The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research.

Abstract Alfalfa (Medicago sativa) is one of the most important forage crop in the world, however, its molecular genetics and breeding research are hindered due to the lack of high-quality reference genome. Here we report a de novo assembled 816 Mb high-quality, chromosome-level haploid genome sequence for “Zhongmu No.1” alfalfa, a heterozygous autotetraploid. The contig N50 is 3.92 Mb, and 49,165 genes are annotated in the genome. The alfalfa genome was estimated to have diverged with M. truncatula around 8 million years ago (Mya). Genomic population analysis of 162 alfalfa accessions revealed high genetic diversity, weak population structure, and extensive gene flow from wild to cultivated alfalfa. Genome-wide association studies discovered many agronomic trait gene candidates. We showed MsFTa2, a Flowering Locus T homolog, may be associated with fall dormancy and salt resistance and has up-regulated expression in salt resistant germplasm. These genomic resources will facilitate alfalfa genetic research and agronomic improvement.