Genome-Wide and Candidate Gene LD In Lolium perenne Cultivars and Selections - The Quest For Associations With Winter Survival

Winter survival is a very complex trait influenced by several abiotic and biotic factors. Breeding for improved winter survival is thus very difficult, and indirect selection using markers, candidate genes or genomic selection could potentially have a huge impact. Freezing tolerance is the single factor which shows highest correlation with winter survival in the field. We have studied the extent of haplotype frequency shifts relative to genetic drift in two candidate genes associated with freezing tolerance, LpPhyC (phytochrome C) and Lp6FT (fructan-6-fructosyltransferase), in populations generated by artificial selection for high and low freezing tolerance. Both loci experienced significant shifts in allele frequencies, and selection towards low frost tolerance resulted in the largest allele frequency shifts. This indicates that there was restricted allelic variation for improved freezing tolerance in the founding population. The lower response observed when selecting for increased freezing tolerance might be explained by purifying (background) selection. Genome-wide linkage disequilibrium (LD) was estimated in the selections and in 2 European and 3 Norwegian cultivars using 278 genic SNPs. Genome-wide LD (r²) decay varied among selections especially for LG5 and LG7, linkage groups that are known to contain QTLs/genes for freezing tolerance. As expected, the cultivars showed much less LD which decayed more rapidly than in the selections, and was correlated with the number of genotypes used to construct the synthetics. Population structure was observed both in the selections and the cultivars. Strategies and prospects of selection for winter hardiness using candidate genes or genome-wide associations will be discussed.