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

Abstract

Alfalfa (Medicago sativa 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 identifi ed 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 signifi cant LD (p < 0.001) between 61.5% of SSR marker pairs separated by less than 1 Mbp. The observed large extent of LD could be explained by the effect of bottlenecking and selection or the high mutation rates of SSR markers. Total marker heterozygosity was positively related to biomass yield in each of fi ve environments, but no relationship was noted for stem composition traits. Of a total of 312 nonrare (frequency >10%) alleles across the 71 SSR markers, 15 showed strong association (p < 0.005) with yield in at least one of fi ve environments, and most of the 15 alleles were identifi ed in multiple environments. Only one allele showed strong association with acid detergent fi ber (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.

Achievements and Challenges in Improving Temperate Perennial Forage Legumes

“…This strategy can work using low density marker systems (Maureira-Butler et al, 2007;Li et al, 2011) in recently combined populations and cases where moderate levels of linkage disequilibrium are detected. This offers the advantage of not having to conduct QTL discovery in biparental populations, and is indicative that genomic selection strategies may be useful in improving yield (see Section VI).…”

Applied Genetics and Genomics in Alfalfa Breeding

“…Alfalfa breeding populations that derive from a relatively narrow range of parental germplasm may have LD that is extensive enough to avoid the need for hundreds of thousands of markers in association mapping experiments. Using SSR markers, we estimated reasonably extensive LD of ~1 Mbp in a tetraploid alfalfa breeding population, although the high mutation rate of SSR markers may result in an overestimate of the LD [94]. In perennial ryegrass, Lolium perenne, also an outcrossing forage crop, a large proportion of the variation in flowering time in a diverse collection of natural populations and synthetic cultivars could be explained by several AFLP markers out of a total of ~600 screened [95].…”

“…In an association mapping study, several SSR markers were found related to yield and quality in an elite alfalfa breeding population [94]. Each identified marker explained about 2-6% of phenotypic variation [94]. One of those markers, associated with yield across multiple environment, was previously identified in an unrelated bi-parental mapping population [38], suggesting that the QTL is possibly responsible for yield in a broad array of alfalfa germplasm.…”

“…This allows for validation and fine mapping QTL identified from different QTL mapping studies and various target traits. In an association mapping study, several SSR markers were found related to yield and quality in an elite alfalfa breeding population [94]. Each identified marker explained about 2-6% of phenotypic variation [94].…”

Association Mapping in Plant Genomes

“…In Brassica napus, several seed oil related loci were identified, with a few corresponding to previously reported genomic regions associated with oil variation (Zou et al, 2010). In tetraploid alfalfa (Medicago sativa), 15 SSR markers showed strong association with yield in different environments (Li et al, 2011a). In sugar beet (Beta vulgaris), genetic variation of six agronomic traits was dissected using GWAS, identifying several QTL with major effects and others with epistatic effects (Würschum et al, 2011).…”