First US alfalfa reference genome sequence completed

Authors: Samac, Deborah; KAUR, HARPREET - University Of Minnesota

Submitted to: Forage Focus
Publication Type: Trade Journal
Publication Acceptance Date: 12/3/2025
Publication Date: 12/22/2025
Citation: Samac, D.A., Kaur, H. 2025. First US alfalfa reference genome sequence completed. Forage Focus. December 2025:8.

Interpretive Summary:

Technical Abstract: Genome sequences are a requirement for modern plant and animal breeding methods. They are characterized by having a high percentage of sequence assembled into chromosomes with few gaps or errors. Alfalfa has lacked a reference genome sequence for US cultivars due to the complex nature of its genome that has four copies of each of the eight chromosomes. In 2020, the USDA-ARS Plant Science Research Unit in St. Paul, MN initiated the development of the first reference genome sequence for alfalfa, selecting Regen-SY27x because it is widely used around the world for biotechnology research and for gene editing. Comparative analyses between the genome sequence of Regen-SY27x and the Chinese alfalfa genome sequences revealed strong conservation of chromosomal organization while also exposing deep structural divergence among haplotypes and between U.S. and Chinese germplasm pools. We found that a single individual alfalfa plant has extraordinarily high genetic variation. Much of this variation stems from abundant repetitive DNA, which is thought to facilitate recombination and movement of sequences within chromosomes and between haplotypes. Our analysis of the Regen-SY27x genome includes the first detailed inventory of the genes involved in disease resistance. Plant breeders and biotechnologists will use the Regen-SY27x genome sequence to investigate polyploid genome evolution, trait-associated genetic variation, and for agronomic improvement in alfalfa.