Genome-wide association studies identifying multiple loci associated with alfalfa forage quality

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

Submitted to: Journal of Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2021
Publication Date: 6/18/2021
Citation: Lin, S., Medina, C., Norberg, S., Combs, D., Wang, G., Shewmaker, G., Fransen, S., Llewellyn, D., Yu, L. 2021. Genome-wide association studies identifying multiple loci associated with alfalfa forage quality. Journal of Genetics and Genomics. 12. Article 648192. https://doi.org/10.3389/fpls.2021.648192.
DOI: https://doi.org/10.3389/fpls.2021.648192

Interpretive Summary: Alfalfa is called the “Queen of Forages” due to it high nutritional quality that benefits livestock performance. The quality of alfalfa can directly effect daily animal response and gains. However, alfalfa quality varies remarkably between different varieties, and the genetic control of quality traits is still poorly understood. The objectives of this study were to evaluate forage quality in diverse alfalfa materials and identify DNA markers associated with forage quality. A panel of 200 diverse alfalfa accessions were used and 34 quality traits were characterized using Near Infrared Reflectance Spectroscopy (NIRS). We identified several DNA markers associated with forage quality that may be useful for developing new alfalfa varieties with improved nutritional qualities.

Technical Abstract: Autotetraploid alfalfa is a major global forage crop due to its adaptation to different environments and high nutritional value for livestock. However, the genetic basis of alfalfa quality is complex and largely unresolved. In this study, a diverse panel of 200 alfalfa accessions and cultivars was used to determine genetic factors that influence forage quality. A total of 34 quality factors were measured from field trials at three locations for two years. Broad sense heritability of 34 quality traits were calculated. Among them, 26 traits had heritability higher than 0.5 with the highest value 0.76 observed for neutral detergent fiber (NDF), suggesting that genetic factors play important roles in the control of forage quality. Plants were genotyped using genotyping by sequencing (GBS) approach and 46,792 single nucleotide polymorphisms (SNPs) were detected. SNPs used for genome wide association studies (GWAS) in combination with phenotypic data. Twenty-eight SNP markers were significantly associated with 17 quality traits related to fiber, protein and sugar content. Among them, several markers were associated with more than one trait, suggesting that discrete genetic factors may control multiple traits. Moreover, several candidate genes encompassing significant markers associated with fiber and sugar content were identified that are involved in the cellulose synthesis and sugar metabolism, respectively. It is notable that significant markers identified using phenotypic data collected in different locations were variable, suggesting strong genotype-by-environment interactions. Further investigation of candidate genes and genetic markers associated with alfalfa quality will provide novel technologies for accelerating the genetic improvement of forage quality in alfalfa.