Abstract
A large set of genome-wide markers and a high-throughput genotyping platform can facilitate the genetic dissection of complex traits and accelerate molecular breeding applications. Previously, we identified about 0.9 million SNP markers by sequencing transcriptomes of 27 diverse alfalfa genotypes. From this SNP set, we developed an Illumina Infinium array containing 9,277 SNPs. Using this array, we genotyped 280 diverse alfalfa genotypes and several genotypes from related species. About 81% (7,476) of the SNPs met the criteria for quality control and showed polymorphisms. The alfalfa SNP array also showed a high level of transferability for several closely related Medicago species. Principal component analysis and model-based clustering showed clear population structure corresponding to subspecies and ploidy levels. Within cultivated tetraploid alfalfa, genotypes from dormant and nondormant cultivars were largely assigned to different clusters; genotypes from semidormant cultivars were split between the groups. The extent of linkage disequilibrium (LD) across all genotypes rapidly decayed to 26 Kbp at r2 = 0.2, but the rate varied across ploidy levels and subspecies. A high level of consistency in LD was found between and within the two subpopulations of cultivated dormant and nondormant alfalfa suggesting that genome-wide association studies (GWAS) and genomic selection (GS) could be conducted using alfalfa genotypes from throughout the fall dormancy spectrum. However, the relatively low LD levels would require a large number of markers to fully saturate the genome.
Highlights
Alfalfa (M. sativa L.) is an important forage legume throughout the world
For the related species evaluated in this study, 97% of the 7,476 SNPs were useful for genotyping in M. prostrata, 91% for M. truncatula and M. secundiflora, 90% for M. lupulina, and 55% for Trifolium pratense
Development and validation of SNP array Illumina Infinium SNP arrays have been developed as a highthroughput genotyping platform for numerous plant species
Summary
Alfalfa (M. sativa L.) is an important forage legume throughout the world. Alfalfa provides high nutrition animal feeds and as a perennial crop, offers numerous environmental benefits. Important agronomic traits such as winter survival and disease resistance have been improved by phenotypic selection, multiple-year phenotypic evaluations per cycle of selection limit rate of genetic gain. Due to the long breeding cycle, the improvement of biomass yield in alfalfa has been much slower compared to that in annual crops [1]. Minimal genetic improvement of biomass yield in alfalfa was found when comparing cultivars released from different eras [2]. Developing cultivars with high yield that are tolerant to abiotic and biotic stresses is crucial to enhance alfalfa productivity and competitiveness in the world market
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