Academic literature on the topic 'QTL (Quantitative trait locus/loci) mapping'
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Journal articles on the topic "QTL (Quantitative trait locus/loci) mapping"
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Xu, Shizhong, and Zhiqiu Hu. "Mapping Quantitative Trait Loci Using Distorted Markers." International Journal of Plant Genomics 2009 (February 21, 2009): 1–11. http://dx.doi.org/10.1155/2009/410825.
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Quantitative trait locus (QTL) mapping is usually performed using markers that follow a Mendelian segregation ratio. We developed a new method of QTL mapping that can use markers with segregation distortion (non-Mendelian markers). An EM (expectation-maximization) algorithm is used to estimate QTL and SDL (segregation distortion loci) parameters. The joint analysis of QTL and SDL is particularly useful for selective genotyping. Application of the joint analysis is demonstrated using a real life data from a wheat QTL mapping experiment.
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Xu, Shizhong, and William R. Atchley. "Mapping Quantitative Trait Loci for Complex Binary Diseases Using Line Crosses." Genetics 143, no. 3 (July 1, 1996): 1417–24. http://dx.doi.org/10.1093/genetics/143.3.1417.
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Abstract A composite interval gene mapping procedure for complex binary disease traits is proposed in this paper. The binary trait of interest is assumed to be controlled by an underlying liability that is normally distributed. The liability is treated as a typical quantitative character and thus described by the usual quantitative genetics model. Translation from the liability into a binary (disease) phenotype is through the physiological threshold model. Logistic regression analysis is employed to estimate the effects and locations of putative quantitative trait loci (our terminology for a single quantitative trait locus is QTL while multiple loci are referred to as QTLs). Simulation studies show that properties of this mapping procedure mimic those of the composite interval mapping for normally distributed data. Potential utilization of the QTL mapping procedure for resolving alternative genetic models (e.g., single- or two-trait-locus model) is discussed.
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Tsilo, T. J., J. B. Ohm, G. A. Hareland, S. Chao, and J. A. Anderson. "Quantitative trait loci influencing end-use quality traits of hard red spring wheat breeding lines." Czech Journal of Genetics and Plant Breeding 47, Special Issue (October 20, 2011): S190—S195. http://dx.doi.org/10.17221/3279-cjgpb.
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Wheat bread-making quality is influenced by a complex group of traits including dough visco-elastic characteristics. In this study, quantitative trait locus/loci (QTL) mapping and analysis were conducted for endosperm polymeric proteins together with dough mixing strength and bread-making properties in a population of 139 (MN98550 × MN99394) recombinant inbred lines that was evaluated at three environments in 2006. Eleven chromosome regions were associated with endosperm polymeric proteins, explaining 4.2–31.8% of the phenotypic variation. Most of these polymeric proteins QTL coincided with several QTL for dough-mixing strength and bread-making properties. Major QTL clusters were associated with the low-molecular weight glutenin gene Glu-A3, the two high-molecular weight glutenin genes Glu-B1 and Glu-D1, and two regions on chromosome 6D. Alleles at these QTL clusters have previously been proven useful for wheat quality except one of the 6D QTL clusters.
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Ungerer, Mark C., Solveig S. Halldorsdottir, Jennifer L. Modliszewski, Trudy F. C. Mackay, and Michael D. Purugganan. "Quantitative Trait Loci for Inflorescence Development in Arabidopsis thaliana." Genetics 160, no. 3 (March 1, 2002): 1133–51. http://dx.doi.org/10.1093/genetics/160.3.1133.
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Abstract Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler × Col and Cvi × Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi × Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.
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REBAÏ, AHMED, and BRUNO GOFFINET. "More about quantitative trait locus mapping with diallel designs." Genetical Research 75, no. 2 (April 2000): 243–47. http://dx.doi.org/10.1017/s0016672399004358.
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We present a general regression-based method for mapping quantitative trait loci (QTL) by combining different populations derived from diallel designs. The model expresses, at any map position, the phenotypic value of each individual as a function of the specific-mean of the population to which the individual belongs, the additive and dominance effects of the alleles carried by the parents of that population and the probabilities of QTL genotypes conditional on those of neighbouring markers. Standard linear model procedures (ordinary or iteratively reweighted least-squares) are used for estimation and test of the parameters.
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Jannink, Jean-Luc, and Ritsert Jansen. "Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches." Genetics 157, no. 1 (January 1, 2001): 445–54. http://dx.doi.org/10.1093/genetics/157.1.445.
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AbstractThe discovery of epistatically interacting QTL is hampered by the intractability and low power to detect QTL in multidimensional genome searches. We describe a new method that maps epistatic QTL by identifying loci of high QTL by genetic background interaction. This approach allows detection of QTL involved not only in pairwise but also higher-order interaction, and does so with one-dimensional genome searches. The approach requires large populations derived from multiple related inbred-line crosses as is more typically available for plants. Using maximum likelihood, the method contrasts models in which QTL allelic values are either nested within, or fixed over, populations. We apply the method to simulated doubled-haploid populations derived from a diallel among three inbred parents and illustrate the power of the method to detect QTL of different effect size and different levels of QTL by genetic background interaction. Further, we show how the method can be used in conjunction with standard two-locus QTL detection models that use two-dimensional genome searches and find that the method may double the power to detect first-order epistasis.
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Paran, I., I. L. Goldman, and D. Zamir. "Morphological Trait QTL Mapping in Tomato Recombinant Inbred Line Population." HortScience 30, no. 4 (July 1995): 788D—788. http://dx.doi.org/10.21273/hortsci.30.4.788d.
