Molecular characterization of tall fescue germplasm using SNP markers: population structure, linkage disequilibrium, and association mapping of yield-related traits

Tall fescue (Festuca arundinacea) from Poaceae family is an allohexaploid (2n=6x=42) and cross pollinated plant that is used throughout the world as a forage plant. This research was conducted to identify the genomic regions associated with 10 agro-morphological traits using 15,881 SNP markers in a diverse tall fescue germplasm. UPGMA, Structure, and PCA analyses illustrated high genetic differentiation between forage, turf, and hybrid tall fescue samples. Correcting r(2) for population structure and kinship effects revealed the fact that the r(2)v (corrected for kinship) is much smaller than r(2) (uncorrected) illustrating the necessity of removing the effect of coancestry to reduce the inflation of r(2) estimates. Analysis of linkage disequilibrium revealed that the amount of SNP pairs in LD differs between sub-genomes and chromosomes and any increase in the distance among SNPs reduces the amount of SNP pairs in LD. A total of 111 and 17 marker-trait associations were identified via GLM and MLM methods for the investigated traits, respectively. Most of the significant MTAs belonged to plant height and days to anthesis. Gene ontology results revealed that 34% of MTAs were located in protein-coding regions. Most of the MTAs were located on chromosomes 1B and 1D. The MTAs for plant height and days to anthesis located within the coding regions can be utilized in genome-based breeding in tall fescue breeding programs.