Heterosis In Hybrid Rice Research Articles

Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (Oryza sativa L.).

The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level.

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

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 F1 hybrids 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, including indica, aus, and japonica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including Ghd8/DTH8, Gn1a, and IPA1 existed 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.

Identification of S23 causing both interspecific hybrid male sterility and environment-conditioned male sterility in rice

BackgroundOryza glumaepatula represents an important resource of genetic diversity that can be used to improve rice production. However, hybrid sterility severely restricts gene flow between Oryza species, and hinders the utilization of distant heterosis in hybrid rice breeding.ResultsIn order to fully exploit the beneficial genes of O. glumaepatula and facilitate the conservation of these gene resources, a set of chromosome single-segment substitution lines (SSSLs) was developed using an indica variety HJX74 as the recurrent parent and an accession of O. glumaepatula as the donor parent. During the process of SSSLs development, S23, a locus conferring hybrid male sterility between O. sativa and O. glumaepatula, was identified and fine mapped to 11.54 kb and 7.08 kb genomic region in O. sativa and O. glumaepatula, respectively, encoding three and two candidate ORFs, respectively. qRT-PCR and sequence analysis excluded one common ORF as the candidate gene. In addition, hybrid male sterility caused by S23 was environment-sensitive, and could be observed only in natural short-day (NSD).ConclusionIdentification and candidate genes analysis of S23 in this study provides a valuable example to study the crosstalk between interspecific F1 hybrid male sterility and environment-conditioned male sterility in rice, facilitates reserving and utilizing favorable genes or alleles of wild Oryza species, and allows for a more efficient exploitation of distant heterosis in hybrid rice breeding.

Research progess of rice erect panicle gene <italic>DEP1</italic>

With the development of molecular biology, several genes relative to grain yield traits have been cloned in rice. Among these genes, only DEP1 (dense and erect panicle 1) has been widely used in rice breeding. The objective of this review is to summarize the previous research for DEP1 and look into its development prospect. DEP1 gene codes a heterotrimeric G protein γ subunit. The loss of its cysteine-rich domain increases signal transmission of G protein, which may result in stronger meristem activity, increased number of branches and grains per panicle, higher nitrogen use efficiency, and consequent increase in grain yield. Moreover, the erect panicle architectures improve the canopy structure and lodging resistance, which lead to higher material production capacity in population. Therefore, the plant type improvement on the basis of the erect panicle gene DEP1 will bring the third breakthrough of grain yield in rice breeding history after the semi-dwarf breeding and the application of heterosis in hybrid rice.

The transcriptomic basis of heterosis in rice

Heterosis, or hybrid vigor, refers to the superior performance of hybrids relative to their parents. Although it has been utilized successfully in agriculture for many years, the genetic basis of heterosis remain largely unclear. The classical explanations of this phenomenon, including dominance, overdominance, and epistasis, ultimately tell us little about the mechanisms driving heterosis at the molecular level. Since heterosis generally manifests in a plurality of observable quantitative traits, it is believed that many genes and/or genetic loci contribute to heterosis. The continued development of genomics and bioinformatics has recently enabled us to conduct whole genome level investigations of gene action in hybrids. The expression of many parental alleles is known to be altered in hybrids, which in turn, changes the transcriptomic activity of hybrids compared to their parents. Consequently, by first comparing the divergences in transcriptomic activity observed between hybrids and their parents, and then determining the connection between this differential gene expression and the altered phenotypes observed in hybrids, it is possible to ascertain the mechanisms driving heterosis at the molecular level. Rice has long been one of the most important crops worldwide. Heterosis in rice has been successfully utilized as a strategy for increasing both the yield and quality of this essential crop for several decades. In recent years, many studies have explored the genomic basis of heterosis in hybrid rice. To date, however, many of these genome-wide analyses of differential gene expression have exhibited a number of inconsistencies in their identification of both differentially expressed genes and patterns of gene expression. These discrepancies may stem from the different hybrid combinations, distinct tissues, and variety of genomic platforms utilized in these studies. Some studies do suggest, however, that the genes differentially expressed in rice hybrids may enhance photosynthesis, carbohydrate metabolism, energy metabolism, and other such integral biological pathways. Furthermore, some key genes required for plant growth have been shown to be unregulated in hybrids, which, in turn, suggests that increased carbon assimilation and more efficient energy utilization may be responsible for the enhanced growth observed in hybrids compared to their parents. Gene expression can be regulated by genetic components, such as cis -elements in the gene promoter regions and the trans -acting factors to which the cis -elements bind. Epigenetic components, such as DNA methylation, histone modification, and small RNAs, were also known to affect gene expression. Previous research has indicated that both genetic and epigenetic variations may contribute to the altered transcriptomic activity documented in rice hybrids. The mechanisms regulating these changes, however, remain unspecified, and thus merit further investigation. In order to gain a deeper understanding of the molecular mechanisms governing heterosis in rice hybrids in the future, it will be necessary to improve the accuracy and specificity of differential gene expression analyses in rice hybrid combinations. Similarly, future heterosis research should focus on the molecular basis of specific biological traits. Finally, we should also combine transcriptomic variation analysis with other methods of quantitative genetics, such as heterosis QTL (quantitative trait loci) mapping and GWAS (genome-wide association studies).

