Fine Mapping of Two Major Quantitative Trait Loci for Rice Chalkiness With High Temperature-Enhanced Additive Effects

Abstract

Chalkiness is a crucial determinant of rice quality. During seed filling period, high temperature usually increases grain chalkiness, resulting in poor grain quality. Rice chalkiness was controlled by quantitative trait loci (QTLs) and influenced by environmental conditions. In this study, we identified two single-segment substitution lines (SSSLs) 22–05 and 15–06 with significantly lower percentage of grain chalkiness (PGC) than recipient Huajingxian 74 (HJX74) over 6 cropping seasons. Two major QTLs for chalkiness, qPGC5 and qPGC6, were located by substitution mapping of SSSLs 22–05 and 15–06, respectively. qPGC5 was located in the 876.5 kb interval of chromosome 5 and qPGC6 was located in the 269.1 kb interval of chromosome 6. Interestingly, the PGC of HJX74 was significantly different between the two cropping seasons per year, with 25.8% in the first cropping season (FCS) and 16.6% in the second cropping season (SCS), while the PGC of SSSLs 22–05 and 15–06 did not significantly differ between FCS and SCS. The additive effects of qPGC5 and qPGC6 on chalkiness in the SSSLs were significantly greater in FCS than in SCS. These results showed that qPGC5 and qPGC6 had major effects on chalkiness and the SSSL alleles were more effective in reducing chalkiness under high temperature condition in FCS. The fine-mapping of the two QTLs will facilitate the cloning of genes for chalkiness and provide new genetic resources to develop new cultivars with low chalkiness even under high temperature condition.

Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

“…High-quality rice cultivars are usually negatively correlated with grain yield (Wang et al 2012a ; Ren et al 2023 ). However, in our previous studies, the six SSSLs, carrying qPGC5 , qPGC6 , qPGC8.1 , qPGC8.2 , qPGC9 and qPGC11 for low grain chalkiness respectively, exhibited similar yield traits to the recipient HJX74 (Yang et al 2021a , b , 2022 ). The six QTLs significantly reduced grain chalkiness without sacrificing its yield.…”

“…Although lots of QTLs for rice chalkiness have been mapped in rice genome, few of them have been used in improvement of rice quality by QTL pyramiding (Fan et al 2022 ; Zhao et al 2022 ). In previous studies, we identified six QTLs, qPGC5 , qPGC6 , qPGC8.1 , qPGC8.2 , qPGC9 and qPGC11 , for chalkiness by using the SSSLs of HJX74 genetic background (Yang et al 2021a , b , 2022 ). In the present research, we used the six QTLs to develop pyramiding lines with different QTL combinations.…”

“…In the double-cropping rice region of southern China, the higher air temperature in first cropping season (FCS) than in second cropping season (SCS) during rice grain-filling stage leads to a higher occurrence of rice chalkiness in FCS (Cheng et al 2005 ; Yang et al 2021a ). Recently, in the double-cropping environments, six QTLs, qPGC5 , qPGC6 , qPGC8.1 , qPGC8.2 , qPGC9 and qPGC11 , for rice chalkiness were fine-mapped, showing different response to HT (Yang et al 2021a , b , 2022 ). Two major QTLs, qPGC5 and qPGC6 , showed higher additive effects enhanced by HT, which are rare QTLs for more effectively reducing rice chalkiness under HT of FCS (Yang et al 2022 ).…”

“…Recently, in the double-cropping environments, six QTLs, qPGC5 , qPGC6 , qPGC8.1 , qPGC8.2 , qPGC9 and qPGC11 , for rice chalkiness were fine-mapped, showing different response to HT (Yang et al 2021a , b , 2022 ). Two major QTLs, qPGC5 and qPGC6 , showed higher additive effects enhanced by HT, which are rare QTLs for more effectively reducing rice chalkiness under HT of FCS (Yang et al 2022 ). These findings provide new genetic resources to improve rice chalkiness even under HT condition.…”

“…Then, the SSSLs carrying the desirable QTL alleles have been used to improve targeted complex traits by QTL pyramiding breeding (Guo et al 2016 ; Luan et al 2019 ; Zhang 2021 ; Tan et al 2022a ). Recently, six QTLs for percentage of grain chalkiness (PGC), named qPGC5 , qPGC6 , qPGC8.1 , qPGC8.2 , qPGC9 and qPGC11 , in rice were fine-mapped in the SSSLs (Yang et al 2021a , b , 2022 ). The six QTLs for low chalkiness were utilized in the present study to develop pyramiding lines with different QTL combinations.…”