数字农科院2.0

Genomic Variation and GWAS Analysis for Salt Tolerance Discovered in Egyptian Rice Germplasm

文献类型： 外文期刊

作者： Wang, Yueying;Yu, Faming;Kongpraphrut, Sirinthorn;Liu, Congcong;Asad, Muhammad Asad Ullah;Kelany, Salma;Sun, Mengrui;Wang, Yuxuan;Lv, Yang;Anis, Galal;Hazman, Mohamed;Qian, Qian;Wang, Yuexing;Guo, Longbiao

作者机构：

关键词： salt tolerance;Egyptian rice;genomic divergence;GWAS;haplotype

期刊名称： PLANTS-BASEL

ISSN： 2223-7747

年卷期： 2026 年 15 卷 1 期

页码：

收录情况： SCIE（2025版）

摘要： Egyptian rice landraces represent a unique genetic reservoir shaped by arid environments, yet their genomic and transcriptional response to salt stress remains largely unexplored. Here, we integrated genomic, transcriptomic, and population genetic analyses to systematically unravel the mechanisms of salt tolerance in this vital germplasm. Resequencing 56 Egyptian accessions uncovered a treasure trove of genetic variation, including 18,204 novel SNPs. An expanded GWAS on 258 accessions discovered 17 novel loci for salt tolerance. Parallel RNA-Seq analysis of a salt-tolerant-susceptible pair (Giza 176 vs. 9311) under stress delineated a defense network centered on phenylpropanoid and lipid metabolic pathways in the tolerant genotype. The power of our integrated approach was exemplified by the convergent identification of ONAC063, where GWAS loci, transcriptional responsiveness, and haplotype-phenotype association collectively validated its role. Furthermore, selection sweep analysis highlighted 62 candidate genes under divergent selection. Our study not only positions Egyptian rice as a key resource for allele mining but also establishes a robust multi-omics pipeline for bridging genetic diversity with complex traits, accelerating the discovery of functional genes for breeding climate-resilient crops.

分类号：

  • 相关文献

[1]Salinity tolerance in soybean is modulated by natural variation in GmSALT3. Guan, Rongxia,Guo, Yong,Yu, Lili,Liu, Ying,Jiang, Jinghan,Chen, Jiangang,Ren, Yulong,Liu, Guangyu,Tian, Lei,Jin, Longguo,Liu, Zhangxiong,Hong, Huilong,Chang, Ruzhen,Qiu, Lijuan,Qu, Yue,Gilliham, Matthew,Qu, Yue,Gilliham, Matthew.

[2]Genome-wide characterization of ZmCRY genes: unveiling stress response mechanisms and the role of ZmCRYPHR2 in salinity tolerance. Runyi Chen,Laikun Xia,Yuying Fan,Jienan Han,Yikai Wang,Xin Lu,Yue Pan,Gongjian Li,Shufeng Sun,Jiayi Liu,Xinyuan Mu,Zhiqiang Zhou,Zhuanfang Hao,Zhennan Xu,Jianfeng Weng. 2025

[3]Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. Rui Ren,Wei Liu,Min Yao,Yuan Jia,Luyao Huang,Wenqian Li,Xin He,Mei Guan,Zhongsong Liu,Chunyun Guan,Wei Hua,Xinghua Xiong,Lunwen Qian. 2022

[4]Genome-Wide Association Study Reveals Novel QTLs and Candidate Genes for Grain Number in Rice. Peiyuan Li,Qing Li,Xueli Lu,Liping Dai,Long Yang,Yifeng Hong,Tiancai Yan,Lan Shen,Qiang Zhang,Deyong Ren,Li Zhu,Jiang Hu,Guojun Dong,Guangheng Zhang,Qian Qian,Dali Zeng. 2022

[5]A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold. Wu, Jiawen,Liu, Huimin,Zhang, Yan,Zhang, Yingdong,Li, Dongling,Liu, Shiyan,Lu, Shan,Wei, Lihui,Hua, Jian,Zou, Baohong. 2024

[6]Integrative genome-wide association and haplotype-based analyses reveal genetic structure and local adaptation in Korean landrace soybeans. Eun Gyeong Kim,Myoung Jae Shin,Xiaohan Wang,Yu Mi Choi,Gi An Lee,Eunae Yoo,Jae Eun Lee,Sookyeong Lee,Kebede Taye Desta,Me Sun Kim,Hyeonseok Oh,Jungyoon Yi. 2025

