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GrainGenes Reference Report: TPJ-95-1039

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Reference	TPJ-95-1039
Title	The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
Journal	The Plant Journal
Year	2018
Volume	95
Pages	1039-1054
Author	Jordan KW [ Show all 15 ]
Abstract	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.
External Databases	https://doi.org/10.1111/tpj.14009 http://wheatgenomics.plantpath.ksu.edu/nam/
Map Data	[ Hide all but 1 of 28 ] Wheat-2018-NAM1-Berkut-x-DharwarDry Wheat-2018-NAM2-Berkut-x-PI572692 Wheat-2018-NAM3-Berkut-x-PI283147 Wheat-2018-NAM4-Berkut-x-PI366716 Wheat-2018-NAM5-Berkut-x-PI382150 Wheat-2018-NAM6-Berkut-x-PI470817 Wheat-2018-NAM7-Berkut-x-PI565213 Wheat-2018-NAM8-Berkut-x-PBW343 Wheat-2018-NAM10-Berkut-x-PI9791 Wheat-2018-NAM11-Berkut-x-CItr4175 Wheat-2018-NAM9-Berkut-x-Vida Wheat-2018-NAM12-Berkut-x-CItr11223 Wheat-2018-NAM13-Berkut-x-PI262611 Wheat-2018-NAM14-Berkut-x-PI70613 Wheat-2018-NAM15-Berkut-x-CItr7635 Wheat-2018-NAM16-Berkut-x-PI8813 Wheat-2018-NAM17-Berkut-x-PI82469 Wheat-2018-NAM18-Berkut-x-CItr15144 Wheat-2018-NAM19-Berkut-x-PI43355 Wheat-2018-NAM20-Berkut-x-PI94567 Wheat-2018-NAM23-Berkut-x-PI192001 Wheat-2018-NAM24-Berkut-x-PI192147 Wheat-2018-NAM25-Berkut-x-CItr15134 Wheat-2018-NAM27-Berkut-x-PI192569 Wheat-2018-NAM28-Berkut-x-PI210945 Wheat-2018-NAM29-Berkut-x-PI220431 Wheat-2018-NAM30-Berkut-x-PI278297 Wheat-2018-NAM26-Berkut-x-PI185715

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