Identification of Genetic Loci Associated with Five Agronomic Traits in
Alfalfa Using Multi-Environment Trials
Abstract
Yield is one of the most important agronomic traits in alfalfa breeding;
however, this is a complex trait affected by genetic and environmental
factors. In this study, we used multi-environment trials to test
yield-related traits in a diverse panel composed of 200 alfalfa
accessions and varieties. Phenotypic data of maturity (MSC), dry matter,
plant height (PH), yield (Yi), and fall dormancy (FD) were collected in
three locations: Idaho, Oregon, and Washington from 2018 to 2020.
Single-trial and stagewise analyses within each environment were used to
obtain estimated means by genotype by trait by environment. Genome-wide
association studies identified a total of 84 non-redundant markers
associated with the traits analyzed. Of those, 55 markers were located
at 44 different loci. Ten significant SNPs at the same locus were
associated with FD and they were linked to a gene annotated as a nuclear
fusion defective 4-like (NFD4) protein. SNPs linked to transcription
factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and
serine/threonine-protein phosphatase 7 proteins were associated with
MSC, PH, and Yi, respectively. Our results provide insight into the
genetic factors that influence alfalfa maturity, yield, and dormancy,
which is helpful to speed up the genetic gain of alfalfa yield
improvement.