Association Mapping of Biomass Yield and Stem Composition in a Tetraploid Alfalfa Breeding Population

Abstract

Alfalfa ( L.), an important forage crop that is also a potential biofuel crop, has advantages of high yield, high lignocellulose concentration in stems, and has low input costs. In this study, we investigated population structure and linkage disequilibrium (LD) patterns in a tetraploid alfalfa breeding population using genome-wide simple sequence repeat (SSR) markers and identified markers related to yield and cell wall composition by association mapping. No obvious population structure was found in our alfalfa breeding population, which could be due to the relatively narrow genetic base of the founders and/or due to two generations of random mating. We found significant LD ( 10%) alleles across the 71 SSR markers, 15 showed strong association ( < 0.005) with yield in at least one of five environments, and most of the 15 alleles were identified in multiple environments. Only one allele showed strong association with acid detergent fiber (ADF) and one allele with acid detergent lignin (ADL). Alleles associated with traits could be directly applied in a breeding program using marker-assisted selection. However, based on our estimated LD level, we would need about 1000 markers to explore the whole alfalfa genome for association between markers and traits.