Document Detail


Whole-genome association mapping in elite inbred crop varieties.
MedLine Citation:
PMID:  21076512     Owner:  NLM     Status:  In-Process    
Abstract/OtherAbstract:
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.
Authors:
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
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Genome / National Research Council Canada = Génome / Conseil national de recherches Canada     Volume:  53     ISSN:  1480-3321     ISO Abbreviation:  Genome     Publication Date:  2010 Nov 
Date Detail:
Created Date:  2010-11-15     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8704544     Medline TA:  Genome     Country:  Canada    
Other Details:
Languages:  eng     Pagination:  967-72     Citation Subset:  IM    
Affiliation:
Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK. Robbie.Waugh@scri.ac.uk
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Investigator
Investigator/Affiliation:
Barbara Alonso / ; Byung-Kee Baik / ; Rex Bernardo / ; Tom Blake / ; Peter Bradbury / ; Victoria Carollo-Blake / ; Wynse Brooks / ; Shiaoman Chao / ; Timothy Close / ; Blake Cooper / ; Julie Dickerson / ; Ruth Dill-Macky / ; Carl Griffey / ; Patrick Hayes / ; Karen Hertsgaard / ; David Hole / ; Richard Horsley / ; Jean-Luc Jannink / ; Jennifer Kling / ; Peggy Lemaux / ; Stefano Lonardi / ; David Matthews / ; Gary Muehlbauer / ; Dolores W Mornhinweg / ; Stephen Neate / ; Donald Obert / ; Mark Schmitt / ; Paul Schwarz / ; Kevin Smith / ; Brian Steffenson / ; Steven Ullrich / ; Doreen Ware / ; Mitch Wise / ; Roger Wise / ; Mike Davis / ; Julie Ho / ; David Marshall / ; Diane Mather / ; Brian Rossnagel / ; Robbie Waugh / ; Gary Hanning / ; Scott Heisel / ; Rebecca Jennings / ; David Ruark / ; Marv Zutz /

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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