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

BMC Plant Biology

Longbiao Guo¹  Huiying He²  Xiaoxia Li²  Tianjiao Liu²  Qiaoling Yuan²  Bin Zhang²  Lianguang Shang²  Chao Zhang²  Quan Wang²  Zhaoran Wei²  Hongsheng Gao²  Hai Lin²  Jianping Yu³  Qian Qian⁴  Chaolei Liu⁵  Shilin Ding⁵ 

[1]Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China

[2]Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

[3]Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

[4]Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China

[5]Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

[6]State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006, Hangzhou, China

[7]State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 310006, Hangzhou, China

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

DOI  :  10.1186/s12870-021-03145-9

来源: Springer

【 摘 要 】

BackgroundCadmium (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.ResultsIn 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 ~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.ConclusionThe 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.

【 授权许可】

CC BY