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Quantitative trait loci influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato (Lycopersicon esculentum) with a related wild species (L. cheesmanii). One-hundred-thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 RIL families. Morphological traits, including plant height, fresh weight, node number, first flower-bearing node, leaf length at nodes three and four, and number of branches, were measured in replicated trials during 1991, 1992, and 1993. Significant (P ≤ 0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. Lower plant height, more branches, and shorter internode length were generally associated with RFLP alleles from the L. cheesmanii parent. QTL with large effects on a majority of the morphological traits measured were detected at chromosomes 2, 3, and 4. Large additive effects were measured at significant marker loci for many of the traits measured. Several marker loci exhibited significant associations with numerous morphological traits, suggesting their possible linkage to genes controlling growth and development processes in Lycopersicon.
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Juenger, Thomas, Michael Purugganan, and Trudy F. C. Mackay. "Quantitative Trait Loci for Floral Morphology in Arabidopsis thaliana." Genetics 156, no. 3 (November 1, 2000): 1379–92. http://dx.doi.org/10.1093/genetics/156.3.1379.
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Abstract A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta × Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler × Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.
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WAYNE, M. L., J. B. HACKETT, C. L. DILDA, S. V. NUZHDIN, E. G. PASYUKOVA, and T. F. C. MACKAY. "Quantitative trait locus mapping of fitness-related traits in Drosophila melanogaster." Genetical Research 77, no. 1 (February 2001): 107–16. http://dx.doi.org/10.1017/s0016672300004894.
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We examined the genetic architecture of four fitness-related traits (reproductive success, ovariole number, body size and early fecundity) in a panel of 98 Oregon-R × 2b3 recombinant inbred lines (RILs). Highly significant genetic variation was observed in this population for female, but not male, reproductive success. The cross-sex genetic correlation for reproductive success was 0·20, which is not significantly different from zero. There was significant genetic variation segregating in this cross for ovariole number, but not for body size or early fecundity. The RILs were genotyped for cytological insertion sites of roo transposable elements, yielding 76 informative markers with an average spacing of 3·2 cM. Quantitative trait loci (QTL) affecting female reproductive success and ovariole number were mapped using a composite interval mapping procedure. QTL for female reproductive success were located at the tip of the X chromosome between markers at cytological locations 1B and 3E; and on the left arm of chromosome 2 in the 30D–38A cytological region. Ovariole number QTL mapped to cytological intervals 62D–69D and 98A–98E, both on the third chromosome. The regions harbouring QTL for female reproductive success and ovariole number were also identified as QTL for longevity in previous studies with these lines.
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Li, Jiahan, Kiranmoy Das, Guifang Fu, Chunfa Tong, Yao Li, Christian Tobias, and Rongling Wu. "EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids." International Journal of Plant Genomics 2010 (January 5, 2010): 1–10. http://dx.doi.org/10.1155/2010/216547.
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Multivalent tetraploids that include many plant species, such as potato, sugarcane, and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such as double reduction. We develop a statistical method for mapping multivalent tetraploid QTLs by considering these cytogenetic properties. This method is built in the mixture model-based framework and implemented with the EM algorithm. The method allows the simultaneous estimation of QTL positions, QTL effects, the chromosomal pairing factor, and the degree of double reduction as well as the assessment of the estimation precision of these parameters. We used simulated data to examine the statistical properties of the method and validate its utilization. The new method and its software will provide a useful tool for QTL mapping in multivalent tetraploids that undergo double reduction.
Dissertations / Theses on the topic "QTL (Quantitative trait locus/loci) mapping"
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Pinheiro, Cassia Renata. "Mapeamento de QTL (Quantitative Trait Loci) associados à resposta do maracujá-doce à bacteriose usando a abordagem de modelos mistos." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-23062015-161305/.
