NDLI: Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Content Provider	PubMed Central
Author	Cockram, James White, Jon Zuluaga, Diana L. Smith, David Comadran, Jordi Macaulay, Malcolm Luo, Zewei Kearsey, Mike J. Werner, Peter Harrap, David Tapsell, Chris Liu, Hui Hedley, Peter E. Stein, Nils Schulte, Daniela Steuernagel, Burkhard Marshall, David F. Thomas, William T. B. Ramsay, Luke Mackay, Ian Balding, David J. Waugh, Robbie O'sullivan, Donal M. Chris, Booer Pike, Steve Hamilton, Graeme Jellis, Graham Davies, Nigel Ross, Anne Bury, Paul Habgood, Rodney Klose, Steve Dominique, Vequaud Christerson, Therese Brosnan, James Newton, Adrian Russell, Joanne Shaw, Paul Bayles, Rosemary Wang, Minghui
Abstract	Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.
Related Links	http://dx.doi.org/10.1073/pnas.1010179107
Ending Page	21616
Page Count	6
Starting Page	21611
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	50
Volume Number	107
Language	English
Publisher	National Academy of Sciences
Publisher Date	2010-12-14
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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