A High-Density Genetic Linkage Map of Autotetraploid Alfalfa Using Genotyping-By-Sequencing

Genetic linkage map is a valuable tool for QTL mapping, map-based gene cloning, comparative mapping, and whole genome assembly. Alfalfa is widely planted forage crop in the world. Highly heterozygous and polyploidy nature of cultivated alfalfa challenges construction of a high-density linkage map. Using genotyping-by-sequencing (GBS), we genotyped an autotetraploid alfalfa F1 population with a cost of $20 per sample and constructed high-density linkage maps for both maternal and paternal parents. The resulted maps contain 3,591 markers on 32 linkage groups of each parental map. Each of the eight chromosomes for both maternal and paternal linkage maps was assigned with four linkage groups representing the four haplotypes. Chromosome rearrangements between chromosome 4 and chromosome 8 were found and located on the genetic and physical maps. A major QTL of fall decumbency was identified on chromosome 2, explaining about 64% of total phenotypic variation. Several major QTLs related to plant height and biomass yield in fall were also identified. The high-density linkage maps greatly improved mapping resolution. GBS could be potentially employed in breeding populations to facilitate genome-wide association study (GWAS) and genomic selection (GS) in alfalfa.