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O maracujazeiro-doce (Passiflora alata Curtis) é uma espécie de cruzamento e diploide (2n = 18) que vem se destacando no Brasil por alcançar melhores cotações no mercado de frutas. Apesar disso, é sensível às adversidades em monocultura, sendo extremamente afetada por variações climáticas, pragas e doenças, dentre elas, a bacteriose causada por Xanthomonas axonopodis pv. passiflorae. O patógeno é endêmico no país, apresentando considerável variabilidade genética nas populações naturais. O presente trabalho teve como objetivo contribuir para o melhoramento genético do maracujazeiro-doce por meio do mapeamento de QTL (Quantitative Trait Loci) relacionados à resistência à bacteriose de uma população F1 segregante, composta de 100 indivíduos e oriunda do cruzamento simples entre dois acessos não endogâmicos. A população foi mantida em casa de vegetação, em delineamento em blocos ao acaso, e foi inoculada com três isolados bacterianos, M129, PA8-2 e AP302, durante 2010, 2012 e 2013, respectivamente. Aos 14 dias após a inoculação, as folhas foram fotografadas e a partir das imagens digitalizadas foram mensuradas as áreas: sadia, de clorose, necrose e lesão (soma das áreas de clorose e necrose), além da área total da folha. Inicialmente, foi realizada uma análise exploratória dos dados e subsequentemente foram selecionados os caracteres área de necrose e de lesão foliar para fins de mapeamento de QTL. Para tanto foi usada uma estratégia desenvolvida para a detecção de QTL em F1 segregantes, com base em modelos mistos, considerando diferentes estruturas de variância e covariância, visando explicar os padrões de variação existentes. A herdabilidade variou de 14% a 64% para o carater necrose, e se manteve estável (28%) para o carater área de lesão, nos três anos de avaliação. Com base em um mapa de ligação integrado previamente construído, foi realizado o mapeamento de QTL por intervalo composto. Foram identificados 20 QTL, sendo 9 deles referentes à necrose e 11 referentes à lesão. Os efeitos individuais variaram de 0,2% a 15,7%, sendo que dois QTL de maior efeito (R² = 15,7%) foram identificados em resposta ao isolado PA8-2, um localizado no grupo de ligação III e o outro no IV do mapa genético integrado do maracujazeiro-doce. Essas informações, aliadas a outros estudos relacionados à produção de frutos, devem contribuir para o melhoramento do maracujazeiro-doce.The sweet passion fruit (Passiflora alata Curtis) is an outcrossing and diploid (2n = 18) species that is achieving a competitive advantage in the fruit markets in Brazil. Nevertheless, the crop is sensitive to monoculture, being greatly affected by weather changes, pests and diseases, among them the bacterial disease caused by Xanthomonas axonopodis pv. passiflorae. The pathogen is endemic in the country, with considerable genetic variability in natural populations. The present study aimed to contribute to genetic improvement of sweet passion fruit through QTL (Quantitative Trait Loci) mapping associated with bacterial resistance using a F1 segregating population containing 100 individuals, which resulted from a single cross between two outbred accessions. The population was kept in a greenhouse, arranged in a randomized block design, and innoculated with three bacterial isolates, M129, PA8-2 and AP302, during 2010, 2012 and 2013, respectively. At 14 days after inoculation, the inoculated leaves were photographed, and the following areas from the scanned images were measured: healthy, with chlorosis, necrosis and leaf lesion (sum of the areas with chlorosis and necrosis), in addition to the total area of the leaf. Initially all data were investigated trough an exploratory analysis and those relative to necrotic and leaf lesion areas were subsequently used for QTLmapping. For that we used a strategy developed for QTL detection in F1 segregating populations based on composite interval mapping and mixed models considering different variance and covariance structures in order to explain the existing patterns of variation. Heritabilities ranged from 14% to 64% for the trait necrosis, and remained stable (28%) for the trait leaf lesion for the three years of evaluation. Based on an integrated linkage map previously constructed, we performed a composite interval mapping of QTL. Twenty QTL were identified, 9 of them related to necrosis and 11 related to the leaf lesion. The individual effects ranged from 0,2% to 15,7%, and two large-effect QTL (R² = 15,7%) were identified in response to isolate PA8-2, one assigned to linkage group III and other to linkage group IV of the integrated genetic map of sweet passion fruit. This information combined with other studies related to fruit production may contribute to sweet passion fruit breeding.
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Sadeque, Abdus. "Genetic mapping of noodle quality characters and rust resistance in hexaploid wheat." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3795.
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Polyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.
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Sadeque, Abdus. "Genetic mapping of noodle quality characters and rust resistance in hexaploid wheat." University of Sydney, 2008. http://hdl.handle.net/2123/3795.
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Doctor of PhilosophyPolyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.
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Logeswaran, Sayanthan. "Mapping quantitative trait loci in microbial populations." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4881.
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Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual the extreme progeny may be selected by multiple generations of asexual reproduction and selection. In this thesis I will analyse this method of measuring phenotype in asexual cross progeny. The aim is to examine the behaviour of marker allele frequency due to selection over many generations, and also to identify statistically significant changes in frequency in the selected population. I will show that stochasticity in marker frequency in the selected population arises due the finite initial population size. For Mendelian traits, the initial population size should be at least in the low to mid hundreds to avoid spurious changes in marker frequency in the selected population. For quantitative traits the length of time selection is applied for, as well as the initial population size, will affect the stochasticity in marker frequency. The longer selection is applied for, the more chance of spurious changes in marker frequency. Also for quantitative traits, I will show that the presence of epistasis can hinder changes in marker frequency at selected loci, and consequently make identification of selected loci more difficult. I also show that it is possible to detect epistasis from the marker frequency by identifying reversals in the direction of marker frequency change. Finally, I develop a maximum likelihood based statistical model that aims to identify significant changes in marker frequency in the selected population. I will show that the power of this statistical model is high for detecting large changes in marker frequency, but very low for detecting small changes in frequency.
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Joehanes, Roby. "Multiple-trait multiple-interval mapping of quantitative-trait loci." Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1605.
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Joehanes, Roby. "Generalized and multiple-trait extensions to Quantitative-Trait Locus mapping." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1919.
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Lu, Yue. "Genetic mapping of quantitative trait loci for slow-rusting traits in wheat." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/32179.
