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Genome Biol. 2015 Feb 26;16:48. doi: 10.1186/s13059-015-0606-4.

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.

Author information

1
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. kwjordan@k-state.edu.
2
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. shichen.wang@gmail.com.
3
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. yanni@k-state.edu.
4
Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA. yanni@k-state.edu.
5
Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. L.Gardiner@liverpool.ac.uk.
6
Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. ron.maclachlan@usask.ca.
7
Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. pierre.hucl@usask.ca.
8
Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. krysta.wiebe@usask.ca.
9
Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. debbie.wong@depi.vic.gov.au.
10
Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. kerrie.forrest@dpi.vic.gov.au.
11
National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada. Andrew.Sharpe@nrc-cnrc.gc.ca.
12
National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0 W9, Canada. Christine.Sidebottom@nrc-cnrc.gc.ca.
13
Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. Neil.Hall@liverpool.ac.uk.
14
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. toomajia@ksu.edu.
15
Department Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA. timothy.close@ucr.edu.
16
Department Plant Sciences, University of California, Davis, CA, 95616, USA. jdubcovsky@ucdavis.edu.
17
Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. jdubcovsky@ucdavis.edu.
18
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. akhunova@ksu.edu.
19
Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA. akhunova@ksu.edu.
20
Department Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717, USA. ltalbert@montana.edu.
21
Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia. urmil.bansal@sydney.edu.au.
22
Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia. harbans.bariana@sydney.edu.au.
23
Department Environment and Primary Industries, Bundoora, VIC, 3083, Australia. matthew.hayden@depi.vic.gov.au.
24
Department Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada. curtis.pozniak@usask.ca.
25
Roche NimbleGen, Inc, Madison, WI, 53719, USA. jeffrey.jeddeloh@roche.com.
26
Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK. Anthony.Hall@liverpool.ac.uk.
27
Department Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. eakhunov@ksu.edu.

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.

PMID:
25886949
PMCID:
PMC4389885
DOI:
10.1186/s13059-015-0606-4
[Indexed for MEDLINE]
Free PMC Article

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