Identification of Candidate Genes for Salt Tolerance at the Germination Stage in Japonica Rice by Genome-Wide Association Analysis

Yuxuan Duan, Hongliang Zheng, Haoran Wen, Di Qu, Jingnan Cui, Chong Li, Jingguo Wang, Hualong Liu, Luomiao Yang, Yan Jia, Wei Xin, Shuangshuang Li and Detang Zou ()
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Yuxuan Duan: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Hongliang Zheng: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Haoran Wen: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Di Qu: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Jingnan Cui: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Chong Li: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Jingguo Wang: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Hualong Liu: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Luomiao Yang: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Yan Jia: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Wei Xin: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Shuangshuang Li: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Detang Zou: Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China

Agriculture, 2022, vol. 12, issue 10, 1-15

Abstract: Rice salt tolerance at the germination stage directly affects the germination rate and seedling establishment of rice directly seeded in saline soils, which in turn affects yield. In this study, we determined the relative germination potential (RGP) and relative germination index (RGI) under 200 mM salt stress and control conditions using 295 japonica rice accessions. Statistical analysis showed extensive phenotypic variations under salt stress conditions. Twenty-one varieties with an RGP ≥ 80% and an RGI ≥ 80% were screened. Based on genotypic data including, 788,396 single-nucleotide polymorphisms (SNPs), 40 quantitative trait loci (QTL) were localized on rice chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, which were shown to be significantly associated with rice salt tolerance at the germination stage, including 20 for RGP and 20 for RGI, using genome-wide association analysis. Six QTL with ≥ 3 consecutive significant SNP loci and localized in the same LD interval were selected for further analysis. Four rice genes ( LOC_Os01g04920 , LOC_Os10g38350 , LOC_Os10g38470 , and LOC_Os10g38489 ) were selected as important candidates for salt tolerance based on haplotype analysis and functional annotation. The findings could facilitate the development of valuable rice varieties for direct seeding in salinized soil and improve japonica rice salt tolerance at the germination stage through molecular breeding.

Keywords: GWAS; japonica rice; germination stage; salt tolerance; candidate gene (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2022
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