Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.)
Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (...
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| creator | Laidò, Giovanni Marone, Daniela Russo, Maria A Colecchia, Salvatore A Mastrangelo, Anna M De Vita, Pasquale Papa, Roberto |
| description | Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker-trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker-trait associations. |
| doi_str_mv | 10.1371/journal.pone.0095211 |
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Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker-trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Finally, the analysis of the selection signature represents a very useful complement to validate marker-trait associations.</description><subject>Agricultural production</subject><subject>Agronomy</subject><subject>Analysis</subject><subject>Barley</subject><subject>Biology and Life Sciences</subject><subject>Breeding</subject><subject>Data analysis</subject><subject>Decay</subject><subject>Divergence</subject><subject>Domestication</subject><subject>Exploitation</subject><subject>Gene loci</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genome, Plant - genetics</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Linkage (Genetics)</subject><subject>Linkage disequilibrium</subject><subject>Linkage Disequilibrium - genetics</subject><subject>Loci</subject><subject>Mapping</subject><subject>Outliers (statistics)</subject><subject>Physiological aspects</subject><subject>Plant breeding</subject><subject>Population</subject><subject>Quantitative genetics</subject><subject>Quantitative trait loci</subject><subject>Quantitative Trait Loci - 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Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker-trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker-trait associations.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24759998</pmid><doi>10.1371/journal.pone.0095211</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Agricultural production Agronomy Analysis Barley Biology and Life Sciences Breeding Data analysis Decay Divergence Domestication Exploitation Gene loci Gene mapping Genes Genetic aspects Genetic diversity Genome, Plant - genetics Genome-Wide Association Study Genomes Genomics Genotype & phenotype Genotypes Linkage (Genetics) Linkage disequilibrium Linkage Disequilibrium - genetics Loci Mapping Outliers (statistics) Physiological aspects Plant breeding Population Quantitative genetics Quantitative trait loci Quantitative Trait Loci - genetics Simple sequence repeats Studies Tetraploidy Triticum Triticum turgidum Wheat |
| title | Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.) |
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