Identification of QTLs for Heat Tolerance at the Flowering Stage Using Chromosome Segment Substitution Lines in Rice

Abstract

High temperature is a major stress in rice production. Although considerable progress has been made in investigating heat tolerance (HT) in rice, the genetic basis of HT at the heading stage remains largely unknown. In this study, a novel set of chromosome segment substitution lines (CSSLs) consisting of 113 lines derived from a heat-resistant indica variety N22 and a heat-sensitive indica variety 9311 was developed and used for the analysis of the genetic basis of HT. The heat sensitivity index (HSI) calculated based on seed-setting rates under natural and high-temperature environments was used to evaluate the influence of HT at the rice heading stage. In total, five quantitative trait loci (QTLs) associated with HT were detected based on seed-setting rate (SSR) evaluation; these were named qSSR6-1, qSSR7-1, qSSR8-1, qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11, respectively. Heat-tolerant alleles of the QTLs were all derived from N22. Among them, qSSR9-1 overlapped with QTLs identified previously, while the remaining QTLs were found novel. In particular, qSSR7-1 explained a high phenotypic variation of 26.35% with a LOD score of 10.75, thus deserved to be further validated. These findings will increase our understanding of the genetic mechanism underlying HT and facilitate the breeding of heat-tolerant rice varieties.

Evaluation of Grain-Filling-Related Traits Using Taichung 65 x DV85 Chromosome Segment Substitution Lines (TD-CSSLs) of Rice

“…The authors envisioned that the detailed genotypes of TD-CSSL obtained with GBS would enable the identification of chromosome regions associated with traits using a model-based approach [ 35 ]. Therefore, the authors tried to map QTLs using QTL IciMapping software [ 36 ].…”

Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice

“…Our study found that QTL qHTT3.1 was close to qhr3-1 ; while qHTT4.2 and qHTT-X4 were close to qHTB4-2 , which corresponds to previous research and provides validation for these findings [ 17 ]. In addition, qSSR6-1 , qSSR7-1 , qSSR8-1 , qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11 from heat-tolerant indica variety N22 and a heat-sensitive indica variety 9311 [ 32 ]. PS et al used recombinant inbred lines of N22 and IR64 to map heat-tolerant QTL qSTIY5.1 / qSSIY5.2 at the booting stage, which overlapped with previously identified QTLs [ 33 ].…”

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

“…A QTL analysis of the genetics underlying HS sensitivity identified a QTL on chromosome 5 in O. rufipogon Griff ( qHTH5 ) coding the HTH5 gene—which affects the pyridoxal phosphate‐binding protein PLPBP—with differential expression patterns in the HS (38 ± 0.5°C from 8:30 am to 3:00 pm) and CS (~30 ± 0.5°C from 3:00 pm to 8:30 am) treatments (Cao et al, 2022). More recently, a genomics study used 113 segment substitution lines derived from heat‐sensitive (9311) and heat‐resistant (N22) indica varieties at the heading stage (38 ± 2°C) (Nguyen et al, 2022). Five QTL associated with HS tolerance were detected based on a seed‐setting rate evaluation: qSSR6‐1 , qSSR7‐1 , qSSR8‐1 , qSSR9‐1 , and qSSR11‐1 located on chromosomes 6, 7, 8, 9, and 11, respectively (Nguyen et al, 2022).…”

“…More recently, a genomics study used 113 segment substitution lines derived from heat‐sensitive (9311) and heat‐resistant (N22) indica varieties at the heading stage (38 ± 2°C) (Nguyen et al, 2022). Five QTL associated with HS tolerance were detected based on a seed‐setting rate evaluation: qSSR6‐1 , qSSR7‐1 , qSSR8‐1 , qSSR9‐1 , and qSSR11‐1 located on chromosomes 6, 7, 8, 9, and 11, respectively (Nguyen et al, 2022).…”