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Doctor of PhilosophyDepartment of Agronomy
Guihua Bai
Allan K. Fritz
Wheat leaf rust, caused by Puccinia triticina, is an important fungal disease worldwide. Growing resistant cultivars is an effective practice to reduce the losses caused by the disease, and using slow-rusting resistance genes can improve the durability of rust resistance in the cultivars. CI13227 is a winter wheat line that shows a high level of slow-rusting resistance to leaf rust and has been studied extensively. In this research, two recombinant inbreed line (RIL) populations derived from CI13227 x Suwon (104 RILs) and CI13227 x Everest (184 RILs) and one doubled haploid (DH) population derived from CI13227 x Lakin with 181 lines were used to identify quantitative trait loci (QTLs) for slow leaf rusting resistance. Each population and its parents were evaluated for slow-rusting traits in two greenhouse experiments. A selected set of 384 simple sequence repeat markers (SSRs), single nucleotide polymorphism markers (SNPs) derived from genotyping-by-sequencing (GBS-SNPs) or 90K-SNP chip (90K-SNPs) were analyzed in the three populations. Six QTLs for slow-rusting resistance, QLr.hwwgru-2DS, QLr.hwwgru-7BL, QLr.hwwgru-7AL, QLr.hwwgru-3B_1, QLr.hwwgru-3B_2, and QLr.hwwgru-1D were detected in the three populations with three stable QTLs, QLr.hwwgru-2DS, QLr.hwwgru-7BL and QLr.hwwgru-7AL. These were detected and validated by Kompetitive Allele-Specific PCR (KASP) markers converted from GBS-SNPs and 90K-SNPs in at least two populations. Another three QTLs were detected only in a single population, and either showed a minor effect or came from the susceptible parents. The KASP markers tightly linked to QLr.hwwgru-2DS (IWB34642, IWB8545 and GBS_snpj2228), QLr.hwwgru-7BL (GBS_snp1637 and IWB24039) and QLr.hwwgru-7AL (IWB73053 and IWB42182) are ready to be used in marker-assisted selection (MAS) to transfer these QTLs into wheat varieties to improve slow-rusting resistance in wheat.
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Lisec, Jan. "Identification and characterization of metabolic Quantitative Trait Loci (QTL) in Arabidopsis thaliana." Phd thesis, Universität Potsdam, 2008. http://opus.kobv.de/ubp/volltexte/2008/2590/.
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Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach.
This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL).
Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis.
The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.
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Huq, Md Nazmul. "The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour." Thesis, Linköpings universitet, Biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-78393.
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Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.
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Podisi, Baitsi Kingsley. "Quantitative trait loci mapping of sexual maturity traits applied to chicken breeding." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5561.
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Many phenotypes are controlled by factors which include the genes, the environment, interactions between genes and interaction between the genotypes and the environment. Great strides have been made to understand how these various factors affect traits of agricultural, medical and environmental importance. The chicken is regarded as a model organism whose study would not only assist efforts towards increased agricultural productivity but also provide insight into the genetic determination of traits with potential application in understanding human health and disease. Detection of genomic regions or loci responsible for controlling quantitative traits (QTL) in poultry has focussed mainly on growth and production traits with limited information on reproductive traits. Most of the reported results have used additive-dominance models which are easy to implement because they ignore epistatic gene action despite indications that it may be important for traits with low heritability and high heterosis. The thesis presents results on the detection of loci and genetic mechanisms involved in sexual maturity traits through modelling both additive-dominance gene actions and epistasis. The study was conducted on an F2 broiler x White Leghorn layer cross for QTL detection for age, weight, abdominal fat, ovary weight, oviduct weight, comb weight, number of ovarian yellow follicles, a score for the persistence of the right oviduct and bone density. In addition, body weight QTL at 3, 6, 12, 24, 48 and 72 weeks of age, QTL for growth rate between the successive ages and QTL for the parameters of the growth curve were also detected. Most of the QTL for traits at sexual maturity acted additively. A few of the QTL explained a modest proportion of the phenotypic variation with most of the QTL explaining a small component of the cumulative proportion of the variation explained by the QTL. Body weight QTL were critical in determining the attainment of puberty. The broiler allele had positive effects on weight at first egg and negative effects on age at first egg. Most QTL affecting weight at first egg overlapped with QTL for age at first egg and for early growth rate (6-9 weeks) suggesting that growth rate QTL are intimately related to the onset of puberty. Specific QTL for early and adult growth were detected but most QTL had varying influence on growth throughout life. Chromosome 4 harboured most of QTL for the assessed traits which explained the highest proportion of the phenotypic variation in the traits confirming its critical role in influencing traits of economic importance. There was no evidence for epistasis for almost all the studied traits. Evidence for role of epistasis was significant for ovary weight and suggestive for both growth rate and abdominal fat.
Books on the topic "QTL (Quantitative trait locus/loci) mapping"
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Saunak, Sen, and SpringerLink (Online service), eds. A Guide to QTL Mapping with R/qtl. New York, NY: Springer-Verlag New York, 2009.
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Quantitative Trait Loci Qtl Methods in Molecular Biology Hardcover. Humana Press, 2012.
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Broman, Karl W., and Saunak Sen. A Guide to QTL Mapping with R/qtl. Springer, 2009.
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Broman, Karl W., and Saunak Sen. A Guide to QTL Mapping with R/qtl. Springer, 2011.
Find full textBook chapters on the topic "QTL (Quantitative trait locus/loci) mapping"
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Powder, Kara E. "Quantitative Trait Loci (QTL) Mapping." In Methods in Molecular Biology, 211–29. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-0716-0026-9_15.
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Hsu, Hui-Chen, Lu Lu, Nengjun Yi, Gary Zant, Robert W. Williams, and John D. Mountz. "Quantitative Trait Locus (QTL) Mapping in Aging Systems." In Methods in Molecular Biology, 321–48. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-361-5_23.
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Yeri, Sharanabasappa B., Varsha Kumari, Radheshyam Sharma, and Sumer Singh Punia. "Quantitative Trait Locus (QTL) Mapping in Crop Improvement." In Biotechnology and Crop Improvement, 227–36. New York: CRC Press, 2022. http://dx.doi.org/10.1201/9781003239932-13.
