Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L
- 1Institute of Animal Science Chinese Academy of Agricultural Sciences Beijing China
- 2State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Beijing China
Abstract
Natural variation in gene expression bridges genetic polymorphisms and phenotypic divergence, yet the regulatory architecture underlying salt stress responses remains largely unexplored in alfalfa. Here, we generated 528 RNA‐seq libraries from 176 alfalfa accessions under well‐watered and salt stress conditions and identified 12,901 differentially expressed genes. Through integration of population transcriptomics, eQTL mapping, TWAS, and Mendelian randomization, we constructed a genome‐wide regulatory landscape comprising 62,423 to 67,405 eQTLs, 346 distant eQTL hotspots, and a predictive TF–eGene interaction network. We prioritized 1,401 genes whose expression variations are associated with salt tolerance. Among these, we functionally validated MsRD26, a NAC transcription factor, as a major candidate positive regulator of salt tolerance. This study provides a comprehensive resource of regulatory variants and candidate genes for salt tolerance in alfalfa, with implications for genomics‐assisted breeding in this polyploid forage crop.
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BibTeX
@article{chen2026conditionally,
title = {{Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L}},
author = {Lin Chen and Yuqi Zhang and Xinyue Ma and Jinpeng Bi and Fei He and Li Zhao and Haiyue Lei and Zhengqin Xiao and Xue Wang and Tiejun Zhang and Ruicai Long and Junmei Kang and Qingchuan Yang},
journal = {Advanced Science},
year = {2026},
month = aug,
doi = {10.1002/advs.77098},
url = {https://doi.org/10.1002/advs.77098},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Conditionally Significant eQTL and TWAS Analyses Identify MsRD26 as a Major Candidate Positive Regulator of Salt Tolerance in Medicago sativa L
AU - Lin Chen
AU - Yuqi Zhang
AU - Xinyue Ma
AU - Jinpeng Bi
AU - Fei He
AU - Li Zhao
AU - Haiyue Lei
AU - Zhengqin Xiao
AU - Xue Wang
AU - Tiejun Zhang
AU - Ruicai Long
AU - Junmei Kang
AU - Qingchuan Yang
PY - 2026
DA - 2026/08/11
JO - Advanced Science
DO - 10.1002/advs.77098
UR - https://doi.org/10.1002/advs.77098
AB - Natural variation in gene expression bridges genetic polymorphisms and phenotypic divergence, yet the regulatory architecture underlying salt stress responses remains largely unexplored in alfalfa. Here, we generated 528 RNA‐seq libraries from 176 alfalfa accessions under well‐watered and salt stress conditions and identified 12,901 differentially expressed genes. Through integration of population transcriptomics, eQTL mapping, TWAS, and Mendelian randomization, we constructed a genome‐wide regulatory landscape comprising 62,423 to 67,405 eQTLs, 346 distant eQTL hotspots, and a predictive TF–eGene interaction network. We prioritized 1,401 genes whose expression variations are associated with salt tolerance. Among these, we functionally validated MsRD26, a NAC transcription factor, as a major candidate positive regulator of salt tolerance. This study provides a comprehensive resource of regulatory variants and candidate genes for salt tolerance in alfalfa, with implications for genomics‐assisted breeding in this polyploid forage crop.
SN - 2198-3844
ER -