1. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
- Author
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Jamie D. Sherman, Eduard Akhunov, Fei He, Luther E. Talbert, Jorge Dubcovsky, Yanni Lun, Katherine W. Jordan, Etienne Paux, Alina Akhunova, Karl D. Glover, Shiaoman Chao, Michael O. Pumphrey, Nancy K. Blake, Pierre Sourdille, Shichen Wang, Department of Plant Pathology, Shizuoka University, USDA-ARS : Agricultural Research Service, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Montana State University (MSU), Integrated Genomics Facility, Kansas State University, Department of Crop and Soil Sciences, Pennsylvania State University (Penn State), Penn State System-Penn State System, Department of Agronomy, Horticulture and Plant Science, South Dakota State University (SDSTATE), Department of Plant Sciences (DPS), University of Cambridge [UK] (CAM), Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Agriculture Food Research Initiative from the USDA National Institute of Food and Agriculture 67007-25939 2016-67013-24473, Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, French Government ANR-10-BTBR-03, FranceAgriMer, French Funds to support Plant Breeding (FSOV), INRA, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Howard Hughes Medical Institute [New York], New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), and NYU System (NYU)-NYU System (NYU)-Columbia University Irving Medical Center (CUIMC)-Rockefeller University [New York]
- Subjects
0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Population ,Quantitative Trait Loci ,Plant Biology & Botany ,Plant Biology ,Single-nucleotide polymorphism ,Plant Science ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,Polyploidy ,polyploid wheat ,03 medical and health sciences ,Gene mapping ,blé ,Genetic ,crossovers ,wheat ,Genetics ,nested association mapping ,Nested association mapping ,Polymorphism ,interstitial CO QTL ,education ,Triticum ,Alleles ,Recombination, Genetic ,recombination rate ,education.field_of_study ,Genome ,food and beverages ,Chromosome Mapping ,Genetic Variation ,Cell Biology ,Original Articles ,Single Nucleotide ,Plant ,Genetic architecture ,Recombination ,Genetic load ,030104 developmental biology ,Genetic marker ,Original Article ,deleterious SNPs ,Genome, Plant ,Genome-Wide Association Study - Abstract
Summary Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes., Significance Statement This study offers insights into the genetic basis of recombination rate variation in allopolyploid wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive recombination rate QTL can be utilized to manipulate crossover frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low recombining pericentromeric regions of chromosomes.
- Published
- 2018