Comprehensive Evaluation of Salt Tolerance and Genome‑Wide Association Study of Japonica Rice Germplasms at Seedling Stage

doi:10.15933/j.cnki.1004-3268.2024.07.001

Abstract

Abstract: To investigate the distribution characteristics of Na⁺and K⁺in japonica rice germplasms at seedling stage under salt stress，identify elite salt‑tolerant germplasms and detect ion homeostasis‑related loci，181 japonica rice germplasms were used to determine the salt tolerance score（STS），shoot Na⁺content（SNC），root Na⁺content（RNC），shoot K⁺content（SKC），root K⁺content（RKC），calculate shoot Na⁺/K⁺（SNK），root Na⁺/K⁺（RNK）and comprehensive evaluation value（D），and conduct genome‑wide association study（GWAS）.The results showed that seven indexes STS，SNC，RNC，SKC，RKC，SNK and RNK showed abundant variation，and the variation coefficient ranged from 23.7% to 70.5%.The correlation analysis result showed that，SNC was extremly significantly positively correlated with RNC，SNK and RNK；RNC was extremly significantly positively correlated with SNK and RNK；SKC was significantly positively correlated with RKC and extremly significantly negatively correlated with SNK.Principal component analysis（PCA）results showed that four major components were extracted，with a cumulative contribution rate of 89. 545%. Subsequently，five salt‑tolerant germplasms，including Bertone，Cigalon，Banat2951，Zaonuodao and Shennong 2，were selected by D value，and Jiahe 1，Yueguang，Xingshi，Shanfuliya and Qianchonglang were salt‑sensitive germplasms.The GWAS analysis revealed a total of 16 salt tolerance related InDel loci and 32 allelic variants，with contribution rate of 10.82%—20.57%.Among them，nine InDel loci were significantly associated with RNC，which were located on chromosomes 1，4，6，8，9 and 11；seven InDel loci were significantly associated with RNK，which were located on chromosomes 4，5，6，7，9 and 10，with contribution rate of 11.04%—18.79%.The allele 6IM20. 68Mb‑2 was detected in RNC and RNK，respectively.The InDel locus 9IM20.21Mb，which was significantly associated with RNK，showed three haplotypes.The RNK of Hap1 was significantly lower than that of Hap2 and Hap3，so it was a typical salt‑tolerant haplotype.

Key words: Japonica rice, Salt tolerance, Comprehensive evaluation, Genome?wide association study（GWAS）

摘要： 为了解析盐胁迫下粳稻种质苗期Na⁺、K⁺分布特征，筛选耐盐优异种质，发掘离子平衡相关位点，以181份粳稻种质为试验材料，测定耐盐级别（STS）、地上部Na⁺含量（SNC）、地上部K⁺含量（SKC）、根系Na⁺含量（RNC）、根系K⁺含量（RKC），计算地上部Na⁺/K⁺（SNK）、根系Na⁺/K⁺（RNK）及耐盐性综合评价值（D），并进行全基因组关联分析。结果表明，STS、SNC、RNC、SKC、RKC、SNK、RNK 7个指标表现出丰富的变异，变异系数介于23.7%~70.5%；相关性分析表明，SNC与RNC、SNK、RNK呈极显著正相关，RNC与SNK、RNK呈极显著正相关，SKC与RKC呈显著正相关，与SNK呈极显著负相关；通过主成分分析共提取到4个主成分，累计贡献率89.545%；参照D值筛选到Bertone、Cigalon、Banat2951、早糯稻和沈农2号5份耐盐种质，加合1号、越光、幸实、山福利亚和千重浪为盐敏感种质。共检测到16个InDel位点，32个等位变异，贡献率为10.82%~20.57%。其中，与RNC显著关联的InDel位点有9个，分布于水稻第1、4、6、8、9、11号染色体上；与RNK显著关联的InDel位点有7个，位于水稻第4、5、6、7、9、10号染色体上，贡献率为11.04%~18.79%。等位变异6IM20.68Mb-2在以上2个指标中被同时检测到。与RNK显著关联的InDel位点9IM20.21Mb表现为3个单倍型，Hap1的RNK显著低于Hap2和Hap3，是1个耐盐优异单倍型。

关键词: 粳稻, 耐盐性, 综合评价, 全基因组关联分析

CLC Number:

S511

FENG Peiyuan, DONG Yue, JIAO Zilan, CHEN Min, KONG Weiru, RAN Jie, LI Peifu, TIAN Lei. Comprehensive Evaluation of Salt Tolerance and Genome‑Wide Association Study of Japonica Rice Germplasms at Seedling Stage[J]. Journal of Henan Agricultural Sciences, 2024, 53(7): 1-9.

冯培媛, 董悦, 焦紫岚, 陈敏, 孔维儒, 冉杰, 李培富, 田蕾. 粳稻种质苗期耐盐性综合评价与全基因组关联分析[J]. 河南农业科学, 2024, 53(7): 1-9.

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