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Agronomy
Volume 15
Issue 12
10.3390/agronomy15122679
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Determining the Genetic Architecture and Breeding Potential of Quality Traits in Alfalfa (Medicago sativa L.) Through Genome-Wide Association Study and Genomic Prediction

by
Ming Xu
1,†,
Kai Zhu
1,†,
Xueqian Jiang
1,†,
Fan Zhang
2,
Bilig Sod
1,
Huajuan Leng
1,
Tian Zhang
1,
Yanchao Xu
1,
Tianhui Yang
3,
Mingna Li
1,
Xue Wang
1,
Qingchuan Yang
1,
Junmei Kang
1,
Tiejun Zhang
1,
Lin Chen
1,*,
Ruicai Long
1,* and
Fei He
1,*
1
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2
State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
3
Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan 75000, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2025, 15(12), 2679; https://doi.org/10.3390/agronomy15122679
Submission received: 19 October 2025 / Revised: 14 November 2025 / Accepted: 21 November 2025 / Published: 21 November 2025
(This article belongs to the Special Issue Breeding Forage and Bioenergy Grasses for Enhanced Productivity and Stress Resistance)
Versions Notes

Abstract

Alfalfa (Medicago sativa L.) is a high-nutritive-value forage crop that provides livestock with abundant protein and essential nutrients. Breeding elite cultivars with superior quality has become a major goal in modern alfalfa improvement. This study systematically evaluated 12 quality-related traits under field conditions using a diverse panel of 176 alfalfa accessions and investigated the genetic basis underlying these traits. Phenotypic analysis revealed variability across all traits, with coefficients of variation ranging from 2.56% to 15.72%. Based on multi-trait clustering analysis, 16 accessions with overall superior quality were identified. Genome-wide association studies (GWAS) detected 45 significant single nucleotide polymorphisms (SNPs) and 12 structural variants (SVs). Within the associated genomic regions, eight candidate genes were prioritized. RT-qPCR validation indicated that three of these genes (Msa.H.0301430, Msa.H.0290550, and Msa.H.0313490) negatively regulate quality traits, while one gene (Msa.H.0479570) acts as a positive regulator. Haplotype analysis further revealed a positive correlation between the number of favorable haplotypes and phenotypic performance. Genomic prediction (GP) achieved accuracies ranging from 0.71 to 0.86 for the traits when incorporating the top 5000 SNPs identified from GWAS. This study provides valuable insights into the genetic architecture of quality-related traits in alfalfa and lays a solid foundation for future molecular design breeding.
Keywords: alfalfa; quality; GWAS; GP alfalfa; quality; GWAS; GP

Share and Cite

MDPI and ACS Style

Xu, M.; Zhu, K.; Jiang, X.; Zhang, F.; Sod, B.; Leng, H.; Zhang, T.; Xu, Y.; Yang, T.; Li, M.; et al. Determining the Genetic Architecture and Breeding Potential of Quality Traits in Alfalfa (Medicago sativa L.) Through Genome-Wide Association Study and Genomic Prediction. Agronomy 2025, 15, 2679. https://doi.org/10.3390/agronomy15122679

AMA Style

Xu M, Zhu K, Jiang X, Zhang F, Sod B, Leng H, Zhang T, Xu Y, Yang T, Li M, et al. Determining the Genetic Architecture and Breeding Potential of Quality Traits in Alfalfa (Medicago sativa L.) Through Genome-Wide Association Study and Genomic Prediction. Agronomy. 2025; 15(12):2679. https://doi.org/10.3390/agronomy15122679

Chicago/Turabian Style

Xu, Ming, Kai Zhu, Xueqian Jiang, Fan Zhang, Bilig Sod, Huajuan Leng, Tian Zhang, Yanchao Xu, Tianhui Yang, Mingna Li, and et al. 2025. "Determining the Genetic Architecture and Breeding Potential of Quality Traits in Alfalfa (Medicago sativa L.) Through Genome-Wide Association Study and Genomic Prediction" Agronomy 15, no. 12: 2679. https://doi.org/10.3390/agronomy15122679

APA Style

Xu, M., Zhu, K., Jiang, X., Zhang, F., Sod, B., Leng, H., Zhang, T., Xu, Y., Yang, T., Li, M., Wang, X., Yang, Q., Kang, J., Zhang, T., Chen, L., Long, R., & He, F. (2025). Determining the Genetic Architecture and Breeding Potential of Quality Traits in Alfalfa (Medicago sativa L.) Through Genome-Wide Association Study and Genomic Prediction. Agronomy, 15(12), 2679. https://doi.org/10.3390/agronomy15122679

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