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Rajesh, M. K., S. V. Ramesh, Lalith Perera, and A. Manickavelu. "Quantitative Trait Loci (QTL) and Association Mapping for Major Agronomic Traits." In The Coconut Genome, 91–101. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-76649-8_6.
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Téoulé, Evelyne, and Carine Géry. "Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing and Cold Acclimation." In Methods in Molecular Biology, 61–84. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0660-5_7.
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Shehzad, Tariq, and Kazutoshi Okuno. "Quantitative trait locus mapping and genetic improvement to strengthen drought tolerance in sorghum." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 433–43. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0025.
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Abstract This chapter overviews the approaches to and application of quantitative trait locus (QTL) mapping and positional cloning of genes controlling important traits related to drought tolerance in sorghum (Sorghum bicolor), which ultimately yields crop improvement and genetic modification. The use of high-throughput phenotyping will help better understand the mechanism involved in response to drought stress by plants. The new paradigm of scientific research should focus on the integration of physiology, genetics, genomics, soil characteristics and breeding to deal with the challenges of food security in the coming years.
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Téoulé, Evelyne, and Carine Géry. "Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation." In Methods in Molecular Biology, 43–64. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0844-8_6.
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Najeeb, Sofi, Anumalla Mahender, Annamalai Anandan, Waseem Hussain, Zhikang Li, and Jauhar Ali. "Genetics and Breeding of Low-Temperature Stress Tolerance in Rice." In Rice Improvement, 221–80. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-66530-2_8.
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AbstractLow-temperature stress (LTS) is one of the major abiotic stresses that affect crop growth and ultimately decrease grain yield. The development of rice varieties with low-temperature stress tolerance has been a severe challenge for rice breeders for a long time. The lack of consistency of the quantitative trait loci (QTLs) governing LTS tolerance for any given growth stage over different genetic backgrounds of mapping populations under different low-temperature stress conditions remains a crucial barrier for adopting marker-assisted selection (MAS). In this review, we discuss the ideal location and phenotyping for agromorphological and physiological parameters as indicators for LTS tolerance and also the traits associated with QTLs that were identified from biparental mapping populations and diverse rice accessions. We highlight the progress made in the fields of genome editing, genetic transformation, transcriptomics, and metabolomics to elucidate the molecular mechanisms of cold tolerance in rice. The stage-specific QTLs and candidate genes for LTS tolerance brought out valuable information toward identifying and improving LTS tolerance in rice varieties. We showed 578 QTLs and 38 functionally characterized genes involved in LTS tolerance. Among these, 29 QTLs were found to be colocalized at different growth stages of rice. The combination of stage-specific QTLs and genes from biparental mapping populations and genome-wide association studies provide potential information for developing LTS-tolerant rice varieties. The identified colocalized stage-specific LTS-tolerance QTLs will be useful for MAS and QTL pyramiding and for accelerating mapping and cloning of the possible candidate genes, revealing the underlying LTS-tolerance mechanisms in rice.
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Hendry, Andrew P. "Genetics and Genomics." In Eco-evolutionary Dynamics. Princeton University Press, 2016. http://dx.doi.org/10.23943/princeton/9780691145433.003.0010.
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This chapter focuses on common empirical methods for studying the genetics of adaptation: quantitative genetics, quantitative trait locus (QTL) linkage mapping, association mapping, genome scans, gene expression, and candidate genes. It addresses various aspects of adaptation, speciation, and eco-evolutionary dynamics. The key questions include examining how much additive genetic variation exists in fitness-related traits, to what extent nonadditive genetic variation (dominance and epistasis) influences phenotypic variation, how many loci are involved in adaptation and how large their effects are, to what extent the adaptation of independent populations to similar environments involves parallel/convergent genetic changes, whether adaptation to changing environments is driven mainly by new mutations or by standing genetic variation, and to what extent the ecological effects of individuals transmitted among generations are.
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Le Roy, Isabelle. "Quantitative Trait Loci (QTL) Mapping." In Neurobehavioral Genetics. CRC Press, 1999. http://dx.doi.org/10.1201/9781420048384.ch6.
Full textReports on the topic "QTL (Quantitative trait locus/loci) mapping"
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.
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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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Levin, Ilan, John Thomas, Moshe Lapidot, Desmond McGrath, and Denis Persley. Resistance to Tomato yellow leaf curl virus (TYLCV) in tomato: molecular mapping and introgression of resistance to Australian genotypes. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7613888.bard.
