Identification of genetic loci associated with protein and fiber digestibility in alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.), known as the queen of forages, is a versatile and valuable forage crop that holds significant importance in agriculture due to its myriad benefits for livestock. Ruminants benefit from alfalfa's digestible fiber and protein, contributing to improved feed efficiency and milk production. However, alfalfa protein is rapidly and extensively degraded in rumen, and it is a challenge to maximize the efficiency of the forage crude protein utilized as metabolizable protein by ruminant livestock. In this study, the phenotypic data of 14 traits related to forage digestibility were collected from 200 alfalfa accessions planted at three different locations for 2 years. The performance of these accessions showed dramatic variations by location, indicating that environmental factors play important roles in alfalfa digestibility. Twenty-two significant genetic markers associated with 12 traits related to forage digestibility were identified by genome-wide association study. Among them, seven markers were associated with more than one trait, although the significant markers varied by year and location. Putative candidate genes associated with these loci were also identified. The digestibility-related markers and associated genes identified in this study will help to better understand the genetic basis of forage digestibility and its interaction with environments. After validation, the closely linked markers and associated genes can be used for marker-assisted selection of alfalfa with improved forage quality.