Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

Abstract

Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

“…Of note, the heterozygote of RH8 was detected initially in five of seven two-line hybrid combinations that showed a yield heterotic phenotype pattern similar to that of LYP9 and then was detected in 51 of 125 two-hybrid commercial hybrid combinations that we later investigated (SI Appendix, Table S4). In parallel with our observation, DTH8 also was found to be one of a few genes with the largest effects on grain yield, which showed the highest correlation with panicle number and grain number in a GWAS survey of 1,495 hybrid rice combinations (15). The DTH8/Ghd8/ LHD1 gene is mainly responsible for HD but also for grain yield in a genetic background-dependent manner.…”

“…Because the SRT is environmentally sensitive, the identification of environmentally insensitive QTLs and their integration into hybrids to mitigate the unstable status of expression of SRT will be greatly beneficial. In contrast, KGW performance in hybrid rice is very stable, and the related QTLs function mainly in an additive manner, as shown in our study and by others (15,36). Thus, improved seed yield will benefit from pyramiding more QTLs from both parents, especially those that do not have a negative effect on other traits (56)(57)(58).…”

“…Recently, Birchler et al (10) suggested that additive partial dominance and over-dominance might be different points on a continuum of dosage effects of alleles. Thus far, by quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS), a number of Mendelian factors, some of which are dominant and others that function in an over-dominant or an epistatic manner, have been identified in hybrid maize, rice, and other crops (11)(12)(13)(14)(15), Nevertheless, only a limited number of these factors have been characterized systematically for their involvement in yield heterosis (16). On the other hand, high-throughput gene-expression profiling in heterotic cross combinations has been carried out in both maize and rice, and a large number of genes have been found to be differentially expressed in the hybrids and their parents (17); some of these genes were reported to display nonadditive expression, in support of over-dominance, but others were mainly additive, supporting the dominance hypothesis.…”

The complete plastid genome and nuclear genome markers provide molecularevidence for the hybrid origin of Pulsatilla × hackelii Pohl.

“…The examined specimens of P. patens and P. vernalis harbored SSR alleles of the same size, which prevented the identification of species-specific alleles. The absence of heterozygosity in the evaluated hybrid could be attributed to hybrid incompatibility in one of the chromosomes (Huang et al, 2015) or the presence of null alleles in parents. SSR markers provided additional evidence that the evaluated species were closely related, because they are generally effective in molecular delimitation of species, even at early stages of divergence (Karlin et al, 2008).…”

Prediction of Hybrid Performance in Crop Plants: Molecular and Recent Approaches

“…Recently, detailed genome wide sequence analysis of a population of 1495 elite hybrid rice varieties along with their inbred parental lines, was done in order to investigate genomic effects on hybrid vigour for 38 agronomic traits Huang et al, (2015). All the inbred parental lines exhibited ~1.3 million polymorphic SNP markers which were subsequently used to study population genetic parameters.…”