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Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomatoes. Although first identified in the Mediterranean region, it is now distributed world-wide. Sequence analysis of the virus by the Australian group has shown that the virus is now present in Australia. Despite the importance of the disease and extensive research on the virus, very little is known about the resistance genes (loci) that determine host resistance and susceptibility to the virus. A symptom-less resistant line, TY-172, was developed at the Volcani Center which has shown the highest resistance level among all tested varieties. Preliminary results show that TY-172 is a good candidate to confer resistance to both TYLCV and to Tomato leaf curl virus (ToLCV) in Queensland conditions. Furthermore, Segregation analysis has previously indicated that the resistance is determined by 2-3 genes. In this proposal we aimed to substantiate that TY-172 can contribute to resistance breeding against TYLCV in Queensland, to develop DNA markers to advance such resistance breeding in both Israel and Queensland, and to exploit these markers for resistant breeding in Australian and Israeli lines. To map quantitative trait loci (QTLs) controlling TYLCVresistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, termed Ty-5, maps to chromosome 4 and accounts for 39.7-to-46.6% of the variation in symptom severity among segregating plants (LOD score: 33-to-35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5. Further analysis of parental lines as well as large F₁, BC₁F₁, F₂ and BC₁F₂ populations originating from crosses carried out, in reciprocal manner, between TY172 and the susceptible processing line M-82 (LA3475) during spring-summer 2010, indicated that: (1) the minor QTLs we have previously identified are in effect not reproducible, (2)Ty-5 alone can yield highly resistant plants with practically no extra-chromosomal effects, and (3) the narrow-sense heritability estimate of resistance levels, attributed to additive factors responsive to selection, does not significantly deviate from 1. All of these results point to Ty-5 as the sole resistance locus in TY172 thus significantly increasing the likelihood of its successful molecular dissection. The DNA markers developed during the course of this study were transferred together with the TY172 genotype to Queensland. TY172 was crossed to a panel of Australian genotypes and the resulting populations were subjected to segregation analysis. Results showed that resistant locus, Ty-5, is highly reproducible in the Australian conditions as well. The Australian group was also able to make improvements to the marker assays by re-designing primer pairs to provide more robust PCR fragments. The Ty-5 locus has now been introgressed into elite Australian germplasm and selection for TYLCV resistance has begun. Cumulatively, our results show that Ty-5 can be effectively used, together with the TY172 genotype to expedite TYLCV resistance breeding and improve our understanding of the genetics that underline the response of tomato to TYLCV. Contributions to agriculture include: (1) the development of tools for more efficient resistance breeding, allowing the incorporation of resistance to local tomato varieties in Australia, Israel and elsewhere; and (2) establish a solid framework for a future attempt to clone the genes that encode such resistance. The latter will enable to decipher the resistance mechanisms that could be applied to other geminiviruses in tomato and possibly in other plant species.
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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.
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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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Lapidot, Moshe, and Vitaly Citovsky. molecular mechanism for the Tomato yellow leaf curl virus resistance at the ty-5 locus. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604274.bard.
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Tomato yellow leaf curl virus (TYLCV) is a major pathogen of tomato that causes extensive crop loss worldwide, including the US and Israel. Genetic resistance in the host plant is considered highly effective in the defense against viral infection in the field. Thus, the best way to reduce yield losses due to TYLCV is by breeding tomatoes resistant or tolerant to the virus. To date, only six major TYLCV-resistance loci, termed Ty-1 to Ty-6, have been characterized and mapped to the tomato genome. Among tomato TYLCV-resistant lines containing these loci, we have identified a major recessive quantitative trait locus (QTL) that was mapped to chromosome 4 and designated ty-5. Recently, we identified the gene responsible for the TYLCV resistance at the ty-5 locus as the tomato homolog of the gene encoding messenger RNA surveillance factor Pelota (Pelo). A single amino acid change in the protein is responsible for the resistant phenotype. Pelo is known to participate in the ribosome-recycling phase of protein biosynthesis. Our hypothesis was that the resistant allele of Pelo is a “loss-of-function” mutant, and inhibits or slows-down ribosome recycling. This will negatively affect viral (as well as host-plant) protein synthesis, which may result in slower infection progression. Hence we have proposed the following research objectives: Aim 1: The effect of Pelota on translation of TYLCV proteins: The goal of this objective is to test the effect Pelota may or may not have upon translation of TYLCV proteins following infection of a resistant host. Aim 2: Identify and characterize Pelota cellular localization and interaction with TYLCV proteins: The goal of this objective is to characterize the cellular localization of both Pelota alleles, the TYLCV-resistant and the susceptible allele, to see whether this localization changes following TYLCV infection, and to find out which TYLCV protein interacts with Pelota. Our results demonstrate that upon TYLCV-infection the resistant allele of pelota has a negative effect on viral replication and RNA transcription. It is also shown that pelota interacts with the viral C1 protein, which is the only viral protein essential for TYLCV replication. Following subcellular localization of C1 and Pelota it was found that both protein localize to the same subcellular compartments. This research is innovative and potentially transformative because the role of Peloin plant virus resistance is novel, and understanding its mechanism will lay the foundation for designing new antiviral protection strategies that target translation of viral proteins. BARD Report - Project 4953 Page 2
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.
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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Smith, Margaret, Nurit Katzir, Susan McCouch, and Yaakov Tadmor. Discovery and Transfer of Genes from Wild Zea Germplasm to Improve Grain Oil and Protein Composition of Temperate Maize. United States Department of Agriculture, 1998. http://dx.doi.org/10.32747/1998.7580683.bard.
