title: A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.
abstract: BACKGROUND
  Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.
  
  
  RESULTS
  A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.
  
  
  CONCLUSIONS
  Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. kwjordan@k-state.edu.
authors.forename: Katherine W
authors.initials: KW
authors.lastname: Jordan
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. shichen.wang@gmail.com.
authors.forename: Shichen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. yanni@k-state.edu.|Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA. yanni@k-state.edu.
authors.forename: Yanni
authors.initials: Y
authors.lastname: Lun
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. L.Gardiner@liverpool.ac.uk.
authors.forename: Laura-Jayne
authors.initials: LJ
authors.lastname: Gardiner
authors.affiliation: Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. ron.maclachlan@usask.ca.
authors.forename: Ron
authors.initials: R
authors.lastname: MacLachlan
authors.affiliation: Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. pierre.hucl@usask.ca.
authors.forename: Pierre
authors.initials: P
authors.lastname: Hucl
authors.affiliation: Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. krysta.wiebe@usask.ca.
authors.forename: Krysta
authors.initials: K
authors.lastname: Wiebe
authors.affiliation: Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. debbie.wong@depi.vic.gov.au.
authors.forename: Debbie
authors.initials: D
authors.lastname: Wong
authors.affiliation: Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. kerrie.forrest@dpi.vic.gov.au.
authors.forename: Kerrie L
authors.initials: KL
authors.lastname: Forrest
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada. Andrew.Sharpe@nrc-cnrc.gc.ca.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada. Christine.Sidebottom@nrc-cnrc.gc.ca.
authors.forename: Christine Hd
authors.initials: CH
authors.lastname: Sidebottom
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. Neil.Hall@liverpool.ac.uk.
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. toomajia@ksu.edu.
authors.forename: Christopher
authors.initials: C
authors.lastname: Toomajian
authors.affiliation: Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA. timothy.close@ucr.edu.
authors.forename: Timothy
authors.initials: T
authors.lastname: Close
authors.affiliation: Department Plant Sciences, University of California, Davis, CA, 95616, USA. jdubcovsky@ucdavis.edu.|Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. jdubcovsky@ucdavis.edu.
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. akhunova@ksu.edu.|Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA. akhunova@ksu.edu.
authors.forename: Alina
authors.initials: A
authors.lastname: Akhunova
authors.affiliation: Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA. ltalbert@montana.edu.
authors.forename: Luther
authors.initials: L
authors.lastname: Talbert
authors.affiliation: Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia. urmil.bansal@sydney.edu.au.
authors.forename: Urmil K
authors.initials: UK
authors.lastname: Bansal
authors.affiliation: Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia. harbans.bariana@sydney.edu.au.
authors.forename: Harbans S
authors.initials: HS
authors.lastname: Bariana
authors.affiliation: Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. matthew.hayden@depi.vic.gov.au.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Hayden
authors.affiliation: Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. curtis.pozniak@usask.ca.
authors.forename: Curtis
authors.initials: C
authors.lastname: Pozniak
authors.affiliation: Roche NimbleGen, Inc, Madison, WI, 53719, USA. jeffrey.jeddeloh@roche.com.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Jeddeloh
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. Anthony.Hall@liverpool.ac.uk.
authors.forename: Anthony
authors.initials: A
authors.lastname: Hall
authors.affiliation: Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. eakhunov@ksu.edu.
authors.forename: Eduard
authors.initials: E
authors.lastname: Akhunov
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D059472:Exome; D005787:Gene Frequency; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D012641:Selection, Genetic; D014908:Triticum / Q000235:genetics*