Loci and alleles for submergence responses revealed by GWAS and transcriptional analysis in rice
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Loci and alleles for submergence responses revealed by GWAS and transcriptional analysis in rice Hongsheng Gao & Chao Zhang & Huiying He & Tianjiao Liu & Bin Zhang & Hai Lin & Xiaoxia Li & Zhaoran Wei & Qiaoling Yuan & Quan Wang & Chunyan Yu & Lianguang Shang
Received: 22 June 2020 / Accepted: 24 July 2020 # Springer Nature B.V. 2020
Abstract The low seedling rate of rice caused by submergence in the process of rice direct seeding has always been an important factor limiting the popularization of rice direct seeding technology. Improving the tolerance of rice to submergence stress will benefit the production of rice and the promotion of direct seeding technology. In this study, we determined the submergence coleoptile length (SCL), submergence shoot length (SSL), and submergence tolerance index (STI) of 166 different cultivated rice seedlings as the phenotypes. Through the genome-wide association analysis (GWAS) of SCL, SSL, and STI, we found multiple quantitative trait locus (QTL) locations, including nine reported QTL locations. To narrow down the candidate gene numbers, we combined data from GWAS, transcriptomic analysis, gene function annotation, and
Hongsheng Gao, Chao Zhang and Huiying He contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11032-020-01160-6) contains supplementary material, which is available to authorized users. H. Gao : C. Zhang : C. Yu (*) College of Agriculture, Ludong University, Yantai 264025, China e-mail: [email protected] H. Gao : C. Zhang : H. He : T. Liu : B. Zhang : H. Lin : X. Li : Z. Wei : Q. Yuan : Q. Wang : L. Shang (*) Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China e-mail: [email protected]
reported QTL locations, and 50 candidate genes for submergence stress were obtained. Some reported genes had been firstly found to play certain roles in submergence-mediated growth response. Combining with reported RNA-seq data and expression profile data, we focused on four adjacent genes (LOC_Os11g47550, LOC_Os11g47570, LOC_Os11g47590, and LOC_Os11g47610) located in qAG11. RNA-seq and expression profile suggested the expression of these genes in sensitive and tolerant types differs hundreds of times (146~510 fold). Based on the diverse germplasms, we determined the natural haplotype of these genes. The haplotype analysis of these four genes showed a large genetic difference between indica and japonica. These results help us to better understand the molecular mechanism of natural variations in submergence tolerance among diverse germplasms and provide materials and new genes for further selection of new submergence tolerance varieties. Keywords GWAS . Transcriptomic analysis . Submergence . Rice coleoptile . Direct seeding
Introduction Submergence and unexpected rain are widespread, recurring problems that negatively
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