Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Michael Francki, Robbie Waugh, David Marshall, Bill Thomas, Jordi Comadran, Joanne Russell, Tim Close, Nils Stein, Pat Hayes, Gary Muehlbauer, James Cockram, Donal O’Sullivan, Ian Mackay, Andrew Flavell, Luke Ramsay

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.
Original languageEnglish
Pages (from-to)967-972
JournalGenome
Volume53
Issue number11
DOIs
Publication statusPrint publication - Nov 2010
Externally publishedYes

Fingerprint

Chromosome Mapping
Brassica
Genetic Models
oilseeds
Hordeum
sustainable agriculture
OECD
Agriculture
genetic improvement
chromosome mapping
genome
barley
Genome
linkage disequilibrium
Gene Pool
crop
Genome-Wide Association Study
Linkage Disequilibrium
crops
disequilibrium

Cite this

Francki, Michael ; Waugh, Robbie ; Marshall, David ; Thomas, Bill ; Comadran, Jordi ; Russell, Joanne ; Close, Tim ; Stein, Nils ; Hayes, Pat ; Muehlbauer, Gary ; Cockram, James ; O’Sullivan, Donal ; Mackay, Ian ; Flavell, Andrew ; Ramsay, Luke. / Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. In: Genome. 2010 ; Vol. 53, No. 11. pp. 967-972.
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Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. / Francki, Michael; Waugh, Robbie; Marshall, David; Thomas, Bill; Comadran, Jordi; Russell, Joanne; Close, Tim; Stein, Nils; Hayes, Pat; Muehlbauer, Gary; Cockram, James; O’Sullivan, Donal; Mackay, Ian; Flavell, Andrew; Ramsay, Luke.

In: Genome, Vol. 53, No. 11, 11.2010, p. 967-972.

Research output: Contribution to journalArticle

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AU - Francki, Michael

AU - Waugh, Robbie

AU - Marshall, David

AU - Thomas, Bill

AU - Comadran, Jordi

AU - Russell, Joanne

AU - Close, Tim

AU - Stein, Nils

AU - Hayes, Pat

AU - Muehlbauer, Gary

AU - Cockram, James

AU - O’Sullivan, Donal

AU - Mackay, Ian

AU - Flavell, Andrew

AU - Ramsay, Luke

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