which was manifested in the projections of genetic relations of breed samples on plane 1 and 2 of the principal coordinates. The first two principal coordinates explained 97-99% of STR variation in the genetic distance matrices. It can be assumed that when assessing the actual differentiation of populations by STR-markers, the methods of group B should be used and among them the statistics of DEST as independent of the level of mean within-subpopulation heterozygosity. In the study of spatial ordination of gene pools of populations, in all probability, it is reasonably to use any method.
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Alemneh, Derebe. "Ethnobotanical Study of Plants Used for Human Ailments in Yilmana Densa and Quarit Districts of West Gojjam Zone, Amhara Region, Ethiopia." BioMed Research International 2021 (February 18, 2021): 1–18. http://dx.doi.org/10.1155/2021/6615666.
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Like other populations of developing countries, most of the populations of Ethiopia depend greatly on the use of traditional herbal medicines as the primary source of health care. However, these resources have been degraded throughout the country. Therefore, recording and documenting medicinal plants are essential for the future conservation of the species. Thus, the current study is related to this issue. Three hundred ninety-five informants participated in this study. The main data collection tools were semistructured interviews, discussions, and observation. The data were analyzed using both qualitative and quantitative methods. The quantitative methods (informant consensus factor, fidelity level) were used to analyze the level of homogeneity of the data, the agreements of informants, and the healing potential of medicinal plants. The ranking exercises (preference and direct matrix ranking) were used to quantify the most preferred and multipurpose medicinal plants. A statistical test was conducted using SPSS version 20 to test knowledge differences among the people. Following the analysis, 112 species of medicinal plants with 62 families were recorded. Most of the species were herbs, of which Fabaceae was the dominant family. Blood pressure and asthma were the most commonly reported human health problems. Most of the remedies were prepared from leaves, and most of them were prepared by pounding and were applied orally. Gastrointestinal diseases had the highest informant consensus. Five medicinal plants were recorded with the highest healing potential value for malaria, asthma, tapeworm, cough, and stomach ulcer. Verbascum sinaiticum Benth. was the most preferred medicinal plant in treating blood pressure. Trigonella foenum-graecum L. had the highest use value. The analysis results showed that local people showed significant knowledge differences ( p < 0.05 ). In conclusion, the indigenous people have a wealth of indigenous herbal knowledge. Therefore, to sustain the wealth of indigenous knowledge of the districts, immediate and well-designed conservation practices of medicinal plants should be conducted.
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Kryukova, A. V., A. N. Mustafina, and L. M. Abramova. "Comparative indicators of morphology and seed productivity in rare <i>Iris</i> L. spp. within their natural habitats and under cultivation in the Southern Urals." Proceedings on applied botany, genetics and breeding 183, no. 3 (October 4, 2022): 171–82. http://dx.doi.org/10.30901/2227-8834-2022-3-171-182.
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Background. Wild irises are promising for cultivation and use in breeding practice. Many of them are included in Red Lists, as they disappear under the impact of anthropogenic factors. It is biologically important to study their morphometric and reproductive parameters, so that the most stable and highly ornamental species could be recommended for expanding the range of flower plants.Materials and methods. Biological features of four Iris L. species rarely occurring in the Southern Urals: I. pseudacorus L., I. pumila L., I. scariosa Wild. ex Link, and I. humilis Georgi, were studied in 2012–2017 in 23 natural and 4 introduced cenopopulations. Individual parameters were compared for 25 medium-age plants from each cenopopulation in their mass-flowering and fruiting phase according to 11 biometric parameters using conventional methods. Statistical significance of the differences was assessed using Student’s t-test.Results. Comparison of morphometric parameters of four rare Iris spp. naturally occurring and introduced in Bashkortostan during six years of research showed significant differences between cenopopulations at a 5% significance level for most traits of I. pumila and I. pseudacorus. As for I. scariosa and I. humilis, differences were mostly insignificant (at tfact< 2.064). Mean values of most reproductive parameters for I. scariosa, I. humilis and I. pseudacorus were significantly lower under introduction conditions than in natural populations. Under cultivation, seed productivity of I. pumila increased. Variability of most morphometric features of the studied irises was within normal response limits for the studied species. When cultivated in the environments of the Bashkir Cis-Urals, they bloom and bear fruit every year, except for I. humilis.Conclusion. Of the four rare Iris spp., I. pumila is recommended for landscaping settlements in the South Urals as the most stable species.
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Belbaraka, Rhizlane, Nada Benhima, Ahmed Laatabi, Mohammed El Fadli, and Ismail Essâdi. "Incidence Trends of Cancer in Morocco: The Tale of the Oncological Center of Marrakech (Morocco) over 8 Years." Journal of Cancer Epidemiology 2022 (February 28, 2022): 1–10. http://dx.doi.org/10.1155/2022/3307194.
