Patterns of polymorphism and linkage disequilibrium in cultivated barley

Jordi Comadran, Luke Ramsay, Katrin MacKenzie, Patrick Hayes, Timothy J. Close, Gary Muehlbauer, Nils Stein, Robbie Waugh

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)523-531
Number of pages9
JournalTheoretical and Applied Genetics
Volume122
Issue number3
DOIs
StatePublished - Feb 2011

Fingerprint Dive into the research topics of 'Patterns of polymorphism and linkage disequilibrium in cultivated barley'. Together they form a unique fingerprint.

Cite this