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Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice

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Abstract

Increasing numbers of rice farmers are adopting methods of direct seeding in flooded paddy fields to save costs associated with labor and transplanting. Successful seedling establishment under anoxic conditions requires rapid coleoptile growth to access oxygen near the water surface. It is important to identify relevant genetic loci for coleoptile growth in rice. In this study, the coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of a germplasm collection consisting of 200 cultivars growing in a low-oxygen environment for 6 days varied extensively. A genome-wide association study (GWAS) was performed using 161,657 high-quality single nucleotide polymorphisms (SNPs), which were obtained via genotyping by sequencing (GBS). A total of 96 target trait-associated loci were detected, of which 14 were detected repeatedly in both the wet and dry seasons. For these 14 loci, 384 genes were located within a 200-kb genomic region (± 100 kb from the peak SNP). In addition, 12,084 differentially expressed genes (DEGs) were identified using transcriptome expression profiling. Based on the GWAS and expression profiling, we further narrowed the candidate genes down to 111. Among the 111 candidate DEGs, Os02g0285300, Os02g0639300, Os04g0671300, Os06g0702600, Os06g0707300, and Os12g0145700 were the most promising candidates associated with anaerobic germination. In addition, we performed a detailed analysis of OsTPP7 sequences from 29 samples in our panel containing 200 diverse germplasms. A total of 11 mutation sites were identified, and four haplotypes were obtained. We found that 7 varieties with the OsTPP7-1 haplotype had higher phenotypic values. This work broadens our understanding of the genetic control of germination tolerance of anaerobic conditions. This study also provides a material basis for breeding superior direct-seeded rice varieties.

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Acknowledgements

We also thank Guangzhou Genedenovo Biotechnology Co., Ltd., for assisting in sequencing and bioinformatic analyses.

Funding

Financial support for this research was provided in part by a grant from the Guangzhou key research and development project (No. 202206010015), the Scientific research fund project of Yunnan Provincial Department of Education (No. 2022J0134) and the earmarked fund for the Modern Agro-Industry Technology Research System (No. CARS-01–17). The funding agency had no input into experimental design, the conduct of the research or the analysis, interpretation of experimental results and in writing the manuscript.

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  1. Kai Liu and Jing Yang contributed equally to this work.

Authors and Affiliations

  1. National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China

    Kai Liu, Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Taotao Zheng, Hui Wang, Zhiqiang Chen & Tao Guo

  2. Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, 650500, China

    Jing Yang

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  1. Kai Liu
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Contributions

H.W., Z.C., and T.G. were responsible for providing ideas and experimental guidance; K.S., D.L., L.L., and T.Z. were responsible for data collection; K.L. and J.Y. were responsible for data analysis and writing. All the authors have read and agreed to the published version of the manuscript.

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Correspondence to Tao Guo.

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Liu, K., Yang, J., Sun, K. et al. Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice. Mol Breeding 43, 9 (2023). https://doi.org/10.1007/s11032-022-01345-1

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