Integrative multi-omics and genomic prediction reveal genetic basis of early salt tolerance in alfalfa

Fei He; Ming Xu; Ruicai Long; Kai Zhu; Mengrui Du; Wenqi Ma; Hui Xue; Yanling Peng; Lin Chen; Junmei Kang; Yongfeng Zhou; Qingchuan Yang; Fan Zhang

doi:10.1016/j.jgg.2025.09.001

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Integrative multi-omics and genomic prediction reveal genetic basis of early salt tolerance in alfalfa

doi: 10.1016/j.jgg.2025.09.001

a. 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, Guangdong 518000, China;
b. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China

Funds:

This work was supported by the National Key Research and Development Program of China (2022YFF1003203), the Major Project in Agricultural Biological Breeding (2022ZD04011), the Central Public-interest Scientific Institution Basal Research Fund (Y2025YC44), the Central Public-interest Scientific Institution Basal Research Fund (2025-YWF-ZYSQ-04), and the China Postdoctoral Science Foundation (2023M733832).

Received Date: 2025-03-15
Accepted Date: 2025-09-01
Rev Recd Date: 2025-09-01

Available Online: 2025-09-10

Abstract

Abstract

The genetic basis of early-stage salt tolerance in alfalfa (Medicago sativa L.), a key factor limiting its productivity, remains poorly understand. To dissect this complex trait, we integrate genome-wide association study (GWAS) and transcriptomics (RNA-seq) from 176 accessions within a machine learning based genomic prediction framework. Analysis reveals weak genetic correlations among four salt-tolerance traits and a gradual decline in performance under increasing salt stress. GWAS identify 60 significant associated SNPs, with the highest number detected under 100 mM salt stress. Salt tolerance exhibits an additive effect from favorable haplotypes, which are most abundant in Chinese accessions. GWAS-associated genes are related to key regulators of hormone signaling and osmotic adjustment, while transcriptome analysis indicates a global repression of stress-responsive transcription factors. Integrating these multi-omics datasets allow us to identify 14 candidate genes, including MsHSD1 (seed dormancy) and MsMTATP6 (energy metabolism). Crucially, incorporating these markers into genomic prediction models improve cross-population predictive accuracy to an average of 54.4%. This study provides insights into the genetic architecture of salt tolerance in alfalfa and offers valuable markers to facilitate molecular breeding.
- Alfalfa,
- GWAS,
- RNA-seq,
- Salt,
- Genomic prediction

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References(47)

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