The pangenome of hexaploid bread wheat

Montenegro, Juan D. , Golicz, Agnieszka A. , Bayer, Philipp E. , Hurgobin, Bhavna, Lee, HueyTyng, Chan, Chon-Kit Kenneth, Visendi, Paul, Lai, Kaitao, Dolezel, Jaroslav, Batley, Jacqueline and Edwards, David (2017) The pangenome of hexaploid bread wheat. Plant Journal, 90 5: 1007-1013. doi:10.1111/tpj.13515

Author Montenegro, Juan D.
Golicz, Agnieszka A.
Bayer, Philipp E.
Hurgobin, Bhavna
Lee, HueyTyng
Chan, Chon-Kit Kenneth
Visendi, Paul
Lai, Kaitao
Dolezel, Jaroslav
Batley, Jacqueline
Edwards, David
Title The pangenome of hexaploid bread wheat
Journal name Plant Journal   Check publisher's open access policy
ISSN 1365-313X
Publication date 2017-04-05
Sub-type Article (original research)
DOI 10.1111/tpj.13515
Open Access Status Not yet assessed
Volume 90
Issue 5
Start page 1007
End page 1013
Total pages 7
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Subject 1311 Genetics
1110 Plant Science
1307 Cell Biology
Abstract There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at, and data are available to download from
Keyword Triticum aestivum
Single nucleotide polymorphisms
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID LP130100925
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
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