Proceedings of the National Academy of Sciences volume 114, issue 6, PE913-E921 2017 DOI: 10.1073/pnas.1619268114

Uncovering hidden variation in polyploid wheat

Ksenia V. Krasileva, Hans A. Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H. Ramirez-Gonzalez, Xiaodong Wang, Philippa Borrill, Christine Fosker, Sarah Ayling, Andrew L. Phillips, Cristobal Uauy, Jorge Dubcovsky
Abstract: Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.wheat | polyploidy | mutations | reverse genetics | exome capture S ince the dawn of agriculture, wheat has been a major dietary source of calories and protein for humans. The cultivated wheat species Triticum turgidum (tetraploid, AABB genome) and Triticum aestivum (hexaploid, AABBDD genome) originated via recent polyploidization events followed by domestication.
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