High Density Array for SNP Genotyping and Mapping in Tetraploid Alfalfa

摘要

The development of an Illumina iSelect Infinium array that includes approximately 9,277 SNPs identified from sequencing 27 diverse alfalfa (Medicago sativa L.) genotypes can be used to accelerate genome-wide association, mapping and molecular breedingefforts in alfalfa. Individuals from a mapping population obtained from a cross between Altet-4 and NECS-141 segregating for aluminum tolerance, fall regrowth, lignin content and other agronomic characteristics were genotyped using the developed array.The dosage status (nulliplex, simplex, duplex, triplex, or quadruplex) of an individual was successfully distinguished using GenomeStudio software for most of the SNPs evaluated. A total of 3,701 SNPs were polymorphic and segregating in the progeny of the mapping population. The number of SNP with segregation ratios suitable for mapping in tetraploid alfalfa were 1,738 SNPs for simplex x nulliplex, 582 SNPs for duplex x nulliplex, and 426 SNPs for simplex x simplex. TetraploidMap software was used to integrate SNPs from the array with an existing framework map. The colinearity between the resulting linkage map and the Medicago truncatula physical map was evaluated. The resulting high-density linkage map in alfalfa generated from this study can be useful to guide the ongoing assembly of the tetraploid alfalfa genome sequence and to identify genie SNPs in relevant loci associated with key traits of agronomic importance. The iSelect Infinium assay represents a platform for high-throughput SNP genotypingin alfalfa that greatly improves genotyping efficiency and enables detection of allelic dosage in a tetraploid species.