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Project Objectives 1. Develop and amplify two interspecific populations (annual and perennial teosintes x elite maize inbred) as the basis for genetic analysis of grain quality. 2. Identify quantitative trait loci (QTLs) from teosinte that improve oil, protein, and essential amino acid composition of maize grain. 3. Develop near isogenic lines (NILs) to quantify QTL contributions to grain quality and as a resource for future breeding and gene cloning efforts. 4. Analyze the contribution of these QTLs to hybrid performance in both the US and Israel. 5. Measure the yield potential of improved grain quality hybrids. (NOTE: Yield potential could not be evaluated due to environmentally-caused failure of the breeding nursery where seed was produced for this evaluation.) Background: Maize is a significant agricultural commodity worldwide. As an open pollinated crop, variation within the species is large and, in most cases, sufficient to supply the demand for modem varieties and for new environments. In recent years there is a growing demand for maize varieties with special quality attributes. While domesticated sources of genetic variation for high oil and protein content are limited, useful alleles for these traits may remain in maize's wild relative, teosinte. We utilized advanced backcross (AB) analysis to search for QTLs contributing to oil and protein content from two teosinte accessions: Zea mays ssp. mexicana Race Chalco, an annual teosinte (referred to as Chalco), and Z diploperennis Race San Miguel, a perennial teosinte (referred to as Diplo). Major Conclusions and Achievements Two NILs targeting a Diplo introgression in bin 1.04 showed a significant increase in oil content in homozygous sib-pollinated seed when compared to sibbed seed of their counterpart non-introgressed controls. These BC4S2 NILs, referred to as D-RD29 and D-RD30, carry the Diplo allele in bin 1.04 and the introgression extends partially into bins 1.03 and 1.05. These NILs remain heterozygous in bins 4.01 and 8.02, but otherwise are homozygous for the recurrent parent (RD6502) alleles. NILs were developed also for the Chalco introgression in bin 1.04 but these do not show any improvement in oil content, suggesting that the Chalco alleles differ from the Diplo alleles in this region. Testcross Fl seed and sibbed grain from these Fl plants did not show any effect on oil content from this introgression, suggesting that it would need to be present in both parents of a maize hybrid to have an effect on oil content. Implications, both Scientific and Agricultural The Diplo region identified increases oil content by 12.5% (from 4.8% to 5.4% oil in the seed). Although this absolute difference is not large in agronomic terms, this locus could provide additive increases to oil content in combination with other maize-derived loci for high oil. To our knowledge, this is the first confirmed report of a QTL from teosinte for improved grain oil content in maize. It suggests that further research on grain quality alleles from maize wild relatives would be of both scientific and agricultural interest.
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Smith, Margaret, Nurit Katzir, Susan McCouch, and Yaakov Tadmor. Discovery and Transfer of Genes from Wild Zea Germplasm to Improve Grain Oil and Protein Composition of Temperate Maize. United States Department of Agriculture, October 2002. http://dx.doi.org/10.32747/2002.7695846.bard.
Full textAbstract:
Project Objectives 1. Develop and amplify two interspecific populations (annual and perennial teosintes x elite maize inbred) as the basis for genetic analysis of grain quality. 2. Identify quantitative trait loci (QTLs) from teosinte that improve oil, protein, and essential amino acid composition of maize grain. 3. Develop near isogenic lines (NILs) to quantify QTL contributions to grain quality and as a resource for future breeding and gene cloning efforts. 4. Analyze the contribution of these QTLs to hybrid performance in both the US and Israel. 5. Measure the yield potential of improved grain quality hybrids. (NOTE: Yield potential could not be evaluated due to environmentally-caused failure of the breeding nursery where seed was produced for this evaluation.) Background: Maize is a significant agricultural commodity worldwide. As an open pollinated crop, variation within the species is large and, in most cases, sufficient to supply the demand for modem varieties and for new environments. In recent years there is a growing demand for maize varieties with special quality attributes. While domesticated sources of genetic variation for high oil and protein content are limited, useful alleles for these traits may remain in maize's wild relative, teosinte. We utilized advanced backcross (AB) analysis to search for QTLs contributing to oil and protein content from two teosinte accessions: Zea mays ssp. mexicana Race Chalco, an annual teosinte (referred to as Chalco), and Z diploperennis Race San Miguel, a perennial teosinte (referred to as Diplo). Major Conclusions and Achievements Two NILs targeting a Diplo introgression in bin 1.04 showed a significant increase in oil content in homozygous sib-pollinated seed when compared to sibbed seed of their counterpart non-introgressed controls. These BC4S2 NILs, referred to as D-RD29 and D-RD30, carry the Diplo allele in bin 1.04 and the introgression extends partially into bins 1.03 and 1.05. These NILs remain heterozygous in bins 4.01 and 8.02, but otherwise are homozygous for the recurrent parent (RD6502) alleles. NILs were developed also for the Chalco introgression in bin 1.04 but these do not show any improvement in oil content, suggesting that the Chalco alleles differ from the Diplo alleles in this region. Testcross Fl seed and sibbed grain from these Fl plants did not show any effect on oil content from this introgression, suggesting that it would need to be present in both parents of a maize hybrid to have an effect on oil content. Implications, both Scientific and Agricultural The Diplo region identified increases oil content by 12.5% (from 4.8% to 5.4% oil in the seed). Although this absolute difference is not large in agronomic terms, this locus could provide additive increases to oil content in combination with other maize-derived loci for high oil. To our knowledge, this is the first confirmed report of a QTL from teosinte for improved grain oil content in maize. It suggests that further research on grain quality alleles from maize wild relatives would be of both scientific and agricultural interest.
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Perl-Treves, Rafael, Rebecca Grumet, Nurit Katzir, and Jack E. Staub. Ethylene Mediated Regulation of Sex Expression in Cucumis. United States Department of Agriculture, January 2005. http://dx.doi.org/10.32747/2005.7586536.bard.
