Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress

Abstract

Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from − 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from − 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.

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

“…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). Further investigations revealed 39 candidate genes associated with non‐synonymous allelic variations under HS conditions (38–41°C) (Kumar et al, 2023a).…”

“…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). Further investigations revealed 39 candidate genes associated with non‐synonymous allelic variations under HS conditions (38–41°C) (Kumar et al, 2023a). The study also screened 185 F12 recombinant inbred lines derived from two US rice cultivars to identify genomic regions associated with grain quality traits under HS conditions (30 ± 1°C day/22.2 ± 1°C night, at the booting stage) (Kumar et al, 2023a).…”

“…Further investigations revealed 39 candidate genes associated with non‐synonymous allelic variations under HS conditions (38–41°C) (Kumar et al, 2023a). The study also screened 185 F12 recombinant inbred lines derived from two US rice cultivars to identify genomic regions associated with grain quality traits under HS conditions (30 ± 1°C day/22.2 ± 1°C night, at the booting stage) (Kumar et al, 2023a). These efforts identified 15 QTLs (nine associated with night‐time HS) containing 6,160 SNPs and 149 DEGs.…”

“…These efforts identified 15 QTLs (nine associated with night‐time HS) containing 6,160 SNPs and 149 DEGs. Eleven potential candidate genes were significantly linked to SNP associations and HS tolerance in rice (Kumar et al, 2023a).…”