Identification of Genetic Loci Associated with Five Agronomic Traits in Alfalfa Using Multi-Environment Trials

Author:

Lin Sen1,Medina Cesar Augusto1ORCID,Wang Guojie2,Combs David3,Shewmaker Glenn4,Fransen Steve5,Llewellyn Don5,Norberg Steven5,Yu Long-Xi1ORCID

Affiliation:

1. USDA-ARS Plant Germplasm Introduction and Testing Research Unit

2. Oregon State University

3. University of Wisconsin-Madison

4. University of Idaho

5. Washington State University

Abstract

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.

Publisher

Research Square Platform LLC

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