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. Core Ideas: Multiple genetic loci contribute to protein digestibility.Different loci control protein and fiber digestibility.Forage digestibility is affected by genetics × environment.Different regulation pathways exist between protein and fiber digestibility. Plain Language Summary: Alfalfa (Medicago sativa L.) is an important forage crop that is known for its high protein content and is often considered the highest‐quality forage. However, alfalfa protein is readily broken down by microbes in the rumen of ruminant animals like cows, which dramatically limits the amount of protein absorbed in the small intestines. Our study was aimed at unveiling the genetic basis of protein digestibility by using genome‐wide association study. Digestibility‐related phenotypic data were collected in three locations for two consecutive years. Combined with the genotype information of each accession, significant associations between twenty‐two significant markers and 12 digestibility‐related traits were identified. Our results demonstrate that genetic factors and environmental factors both play important roles in regulating protein digestibility. The associated markers and candidate genes regulate protein digestibility in an environment‐dependent manner. [ABSTRACT FROM AUTHOR]