Full textAbstract:
Monoecious species such as melon and cucumber develop separate male and female (or bisexual) flowers on the same plant individual. They display complex genetic and hormonal regulation of sex patterns along the plant. Ethylene is known to play an important role in promoting femaleness and inhibiting male development, but many questions regarding critical sites of ethylene production versus perception, the relationship between ethylene and the sex determining loci, and the possible differences between melon and cucumber in this respect are still open. The general goal of the project was to elucidate the role of ethylene in determining flower sex in Cucumis species, melon and cucumber. The specific Objectives were: 1. Clone and characterize expression patterns of cucumber genes involved in ethylene biosynthesis and perception. 2. Genetic mapping of cloned genes and markers with respect to sex loci in melon and cucumber. 3. Produce and analyze transgenic melons altered in ethylene production or perception. In the course of the project, some modifications/adjustments were made: under Objective 2 (genetic mapping) a set of new mapping populations had to be developed, to allow better detection of polymorphism. Under Objective 3, cucumber transformation systems became available to us and we included this second model species in our plan. The main findings of our study support the pivotal role of ethylene in cucumber and melon sex determination and later stages of reproductive development. Modifying ethylene production resulted in profound alteration of sex patterns in melon: femaleness increased, and also flower maturation and fruit set were enhanced, resulting in earlier, more concentrated fruit yield in the field. Such effect was previously unknown and could have agronomic value. Our results also demonstrate the great importance of ethylene sensitivity in sex expression. Ethylene perception genes are expressed in sex-related patterns, e.g., gynoecious lines express higher levels of receptor-transcripts, and copper treatments that activate the receptor can increase femaleness. Transgenic cucumbers with increased expression of an ethylene receptor showed enhanced femaleness. Melons that expressed a defective receptor produced fewer hermaphrodite flowers and were insensitive to exogenous ethylene. When the expression of defective receptor was restricted to specific floral whorls, we saw that pistils were not inhibited by the blocked perception at the fourth whorl. Such unexpected findings suggest an indirect effect of ethylene on the affected whorl; it also points at interesting differences between melon and cucumber regarding the mode of action of ethylene. Such effects will require further study. Finally, our project also generated and tested a set of novel genetic tools for finer identification of sex determining genes in the two species and for efficient breeding for these characters. Populations that will allow easier linkage analysis of candidate genes with each sex locus were developed. Moreover, effects of modifier genes on the major femaleness trait were resolved. QTL analysis of femaleness and related developmental traits was conducted, and a comprehensive set of Near Isogenic Lines that differ in specific QTLs were prepared and made available for the private and public research. Marker assisted selection (MAS) of femaleness and fruit yield components was directly compared with phenotypic selection in field trials, and the relative efficiency of MAS was demonstrated. Such level of genetic resolution and such advanced tools were not used before to study these traits, that act as primary yield components to determine economic yields of cucurbits. In addition, this project resulted in the establishment of workable transformation procedures in our laboratories and these can be further utilized to study the function of sex-related genes in detail.
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Paterson, Andrew H., Yehoshua Saranga, and Dan Yakir. Improving Productivity of Cotton (Gossypsum spp.) in Arid Region Agriculture: An Integrated Physiological/Genetic Approach. United States Department of Agriculture, December 1999. http://dx.doi.org/10.32747/1999.7573066.bard.
Full textAbstract:
Objectives: We seek to establish the basis for improving cotton productivity under arid conditions, by studying the water use efficiency - evaporative cooling interrelationship. Specifically, we will test the hypothesis that cotton productivity under arid conditions can be improved by combining high seasonal WUE with efficient evaporative cooling, evaluate whether high WUE and/or evaporative cooling are based on specific physiological factors such as diurnal flexibility in stomatal conductance, stomatal density, photosynthetic capacity, chlorophyll fluorescence, and plant water status. Genes influencing both WUE and evaporative cooling, as well as other parameters such as economic products (lint yield, quality, harvest index) of cotton will also be mapped, in order to evaluate influences of water relations on these parameters. Approach: Carbon isotope ratio will be used to evaluate WUE, accompanied by additional parameters to elucidate the relationship between WUE, evaporative cooling, and cotton productivity. A detailed RFLP map will be used to determine the number, location, and phenotypic effects of genes underlying genetic variation in WUE between cultivated cottons, as well as test associations of these genes with traits of economic importance such as harvest index, lint yield, and lint quality. Major Conclusions: Productivity and quality of cotton grown under well-watered versus water-limited conditions was shown to be partly accounted for by different quantitative trait loci (QTLs). Among a suite of physiological traits often found to differ between genotypes adapted to arid versus well-watered conditions, genetic mapping implicated only reduced plant osmotic potential in improved cotton productivity under arid conditions. Our findings clearly implicate OP as a major component of cotton adaptation to arid conditions. However, testing of further physiological hypotheses is clearly needed to account for additional QTL alleles conferring higher seed-cotton yield under arid conditions, such as three of the five we found. Near-isogenic lines being made for QTLs discovered herein will offer a powerful new tool useful toward identification of the underlying gene(s) by using fine-scale mapping approaches (Paterson et al 1990). Implications: Adaptation to both arid and favorable conditions can be combined into the same genotype. We have identified diagnostic DNA markers that are being applied to creation of such desirable genotypes. Simultaneous improvement of productivity (and/or quality) for both arid and irrigated conditions will require more extensive field testing and the manipulation of larger numbers of genes, reducing the expected rate of genetic gain These difficulties may be at least partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers. Genomic tools and approaches may expedite adaptation of crops to arid cultivation, help to test roles of additional physiological factors, and guide the isolation of the underlying genes that protect crop performance under arid conditions.
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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.
Full textAbstract:
The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.