Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203

Abstract

The yield heterosis of rice is sought by farmers and strong contributes to food safety, but the quality of hybrid rice may be reduced. Therefore, developing new varieties with both high yield and good quality is a heavily researched topic in hybrid rice breeding. However, the molecular mechanism governing yield heterosis and high rice quality has not been elucidated to date. In this study, a comparative transcriptomics and genomic analysis was performed on a hybrid rice variety, Chuanyou6203 (CY6203), and its parents to investigate the molecular mechanism and gene regulation network governing the formation of yield and quality stages. A total of 66,319 SNPs and InDels between CH3203 and C106B were detected in the 5′-UTR, exon, intronic, and 3′-UTR regions according to the reference genome annotation, which involved 7473 genes. A total of 436, 70, 551, 993, and 1216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. Of the common DEGs, the numbers of upregulated DEGs between CY6203 and CH3203 were all greater than those of upregulated DEGs between CY6203 and C106B in panicles and flag leaves at the booting, flowering, and middle filling stages. Approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6, and 1.68% of mRNA editing events (editing ratio ≥ 0.8) in CY6203 favored one of its parents at three stages or a particular stage, suggesting that the hypothetical heterosis mechanism of CY6203 might involve dominance or epistasis. Also 15,934 DEGs were classified into 19 distinct modules that were classified into three groups by the weighted gene coexpression network analysis. Through transcriptome analysis of panicles and flag leaves in the yield and quality stages, the DEGs in the green-yellow module primarily contributed to the increase in the source of CY6203 due to an in increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the outstanding quality of CY6203. Our transcriptome and genome analyses offer a new data set that may help to elucidate the molecular mechanism governing the yield heterosis and high quality of a hybrid rice variety.

Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis

“…The success of hybrid rice has made a great contribution to the self-sufficiency of the food supply in China and world food security. However, the molecular mechanism governing yield heterosis has not been elucidated to date [ 3 ].…”

Assembly of yield heterosis of an elite rice hybrid is promising by manipulating dominant quantitative trait loci

“…Without exception, one parent carried functional alleles and another one carried nonfunctional alleles of all four genes, which indicates that complementary function between parents underlies MPH. Many transcriptome studies on rice heterosis have compared the amounts of two parental alleles in hybrids with their parents, providing a useful resource for rice consortium (Wei et al, 2009; He et al, 2010; Li et al, 2016; Chen et al, 2018; Shao et al, 2019; Ren et al, 2020). However, amounts of nonfunctional alleles are not appropriate for trait performance.…”

Overdominant expression of genes plays a key role in root growth of tobacco hybrids

“…In different crops, gene expression shows different additive and non-additive expression patterns ( Tian et al., 2018 ; Shahzad et al., 2020 ; Shalby et al., 2021 ). In recent years, a large number of transcriptome research advances have provided new insights into the molecular basis of heterosis in species such as Arabidopsis ( Fujimoto et al., 2012 ; Wang et al., 2019 ; Liu et al., 2020 ), rice ( Shao et al., 2019 ; Ren et al., 2020 ), maize ( Ko et al., 2016 ), and rape ( Xiong et al., 2022 ).…”