Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice

作者：Ling Su, Jing Yang, Dandan Li, Ziai Peng, Aoyun Xia, Meng Yang, Lixin Luo, Cuihong Huang, Jiafeng Wang, Hui Wang, Zhiqiang Chen, Tao Guo · 发表于：Rice · 年份：2021 · DOI：10.1186/s12284-020-00444-x · 被引用次数：57 · 研究领域：Plant responses to water stress、Rice Cultivation and Yield Improvement、Plant Stress Responses and Tolerance

Abstract Background In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. Results In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (−log 10 ( P ) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 ( OsVP1 ), Os05g0560900 ( OsGA2ox8 ), Os05g0562200 ( OsDi19–1 ) and Os06g0548200 . Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidat...