Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.)

Abstract

Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

A wild rice CSSL population facilitated identification of salt tolerance genes and rice germplasm innovation

“…In this study, we identified a total of 17 QTLs related to four STG indices. These indices have been successfully used in previous studies on salt tolerance at the rice germination stage (Shi et al, 2017; Yu et al, 2018; Li et al, 2022). Although eight QTLs harboured previously reported genes, these genes (except AGO2 and WRKY53 ) were not reported to be involved in STG or salt stress response.…”

“…The germination rate (GR) was counted on the 10th day, and five plant replicates were randomly selected to measure shoot length (SL) and root length (RL). Relative values were calculated by dividing the value under salt treatment by that of the control (Li et al, 2022).…”

“…As one of the most important food crops in the world, rice ( Oryza sativa ) is the staple food source for around 4 billion people, but it is highly sensitive to salt stress, especially in germination and seedling stages (Sasaki & Burr, 2000). Salt tolerance germinability (STG) is vital for rice to survive under salt stress conditions and is also an important trait for direct‐seeding rice, which has become popular in recent years in China and South East Asia (Li et al, 2022; Wang et al, 2011). Salinized rice paddy area is continuously increasing as a result of exacerbated climate change, irrational irrigation, and other factors (Hickey et al, 2019).…”

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

“…Efficient seed germination under salt stress is a crucial prerequisite for seedling establishment and subsequent crop production in saline land, and is a quantitative trait regulated by multiple genes ( Shi et al., 2017 ; Li et al., 2022 ). In this study, we conducted GWAS to investigate the genetic basis of seed germination under salt stress utilizing a set of 541 rice varieties collected worldwide.…”

“…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.…”