Genome-Wide Association and Genomic Prediction of Alfalfa (Medicago sativa L.) Biomass Yield Under Drought Stress

Authors: MEDINA, CESAR - University Of Minnesota; HANSEN, JULIE - Cornell University; CROFORD, JAMIE - Cornell University; VIANDS, DONALD - Cornell University; SAPKOTA, MANJO - Cornell University; Xu, Zhanyou; Peel, Michael; Yu, Long-Xi

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2025
Publication Date: 1/13/2025
Citation: Medina, C.A., Hansen, J., Croford, J., Viands, D., Sapkota, M., Xu, Z., Peel, M., Yu, L. 2025. Genome-wide association and genomic prediction of alfalfa (medicago sativa L.) biomass yield under drought stress. International Journal of Molecular Sciences. 26(2). Article 608. https://www.mdpi.com/1422-0067/26/2/608.
DOI: https://doi.org/10.3390/ijms26020608

Interpretive Summary: Alfalfa is considered a drought-tolerant crop that under water stress often goes dormant until sufficient moisture is available for growth. Developing alfalfa that maintains a high biomass yield under drought stress is a breeding goal for enhancing alfalfa productivity in water-limited areas. In this study, 424 genetically related alfalfa lines were characterized for forage yield under drought stress from multiple harvests in 2020 through 2023. Forage yield for each line was statistically modeled for harvests during each year for correlation with genetic markers. The research identified 131 markers were associated with forage yield, with 80 of them specifically linked to yield under drought stress and among the 80, 19 markers associated with multiple harvests during the growing season. Additionally, the research identified 38 markers were specific to a particular harvest indicating different genetic expression during the growing season. The identification of specific genetic markers identified in this research are useful for genetically improving alfalfa yield under drought stress.

Technical Abstract: Background Although alfalfa is considered a drought-tolerant crop, it’s response under water stress is often going dormant until moisture is available. Therefore, developing drought-resistance alfalfa that maintains a high biomass yield is a breeding goal for enhancing alfalfa productivity in water-limited areas. Results In this study, 424 half-sib families (HSFs) of alfalfa from backcross populations were genotyped and phenotyped to predict biomass yield under drought stress across multiple harvests from 2020 to 2023, in a field trial with an imposed deficit irrigation. Biomass yield for each HSF by harvest, month, year, and overall yield was modeled using mixed linear models. Predicted values were utilized for genome-wide association studies (GWAS) and genomic prediction (GP). One hundred and thirty-one significant markers were associated with biomass yield, with 80 markers specifically linked to yield under drought stress and among those, 19 markers associated with multiple harvests. Thirty-eight markers were specific to a single harvest, suggesting genotype-by-environment interactions. Significant markers and previous transcriptomic data were used to prioritize candidate genes within a window of 2 Mb and, 50 high-confidence genes associated with drought stress were identified. Genomic best linear unbiased prediction was employed for GP to obtain predictive accuracies (PAs) and genomic estimated breeding values (GEBVs). The incorporation of -log10(p-values) of the additive GWAS model of overall yield into genomic relationship matrices increased the PA by 41%. Additionally, removing SNPs with a p-value > 0.05 before developing the genomic relationship matrix increased the PA by 47.3%. Conclusion The SNP markers identified in this study are useful for marker-assisted selection to genetically improve alfalfa yield under drought stress. Finally, the highest PA (0.9) was obtained for overall yield and the GEBV enabled the selection of high-yielding plants for advancing breeding cycles.