Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses

Mohammad Rafiqul Islam; Shahzad Amir Naveed; Yue Zhang; Zhikang Li; Xiuqin Zhao; Sajid Fiaz; Fan Zhang; Zhichao Wu; Zhiqing Hu; Binying Fu; Yingyao Shi; Shahid Masood Shah; Jianlong Xu; Wensheng Wang

doi:10.3389/fgene.2022.822516

Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses

Front Genet. 2022 Feb 23:13:822516. doi: 10.3389/fgene.2022.822516. eCollection 2022.

Authors

Mohammad Rafiqul Islam¹, Shahzad Amir Naveed¹, Yue Zhang¹, Zhikang Li^{1

2

3}, Xiuqin Zhao¹, Sajid Fiaz⁴, Fan Zhang^{1

2}, Zhichao Wu¹, Zhiqing Hu¹, Binying Fu¹, Yingyao Shi², Shahid Masood Shah⁵, Jianlong Xu^{1

3}, Wensheng Wang^{1

2

6}

Affiliations

¹ Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
² College of Agronomy, Anhui Agricultural University, Hefei, China.
³ Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁴ Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan.
⁵ Department of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, Abbottabad, Pakistan.
⁶ National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China.

Abstract

Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.

Keywords: GWAS; QTL mapping; anaerobic; direct seeding; salinity.