Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

Abstract

Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672–17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice.

Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress

“…To accurately measure seed germination in such a manner, we did the germination experiments on water- or NaCl solution-immersed filter paper in petri dishes (with a cover, but without seal), and refreshed the solutions in every two days. After counting germinated seeds, germination rate and germination index were calculated to evaluate seed germination status under salt stress ( Shi et al., 2017 ; Ju et al., 2022 ; Li et al., 2022 ; Mei et al., 2022 ; Zhan et al., 2023 ). In this study, we established germination grades (1 to 11) using the GR3, GR4 and GI ratios of salt stress condition to the control condition.…”

“…Although GWASs have been performed in rice to decipher seed germination under salt stress ( Shi et al., 2017 ; Yu et al., 2018 ; Islam et al., 2022 ; Ju et al., 2022 ; Li et al., 2022 ), no genes have been identified so far. In this study, three QTLs, two for GRG3 ( qGRG3-1 and qGRG3-2 ) and one for GRG4 ( qGRG4 ), were consistently detected under 0.3% and 0.5% NaCl treatments.…”

“…The general linear model (GLM) with the first three principal components matrix calculated from genotypes was employed using Tassel 5.2.54 software ( Bradbury et al., 2007 ) to perform GWAS for seed germination under salt stress. Across the whole panel of varieties, 302,900 high-quality SNPs were used for GWAS after removing SNPs with missing rates of more than 20% and minor allele frequencies of less than 5% ( Ju et al., 2022 ; Mei et al., 2022 ). To identify significant SNPs, the Bonferroni correction method was used to calculate suggestive significance thresholds of associations, resulting in a p value of 1.65 × 10 -7 (0.05/N, with N = number of SNPs) ( Shi et al., 2017 ).…”

Cold Tolerance SNPs and Candidate Gene Mining in the Soybean Germination Stage Based on Genome-Wide Association Analysis

“…The germination characteristics evaluated included germination potential (GP = number of germinated seeds in 3 days/number of seeds tested) (Zhou X et al 2023;Wang R et al 2023); germination rate (GR = number of germinated seeds/number of seeds tested); mean germination time [MGT = ∑ (Gt × Tt)/∑ Gt, where "Gt" represents the number of seeds germinated on day t and "Tt" is the time corresponding to Gt in days] (Alvarado AD et al 1987); and germination index (GI = ∑ Gt/Dt, where "Gt" represents the number of seeds germinated on day t "Dt" is the corresponding germination days) (Kan G et al 2015;Zhou X et al 2023;Ju C et al 2022). The GP and GR of each variety were calculated on the 3rd and 7th days of cultivation, respectively.…”

Haplotype analysis and marker development of five salt-tolerant–related genes in rice (Oryza sativa L.)

“…Up to now, large quantities of genetic studies on mining quantitative trait loci (QTL) and genes related to salt tolerance have been conducted, and hundreds of related QTL have been identified ( Lin et al., 2004 ; Quan et al., 2018 ; Ju et al., 2022 ; Li et al., 2022 ; Lv et al., 2022 ; Yin et al., 2022 ; Yuan et al., 2022 ; Geng et al., 2023 ). However, only five genes with natural variations have been cloned ( Table 1 ).…”