QTL mapping and identification of candidate genes using a genome-wide association study for heat tolerance at anthesis in rice (Oryza sativa L.)

Abstract

Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice accessions were investigated in two environments and showed abundant variations. We performed a genomewide association study on RSF using 1.2 million single nucleotide polymorphisms (SNPs). Five QTLs were significantly associated with RSF were identified, four were found in previously reported QTLs/genes, and one was novel. The novel QTL qRSF9.2 was mapped into the 22,059,984-22,259,984 bp region, which had 38 positional candidate genes. By combining the linkage disequilibrium analysis, the QTL region was narrowed to 22,110,508-22,187,677 bp, which contained 16 candidate genes. Among them, only gene LOC_Os09g38500 contained nonsynonymous SNPs that were significantly associated with RSF. In addition, accessions with large and small RSF values had corresponding respective high and low gene expression levels. Furthermore, the RSF of the CC allele was significantly higher than that of the TT allele. Hap 2 and Hap 3 can increase heat tolerance by 7.9 and 11.3%, respectively. Our results provide useful information that recommends further cloning of qRSF9.2 and breeding heat-tolerant rice varieties by marker-assisted selection.

Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance

“…We also observed important AS events in mitochondria-related genes. For example, LOC_Os09g38500.1 (cluster 2) codes for a mitochondrial glycoprotein, probably responsible for protecting the mitochondrial membrane system from HS damage ( Hu et al, 2022 ), while isoforms LOC_Os09g38500.2 and LOC_Os09g38500.3 have exon junction complexes > 50 nt downstream their stop codon, a frequent NMD-targeting feature ( Hug et al, 2016 ), meaning they might not be translated. We observed that these three transcripts switch in their relative proportions upon different exposure times to high temperatures ( Figure 2C ), suggesting that LOC_Os09g38500 splicing regulation can be crucial for HS responses.…”

“…Our approach considerably facilitated the discovery of previously unknown candidates involved in the HS response and expanded our knowledge of known heat-responsive genes. For example, Hu et al (2022) carried out a genome-wide association analysis that identified LOC_Os09g38500 as a candidate gene for thermotolerance. This gene is present in our network and we suggest that LOC_Os09g38500 splicing regulation ( Figure 2C ) can be crucial for HS responses.…”

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

“…A recent study identified five QTL associated with relative spikelet fertility (RSF) rate, one of which ( qRSF9.2 ) contained 16 candidate genes for HS tolerance (Hu et al, 2022). One specific gene ( LOC_Os09g38500 ) contained non‐synonymous SNPs significantly associated with RSF (Hu et al, 2022). A meta‐QTL analysis was conducted to identify potential candidate genes associated with the rice grain chalkiness trait, retrieving 64 meta‐QTL from a pool of 403 previously identified QTL comprising 5,262 non‐redundant genes (Kumar et al, 2023a).…”

“…Anthesis is a critical phase in the rice development cycle, significantly influencing grain yield and quality. A recent study identified five QTL associated with relative spikelet fertility (RSF) rate, one of which ( qRSF9.2 ) contained 16 candidate genes for HS tolerance (Hu et al, 2022). One specific gene ( LOC_Os09g38500 ) contained non‐synonymous SNPs significantly associated with RSF (Hu et al, 2022).…”

Genetic Research Progress: Heat Tolerance in Rice

“…Hu et al used relative spikelet fertility as an index of heat tolerance and carried out genome-wide association analysis on the characters of 173 rice materials under two environments. Five significantly related QTLs were detected, of which a new QTL, qRSF9.2 , was located and its region narrowed to the 22,110,508–22,187,677 bp region on chromosome 9 [ 33 ]. There are similar heat-tolerant QTLs in rice, indicating that the metabolic pathway of heat tolerance among different rice varieties may be conservative, and some effective QTLs can be stably expressed.…”