Identification of Loci Controlling Forage Yield and Nutritive Value in Diploid Alfalfa Using GBS-GWAS

Alfalfa is one the most widely cultivated forage legumes worldwide and improving alfalfa forage yield and nutritive value is a major global breeding goal. Genotyping-by-sequencing (GBS) provides cost effective molecular marker genotyping for genome-wide association studies (GWAS). The tetraploid nature of cultivated alfalfa possesses challenges for mapping procedures, so to circumvent these problems, we previously used a panel of 365 diploid individuals and 89 SSR markers to map 22 forage yield and nutritive value related traits over two years. The limited marker number, unsurprisingly did not identify any associations. Using GBS, we were able to do a true GWAS to investigate association between forage yield and nutritive value-related traits over two years. More than 16,700 genome-wide SNPs passed the quality criterion after filtering and were used for subsequent analyses. We used an independent set of 89 SSR markers to account for the presence of population structure. We have detected a large number of associations for all the traits evaluated and are currently in the process of further investigating the the top associations and locating them on the Medigaco truncatula genome.  The alleles we identify with the major impact on forage yield and nutritive value can be rapidly incorporated into our breeding program.