[7]Genome-Wide Identification of Wheat Gene Resources Conferring Resistance to Stripe Rust. Ma, Qiaoyun,Yan, Dong,Pang, Binshuang,Bai, Jianfang,Yang, Weibing,Gao, Jiangang,Chen, Xianchao,Hou, Qiling,Zhang, Honghong,Tian, Li,Li, Yahui,Jia, Jizeng,Zhang, Lei,Chen, Zhaobo,Gao, Lifeng,Liao, Xiangzheng. 2025

[8]Genome-wide assessment of genetic diversity and association mapping for salt tolerance traits in okra (Abelmoschus esculentus L. Moench) using genotyping-by-sequencing. Jian Sun,Gaowen Xu,Yudie Hu,Yujing Cheng,Xiaoqiu Wang,Jing Yang,Meng Yang,Dongwei Xie,Zhigang Dai. 2023

[9]Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat (Triticum aestivum L.). Xiaoyan Quan,Jindong Liu,Ning Zhang,Chunjuan Xie,Hongmei Li,Xianchun Xia,Wenxing He,Yuxiang Qin. 2021

[10]Genome-Wide Association Study Uncover the Genetic Architecture of Salt Tolerance-Related Traits in Common Wheat (Triticum aestivum L.). Xiaoyan Quan,Jindong Liu,Ning Zhang,Chunjuan Xie,Hongmei Li,Xianchun Xia,Wenxing He,Yuxiang Qin. 2021

[11]Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study. Gaowen Xu,Yujing Cheng,Xiaoqiu Wang,Zhigang Dai,Zepei Kang,Zhichao Ye,Yangyang Pan,Linkang Zhou,Dongwei Xie,Jian Sun. 2024

[12]Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice. Hua Wei,Xianmeng Wang,Zhipeng Zhang,Longbo Yang,Qianqian Zhang,Yilin Li,Huiying He,Dandan Chen,Bin Zhang,Chongke Zheng,Yue Leng,Xinglan Cao,Yan Cui,Chuanlin Shi,Yifan Liu,Yang Lv,Jie Ma,Wenchuang He,Xiangpei Liu,Qiang Xu,Qiaoling Yuan,Xiaoman Yu,Tianyi Wang,Hongge Qian,Xiaoxia Li,Bintao Zhang,Hong Zhang,Wu Chen,Mingliang Guo,Xiaofan Dai,Yuexing Wang,Xiaoming Zheng,Longbiao Guo,Xianzhi Xie,Qian Qian,Lianguang Shang. 2024

[13]Domestication of Tartary Buckwheat Shaped a Regulatory Module for Seedling Salt Tolerance by Targeting the Magnesium Transporter Gene FtMGT2. Lu, Xiang,He, Yuqi,Weng, Wenfeng,Liu, Zebin,Gao, Yuanfen,Shi, Yaliang,Li, Wei,Lai, Dili,Zhao, Mengyu,Jha, Rintu,Zhao, Hui,Li, Guangsheng,Guan, Chaonan,Shao, Shuai,Ruan, Jingjun,Woo, Sun Hee,Ouyang, Yinan,Quinet, Muriel,Georgiev, Milen I.,Fernie, Alisdair R.,Hou, Congcong,Zhang, Kaixuan,Liu, Xu,Zhou, Meiliang. 2025

[14]Genome-wide association study using an aus Rice panel identifies a Salinity Sensitive Gene on Chromosome 6 at seedling stage. Hu, Shiqin,Chen, Yuetong,Zhao, Qing,Zou, Wenli,Wang, Xiwei,Meng, Lijun,Liu, Changhua,Ye, Guoyou. 2025

[15]IMPACT OF AGRICULTURAL POLICY ON EGYPTIAN RICE. Eliw, Moataz,Alim, Samim S.,Soliman, Sarhan A.. 2022

[16]蛋鸡资源群体的盲肠长度全基因组关联分析. 王星果,曲亮,卢建,窦套存,马猛,胡玉萍,沈曼曼,郭军,李尚民,王克华. 2018

[17]中国籼稻群体的遗传结构解析及12个株型性状的全基因组关联分析. 鲁清,章孟臣,魏兴华. 2015

[18]北京油鸡血清IgG含量的GWAS初步分析. 张磊,刘冉冉,赵桂苹,文杰,郑麦青,吴丹,胡耀东,李鹏,刘丽. 2011

[19]黄瓜发芽期耐热性评价及全基因组关联分析. 张松,苗晗,宋子超,薄凯亮,王烨,顾兴芳,张圣平. 2019

[20]功能基因筛选方法的研究进展. 姚雅馨,喇永富,汤继顺,贺小云,张壮彪,储明星. 2020

作者其他论文 更多>>