Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice

Abstract

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, includingindica,aus, andjaponica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, includingGhd8/DTH8,Gn1a, andIPA1existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.

Gene disruption by structural mutations drives selection in US rice breeding over the last century

“…Still, the genes implicated in this analysis only account for~5% of disrupted genes, suggesting that the bulk of the effect is driven by a general disruption of metabolic function [7]. There was a slight enrichment in overlap with loci found to effect heterosis in rice [28], though the significance of the bias (18 observed versus 10 expected) is difficult to assess in this context.…”

An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’, as revealed by genome-wide gene expression analysis

“…In previous years, many important genes or QTLs associated with heterosis have been identi ed in many species, such as WUSCHEL (WUS), (AUXIN-REGULATED GENE INVOLVED IN ORGAN SIZE) ARGOS in Arabidopsis [39], SINGLE FLOWER TRUSS (SFT) and fw2.2 in tomato [40,41], GW3p6 (OsMADS1), OsNramp5 (Natural Resistance-Associated Macrophage Protein 5), Ghd8/DTH8, Gn1a (OsCKX2), IPA1 (OsSPL14), Hd3a (Heading date3a) in rice [42][43][44][45] and CNR in maize [46]. These genes involved in various functions including cell number or cell cycle regulation; environmental adaption; heading date, plant height and grain-yield controlling.…”

Transcriptional and post‐transcriptional regulation of heading date in rice

“…The heterozygous state, consisting of a strong allele and a nonfunctional allele of DTH8 (DTH8/dth8), is present in many Chinese hybrids, particularly in the two-line hybrids (40.8%), including the well known superhybrid rice Liangyou-pei 9 (LYP9) (Li et al, 2016). More recently, studies have shown that the DTH8 locus has been divergently selected among New Phytologist (2021) 230: 943-956 www.newphytologist.com © 2020 The Authors New Phytologist © 2020 New Phytologist Foundation rice subpopulations, and the genetic segment carrying japonica type DTH8 was introgressed into the male parent in modern indica hybrid cultivar breeding, and contributed to heterosis with overdominance effects (Huang et al, 2016;Lin et al, 2020). Similarly, Ghd7 has been divergently selected in the male and female parents of hybrid rice and that heterozygous state of Ghd7 consisting of a strong allele and a weak or nonfunctional allele was also found to be common in Chinese hybrid rice cultivars (Li et al, 2016;Lin et al, 2020).…”