title: Uncovering hidden variation in polyploid wheat.
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.
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.|The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom.|The Earlham Institute, Norwich NR4 7UG, United Kingdom.
authors.forename: Ksenia V
authors.initials: KV
authors.lastname: Krasileva
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Hans A
authors.initials: HA
authors.lastname: Vasquez-Gross
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Tyson
authors.initials: T
authors.lastname: Howell
authors.affiliation: The Earlham Institute, Norwich NR4 7UG, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Bailey
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Francine
authors.initials: F
authors.lastname: Paraiso
authors.affiliation: The Earlham Institute, Norwich NR4 7UG, United Kingdom.
authors.forename: Leah
authors.initials: L
authors.lastname: Clissold
authors.affiliation: John Innes Centre, Norwich NR4 7UH, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Simmonds
authors.affiliation: The Earlham Institute, Norwich NR4 7UG, United Kingdom.|John Innes Centre, Norwich NR4 7UH, United Kingdom.
authors.forename: Ricardo H
authors.initials: RH
authors.lastname: Ramirez-Gonzalez
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Wang
authors.affiliation: John Innes Centre, Norwich NR4 7UH, United Kingdom.
authors.forename: Philippa
authors.initials: P
authors.lastname: Borrill
authors.affiliation: The Earlham Institute, Norwich NR4 7UG, United Kingdom.
authors.forename: Christine
authors.initials: C
authors.lastname: Fosker
authors.affiliation: The Earlham Institute, Norwich NR4 7UG, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Ayling
authors.affiliation: Rothamsted Research, Harpenden AL5 2JQ, United Kingdom.
authors.forename: Andrew L
authors.initials: AL
authors.lastname: Phillips
authors.affiliation: John Innes Centre, Norwich NR4 7UH, United Kingdom; cristobal.uauy@jic.ac.uk jdubcovsky@ucdavis.edu.
authors.forename: Cristobal
authors.initials: C
authors.lastname: Uauy
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA 95616; cristobal.uauy@jic.ac.uk jdubcovsky@ucdavis.edu.|Howard Hughes Medical Institute, Chevy Chase, MD 20815.
authors.forename: Jorge
authors.identifier: 0000-0002-7571-4345
authors.initials: J
authors.lastname: Dubcovsky
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods; D019143:Evolution, Molecular; D059472:Exome / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D009154:Mutation; D000069600:Plant Breeding; D010940:Plant Proteins / Q000235:genetics; D011123:Polyploidy; D012641:Selection, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: exome capture; mutations; polyploidy; reverse genetics; wheat