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Background. Determining cancer incidence and mortality is a key factor in the implementation of health policies and cancer prevention strategies. This report aims to describe the trends of cancer incidence in a single referral oncology department from the Marrakech region (Morocco). Material and Methods. All new cancer cases of age ≥ 15 years registered at the Medical Oncology department of Mohammed VI University Hospital of Marrakesh between January 1, 2012, and December 31, 2019, were included. Central nervous system (CNS) cancers, tumors of hematopoietic and lymphoid tissues, and thyroid cancers for which chemotherapy was not indicated or was managed in other cancer-specialized departments were excluded from the analysis. Manual data collection from printed archived medical records of the study population was performed. Descriptive statistics were analyzed using R software and Joinpoint Regression Program. Results. A total of 15648 new cancer cases were analyzed. Missing data ( n = 1822 ) accounted for 11.64%, and 4.1% ( n = 652 ) were excluded. The final statistical analysis and registration included 13174 cases. The median age at diagnosis is 54 years for females and 61 years for males. Female patients outnumbered males with a ratio of 1.58 among all age groups except those aged ≥75 y. The age-standardized incidence rate (ASIR) for all sites was 68,0 per 100.000 person-years, which has increased with an annual percent change (APC) of 10.61%. The five most common malignancies among males are lung, stomach, prostate, colic, and rectal cancers. Among females, the five most frequent cancers are breast, cervix, ovary, colon, and stomach. Conclusion. The higher incidence observed in our results translates into a growing burden on the center and is expected to impact our ability to deliver cancer care. Epidemiological studies to identify risk factors and effective efforts are needed to further invest in cancer control and prevention plans.
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Zou, Wei, and Zhao-Bang Zeng. "Statistical Methods for Mapping Multiple QTL." International Journal of Plant Genomics 2008 (June 8, 2008): 1–8. http://dx.doi.org/10.1155/2008/286561.
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Since Lander and Botstein proposed the interval mapping method for QTL mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for QTL analysis. Recent research progress has been focused on statistical methods and issues for mapping multiple QTL together. In this article, we review this progress. We focus the discussion on the statistical methods for mapping multiple QTL by maximum likelihood and Bayesian methods and also on determining appropriate thresholds for the analysis.
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Gudova, Lyudmila Aleksandrovna, Sergey Aleksandrovich Zaytsev, Valeriy Ivanovich Zhuzhukin, Lyudmila Gennadievna Kurasova, and Andrey Vladimirovich Lekarev. "Using multivariate statistical methods to estimate the model maize population." Agrarian Scientific Journal, no. 7 (August 5, 2021): 9–15. http://dx.doi.org/10.28983/asj.y2021i7pp9-15.
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In order to objectively assess the degree of similarity of varieties and hybrids by a set of indicators and to interpret a large amount of data in breeding practice, methods of multidimensional statistics are used, including factor and cluster analyzes. The study included 42 maize hybrids (FAO 100-499) of the selection of various scientific institutions of Russia, which were assessed according to the following characteristics: the length of the interphase stage of seedlings - flowering of panicles and ears, plant height, ear attachment height, grain yield, number of grains per ear, crude protein and crude fat content. Factor analysis made it possible to calculate the correlation coefficients between the variables under consideration and to reveal high positive correlations between the interfacial stages of a panicle seedlings–flowering and seedlings–-flowering of ears (r = 0.99), plant height and ear attachment height (r = 0, 81), the length of the interphase periods and the ear height (r = 0.77). A significant correlation coefficient was determined between the traits, the length of the interphase periods, seedlings – flowering of panicles and ears with grain yield (r = 0.34 and 0.36, respectively), grain yield and number of grains per ear (r = 0.37). When calculating the weights of the variables for the components, it was found out that the largest contribution (variance 54.814%) to the first hypothetical factor was made by the following signs: interphase periods of panicle seedlings–flowering and of ear seedlings–flowering, plant height, ear attachment height, grain yield, 1000 grain weight. The use of cluster analysis made it possible to group the studied hybrids at 32 iteration steps (Euclidean distance - 7.340) into 10 clusters with different breeding values. The hybrids that make up the clusters are characterized by a similar set of features within the clusters and significant differences between the clusters, confirmed by the method of unorganized repetitions of one-way ANOVA.
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Beaumont, Mark A., Wenyang Zhang, and David J. Balding. "Approximate Bayesian Computation in Population Genetics." Genetics 162, no. 4 (December 1, 2002): 2025–35. http://dx.doi.org/10.1093/genetics/162.4.2025.
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Abstract We propose a new method for approximate Bayesian statistical inference on the basis of summary statistics. The method is suited to complex problems that arise in population genetics, extending ideas developed in this setting by earlier authors. Properties of the posterior distribution of a parameter, such as its mean or density curve, are approximated without explicit likelihood calculations. This is achieved by fitting a local-linear regression of simulated parameter values on simulated summary statistics, and then substituting the observed summary statistics into the regression equation. The method combines many of the advantages of Bayesian statistical inference with the computational efficiency of methods based on summary statistics. A key advantage of the method is that the nuisance parameters are automatically integrated out in the simulation step, so that the large numbers of nuisance parameters that arise in population genetics problems can be handled without difficulty. Simulation results indicate computational and statistical efficiency that compares favorably with those of alternative methods previously proposed in the literature. We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC.
