Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Genome-Wide Linkage Disequilibrium Analysis And Association Study For Agronomic Traits In Canadian Barley

Liyi Zhang , Suzanne Marchand , Francois Belzile

  Département de phytologie, 1243 Marchand Building, Université Laval, Québec QC Canada G1V 0A6

Linkage disequilibrium (LD) mapping could be a valuable approach for identifying QTLs controlling complex traits in barley. A collection of 188 lines representative of barley cultivated in Canada was genotyped with >1,000 DArT markers. The population was clearly defined into two groups based on row number with two-row and six-row types falling into the appropriate group with only a few exceptions. LD between pairs of markers on the same chromosome was estimated using the squared allele-frequency correlation (r²). On average, 22.4% of all marker pairs showed significant LD (P<0.001). There was a clear relationship between genetic distance and LD and the average r² value dropped below 0.2 for markers located 3-5 cM apart. Using a subset of 65 elite cultivars for which historical data were available, we measured marker-trait associations for plant height and test weight. In total, 16 QTLs for plant height (with R² between 0.0346 and 0.1467) and 22 QTLs for test weight (with R² between 0.0506 and 0.1477) were identified. These were located on all of the chromosomes except 4H. Of the 16 QTLs for height, 7 mapped to a location where previous studies had reported height QTLs and of the 22 QTLs for test weight, 12 colocalized with previously reported test weight QTLs. In many instances where no such colocalization was found, poor marker coverage in the conventional QTL mapping populations was noted. Our results suggest that association mapping represents an attractive alternative to classical QTL methods and would increase the efficiency of marker-assisted selection.