The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping

Authors: JORDAN, KATHERINE - Kansas State University; WANG, SHICHEN - Kansas State University; Chao, Shiaoman; LUN, YANNI - Kansas State University; PAUX, ETIENNE - Institut National De La Recherche Agronomique (INRA); SOURDILLE, PIERRE - Institut National De La Recherche Agronomique (INRA); SHERMAN, JAMIE - Montana State University; AKHUNOVA, ALINA - Kansas State University; BLAKE, NANCY - Montana State University; PUMPHREY, MICHAEL - Washington State University; GLOVER, KARL - South Dakota State University; KING, ROBERT - Rothamsted Research; PHILLIPS, ANDREW - Rothamsted Research; UAUY, CRISTOBAL - John Innes Center; JUBCOVSKY, JORGE - University Of California; TALBERT, LUTHER - Montana State University; AKHUNOV, EDUARD - Kansas State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/6/2018
Publication Date: 7/1/2018
Citation: Jordan, K.W., Wang, S., He, F., Chao, S., Lun, Y., Paux, E., Sourdille, P., Sherman, J., Akhunova, A., Blake, N.K., Pumphrey, M.O., Glover, K., Dubcovsky, J., Talbert, L., Akhunov, E. 2018. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. The Plant Journal. 10.1111/tpj.14009.
DOI: https://doi.org/10.1111/tpj.14009

Interpretive Summary: Recombination affects the fate of genetic variation in populations by imposing constraints on the reshuffling of genetic information. Understanding the nature of these constraints and the determinants of recombination would help plant breeders effectively manipulate genetic diversity during the breeding process. In this study, large spring wheat mapping populations consisting of 2100 individuals were developed and used to uncover gene regions affecting recombination rate variation. Results from further genetic analyses indicated that those regions discovered coincided with regions containing genes known for controlling recombination in plants, animals, and fungi. Those genes were part of the conserved network affecting recombination, and thus providing targets for manipulating recombination in wheat using genetics and biotechnology-based approaches.

Technical Abstract: Recombination affects the fate of allelic variation in populations by imposing constraints on the reshuffling of genetic information. Understanding the nature of these constraints is critical for manipulating recombination in crops. Using high-density genotyping of the spring wheat nested association mapping (NAM) population derived by crossing 28 genetically and geographically diverse wheat landraces and cultivars (founders) with broadly adapted cultivar Berkut, we identified 102,000 recombination breakpoints (RBs). At the genome-wide level recombination rate variation was mostly defined by multiple low frequency alleles with small effects together explaining up to 48.3% of variation. The majority of recombination rate QTL were rare in the population, and acted additively showing predominantly trans-acting effects. The QTL for interstitial RBs showed additive effects without increasing the frequency of distal RBs. The identified QTL regions were significantly enriched for conserved genes known to affect recombination in plants, animals and fungi. Using exome-wide data available for two wheat EMS mutant populations of 2,735 lines, we assessed recombination frequency in individual mutant lines and showed that strong effect mutations in 19 meiotic genes located within the QTL regions affect recombination rate in both tetraploid and hexaploid wheat. These genes were part of the conserved network controlling recombination in different organisms, providing targets for manipulating recombination in wheat using genetics and biotechnology-based approaches.