Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

文献类型： 外文期刊

第一作者： Yu, Jianping

作者： Yu, Jianping;Lin, Hai;Zhang, Bin;Li, Xiaoxia;Yuan, Qiaoling;Liu, Tianjiao;He, Huiying;Wei, Zhaoran;Zhang, Chao;Gao, Hongsheng;Wang, Quan;Qian, Qian;Shang, Lianguang;Yu, Jianping;Guo, Longbiao;Liu, Chaolei;Ding, Shilin;Qian, Qian

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关键词： Cadmium-mediated growth responses; Genome-wide association study; Natural haplotypes; Transcriptome analysis; Glutathione S-transferase

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2021 年 21 卷 1 期

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收录情况： SCI

摘要： Background: Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results: In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on similar to 3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion: The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

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