Uncovering hidden variation in polyploid wheat

Research output: Contribution to journalArticle

Authors

  • Ksenia V Krasileva
  • Hans A Vasquez-Gross
  • Tyson Howell
  • Paul Bailey
  • Francine Paraiso
  • Leah Clissold
  • James Simmonds
  • Ricardo H Ramirez-Gonzalez
  • Xiaodong Wang
  • Christine Fosker
  • Sarah Ayling
  • Andrew L Phillips
  • Cristobal Uauy
  • Jorge Dubcovsky

Colleges, School and Institutes

External organisations

  • The Earlham Institute, Norwich NR4 7UG, United Kingdom.
  • Department of Plant Sciences, University of California, Davis, CA 95616.
  • John Innes Centre, Norwich, NR4 7UH, United Kingdom.
  • Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom.
  • John Innes Centre, Norwich NR4 7UH, United Kingdom; cristobal.uauy@jic.ac.uk jdubcovsky@ucdavis.edu.
  • Howard Hughes Medical Institute, Chevy Chase, MD 20815.

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.

Details

Original languageEnglish
Pages (from-to)E913-E921
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number6
Early online date17 Jan 2017
Publication statusPublished - 7 Feb 2017

Keywords

  • DNA Mutational Analysis/methods, Evolution, Molecular, Exome/genetics, Genome, Plant/genetics, Mutation, Plant Breeding, Plant Proteins/genetics, Polyploidy, Selection, Genetic, Triticum/genetics