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Identification of Genetic Loci Associated with Five Agronomic Traits in Alfalfa Using Multi-Environment Trials
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  • Cesar Medina,
  • Sen Lin,
  • Guojie Wang,
  • David Combs,
  • Glenn Shewmaker,
  • Steven Fransen,
  • Don Llewellyn,
  • Steven Norberg,
  • Long-Xi Yu
Cesar Medina
USDA-ARS Plant Germplasm Introduction and Testing Research Unit

Corresponding Author:[email protected]

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Sen Lin
USDA-ARS Plant Germplasm Introduction and Testing Research Unit
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Guojie Wang
Oregon State University
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David Combs
University of Wisconsin-Madison
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Glenn Shewmaker
Kimberly Research and Extension Center
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Steven Fransen
Washington State University Prosser Irrigated Agriculture Research and Extension Center
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Don Llewellyn
Washington State University
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Steven Norberg
Washington State University Extension
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Long-Xi Yu
USDA-ARS Plant Germplasm Introduction and Testing Research Unit
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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.