Patterns of polymorphism and linkage disequilibrium in cultivated barley |
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Authors: | Jordi Comadran Luke Ramsay Katrin MacKenzie Patrick Hayes Timothy J Close Gary Muehlbauer Nils Stein Robbie Waugh |
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Institution: | (1) Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA, Scotland, UK;(2) BIOSS, Invergowrie, Dundee, DD2 5DA, Scotland, UK;(3) Oregon State University, Barley Project Crop Science Bldg. 30th and Campus Way, Corvallis, OR 97333, USA;(4) Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA;(5) Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA;(6) Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany; |
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Abstract: | We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent
the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure,
patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely
recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the
‘genetic centromeres’. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10
by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current
marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing
they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively
controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical
mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable
genome and genetic features. |
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