Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials

Authors: LIN, SEN - Washington State University; MEDINA, CESAR - Washington State University; WANG, GUOJIE - Eastern Oregon University; COMBS, DAVID - University Of Wisconsin; SHEWMAKER, GLENN - University Of Idaho; FRANSEN, STEVEN - Washington State University; LLEWELLYN, DON - Washington State University; NORBERG, STEVEN - Washington State University; Yu, Long-Xi

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2023
Publication Date: 4/29/2023
Citation: Lin, S., Medina, C., Wang, G., Combs, D., Shewmaker, G., Fransen, S., Llewellyn, D., Norberg, S., Yu, L. 2023. Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials. Journal of Theoretical and Applied Genetics. 136. Article 121. https://doi.org/10.1007/s00122-023-04364-4.
DOI: https://doi.org/10.1007/s00122-023-04364-4

Interpretive Summary: Alfalfa is the most widely grown legume forage crop worldwide due to its adaptation to various environments and high quality as livestock feed. However, the productivity of alfalfa has reached a bottleneck. Genetic improvement of yield is a priority in alfalfa breeding goals. Yield is a complex trait and interacts with 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. Maturity traits including mean stage by count (MSC), dry matter (DM), plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. The same accessions were genotyped using genotyping-by-sequencing. Genome-wide association studies identified a total of 142 DNA markers associated with the traits analyzed with 84 non-redundant markers. Of those, 55 markers were located at 44 different genetic loci. Markers 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 yield, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed genetic gain of alfalfa yield improvement.

Technical Abstract: Alfalfa is the most widely grown legume forage crop worldwide due to its adaptation to various environments and high quality as livestock feed. However, the productivity of alfalfa has reached a bottleneck. Genetic improvement of yield is a priority in alfalfa breeding goals. Yield is a complex trait and interacts with 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. Maturity traits including mean stage by count (MSC), dry matter (DM), plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses within each environment were used to obtain the best linear unbiased estimate (BLUE) and best linear unbiased prediction (BLUP) values. The same accessions were genotyped using genotyping-by-sequencing followed by single nucleotide polymorphism (SNP) calling and filtering. Genome-wide association studies identified a total of 142 markers associated with the traits analyzed with 84 non-redundant markers. Of those, 55 markers were located at 44 different loci and 29 markers were in intergenic regions. 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) gene with five missense mutations . 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 yield, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed genetic gain of alfalfa yield improvement.