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Yousefzadeh, Hamed, Shahla Raeisi, Omid Esmailzadeh, Gholamali Jalali, Malek Nasiri, Łukasz Walas, and Gregor Kozlowski. "Genetic Diversity and Structure of Rear Edge Populations of Sorbus aucuparia (Rosaceae) in the Hyrcanian Forest." Plants 10, no. 7 (July 19, 2021): 1471. http://dx.doi.org/10.3390/plants10071471.
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Sorbus aucuparia (Rosaceae) is a small tree species widely distributed in Eurasia. The Hyrcanian forest is the southernmost distribution limit of this species. Severe habitat degradation and inadequate human interventions have endangered the long-term survival of this species in this region, and it is necessary to develop and apply appropriate management methods to prevent the loss of its genetic diversity. In this study, we used 10 SSR markers in order to evaluate the genetic diversity of this taxon. Leaf samples were collected from five known populations of S. aucuparia throughout its distribution area in the Hyrcanian forest. Expected heterozygosity ranged from 0.61 (ASH) to 0.73, and according to the M-ratio, all populations showed a significant reduction in effective population size, indicating a genetic bottleneck. Global FST was not statistically significant and attained the same values with and without excluding null alleles (ENA) correction (FST = 0.12). Bayesian analysis performed with STRUCTURE defined two genetic clusters among the five known populations, while the results of discriminant analysis of principal components (DAPC) identified three distinct groups. The average proportion of migrants was 22. In general, the gene flow was asymmetrical, with the biggest differences between immigration and emigration in Barzekoh and Asbehriseh. The Mantel test showed that there was no significant correlation between genetic distance (FST) and geographic distance in S. aucuparia. The best pathway for theoretical gene flow is located across the coast of the Caspian Sea and significant spatial autocorrelation was observed in only one population. In order to reduce the extinction risk of very small and scattered populations of S. aucuparia in the Hyrcanian forest, it is very important to establish and/or enhance the connectivity through habitat restoration or genetic exchange.
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Velcheva, N., and S. Petrova. "Statistical analysis of genetic diversity using faba bean landraces database." Agricultural Science and Technology 12, no. 3 (September 2020): 211–15. http://dx.doi.org/10.15547/ast.2020.03.033.
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Abstract. Evaluation of genetic diversity among landraces could be an invaluable aid related to the sustainable use of ex situ collections. Statistical methods are currently available for analysis of databases from investigation of stored germplasm. Faba bean (Vicia faba L.) is a self-pollinating with high percentage of foreign pollination legume crop with a great importance for food and forage due to its high protein content as well as the important role in soil fertility and nitrogen fixation. The local populations are well adapted to specific agro-climatic conditions in the growing areas and are a rich initial material for the breeding programs. The purpose of this study is to establish the genetic diversity of 21 Bulgarian faba bean landraces by important traits in order to review the current potential of conserved germplasm for its sustainable use. All genotypes, included in the study, are collected from expeditions in the country, recorded in the National Register for Plant Genetic Resources and long term stored at the National Genebank. They are characterized according to the International Faba Bean Descriptors. The cluster analysis results show a high genetic diversity in the collection and the variability of each studied trait is presented. The factor analysis, which complements the cluster analysis, gives a reason to group the genotypes with their features into groups that have a breeding value. Genetic diversity in the studied collection has been identified and some of the landraces could be included in future breeding programs.
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Reyes-Ortiz, José Luis, Pablo Octavio-Aguilar, Lauro López-Mata, and Arturo Sánchez-González. "Diversity and Genetic Structure of Dicksonia navarrensis (Dicksoniaceae) Populations in the Mexican Sierra Madre Oriental." Tropical Conservation Science 15 (January 2022): 194008292211285. http://dx.doi.org/10.1177/19400829221128539.
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Background and Research Aims Dicksonia navarrensis is a species of tree fern at risk of extinction, distributed in the montane cloud forest (MCF) of the Americas from the central region of Mexico to Ecuador. In Mexico, populations of this species grow in primary vegetation of the MCF, in a matrix with a high degree of fragmentation and under threat of disappearance. Methods In the present study, the diversity and genetic structure of seven populations of D. navarrensis that are distributed in the cloud forest of the Sierra Madre Oriental were evaluated, with both standard laboratory and statistical analysis techniques, using 11 microsatellites developed for the genus Dicksonia. Results A total of 33 alleles were found. Genetic diversity differed between populations, and some presented low heterozygosity. Using assignment tests, three genetic groups were identified, associated with the geographical distribution of the populations; those from the north maintain connectivity with each other but diverge highly from the populations in the south, probably due to processes of isolation by distance (local environment), genetic drift, and natural selection. Conclusion The northernmost population, which is more isolated from the rest, has a broader genetic reservoir, which can be useful for maintaining the genetic diversity of the species. In the other populations, with less genetic diversity, the introduction of individuals and/or the dispersion of spores is important, to maintain and increase the genetic variability that they still possess, but which could disappear in a short time if their habitat continues to deteriorate at a high degree. Implications for Conservation The results obtained provide basic information that can be used in management and conservation plans, because the populations with the greatest genetic diversity and the possible processes that are influencing the genetic structure of the species were identified.