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. Generich
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 substructure 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.
Year
2011
Category
Refereed journal