Different effects of DEP1 on vascular bundle- and panicle-related traits under indica and japonica genetic backgrounds

Rice (Oryza sativa L.) is a major food for more than half of the world’s population and serves as a model monocot plant. DEP1 (dense and erect panicle 1), corresponding to an erect-panicle architecture, may bring the third breakthrough in rice breeding after the introduction of the semi-dwarf trait and the application of heterosis in hybrid rice. The aim of this study was to determine the effects of DEP1 on yield components and vascular bundle-related traits under indica and japonica genetic backgrounds. We analyzed a series of recombinant inbred lines, which were derived from a cross between the japonica variety SN265 with an erect panicle and the indica variety R99 with a curved panicle. The results showed that effects of the DEP1/dep1 allele were much stronger than the effects of the indica/japonica genetic background on vascular bundle-related traits and yield components. As the frequency of indica alleles increased, the grain yield per plant and the harvest index significantly increased in lines with the dep1 allele. Among the indica-type lines, those with the dep1 allele showed superior values for almost all of the vascular bundle-related traits and yield components. Our results provide new insights into the use of a high-yield-related gene derived from japonica in the indica genetic background.

The Effect of Environment on Combining Ability and Heterosis in Hybrid Rice

The Effect of Environment on Combining Ability and Heterosis in Hybrid Rice

The Effect of Environment on Combining Ability and Heterosis in Hybrid Rice

Study was undertaken to estimate the combining ability and heterosis for yield and yield contributing characters over environments. Environment, Crosses, GCA and SCA, and their various interactions with environment were significant suggesting that the hybrids did not have the same relative performances among environments. An evaluation of combining ability across the environment indicated that both general and specific combining ability effects are important but predominance of non-additive genetic variance indicated the presence of heterozygosity in the population. As such this type of genetic variance is non-fixable hence; heterosis breeding is effective for crop improvement. Line IR-79156A, IR-68897 and tester R-51 during both the seasons and testers R-47, R-48, R-49, R-52, IR-64 and IR-10198 during kharif and line R-42, IR-66, R-43, R-46, R-56 and IR-13419 during rabi were the promising general combiners for grain yield per plant and other traits. These parents used as testers and lines in the cross combinations would be able to realize good hybrids. Considering high physical grain quality parameters as well as per se performance, sca effects (High x high or high x low gca effects of each cross) and standard heterosis, hybrids viz., IR-80555A x R-51 and IR-79156A x R-44 during kharif and IR-79156A x R-43, IR-68897A x R-51 and IR-68897A x R52 during rabi have been identified as promising rice hybrids.

Studying heterosis for grain yield and its components in hybrid rice

Heterosis in hybrid rice was studied in the 1995 wet season under irrigated conditions. Some 22 F1 hybrids developed by using cytoplasmic male sterile lines IR58025A, PMS1A, PMS2A, PMS3A, and PMS10A and 18 restorers were grown along with the standard variety HKR126 in a randomized block design with three replications. Each line was planted in a single row 3 m long. Spacing between rows and plants was kept at 30 15 cm. Observations were recorded for grain yield plant-1, panicles plant-1, grains panicle-1, and 1,000-grain weight.

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F1 hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F1 hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

Production and Heterosis Analysis of Rice Autotetraploid Hybrids

Poor fertility is the main barrier for utilizing heterosis between the two rice (Oryza sativa L.) subspecies, indica and japonica Recently, the development of autotetraploid hybrids (2n = 4x = 48) has been suggested as a new method for increasing heterosis in hybrid rice. Using standard experimental protocols, the elite diploid rice male sterile, maintainer, and restorer lines were colchicine‐doubled, and autotetraploid counterparts were obtained. Seven resulting hybrids were analyzed for heterobeltiosis (HB), where the F1 was compared to the male parent, and the degree of heterosis, where the F1 was compared to the diploid commercial hybrid, Shanyou 63. The HB among the autotetraploid hybrids ranged from 1.4 to 105.9% for the productive panicles per plant, 0.5 to 74.3% for total kernels per panicle, 17.6 to 255.7% for filled kernels per panicle, and 9.6 to 130.4% for seed set. Improvements in these yield components resulted in the HB for kernel yield ranging from 64.8 to 672.7% among the seven hybrids. Hybrids T461A/T4002 and T461A/T4193 yielded 46.3 and 38.3% more, respectively, than Shanyou 63, and all other hybrids but one yielded the same or more than Shanyou 63. The high heterosis for yield suggests that hybrid sterility between two rice subspecies may be overcome by using tetraploid lines followed by intensive selection. Also, the gigantic features of the autotetraploid hybrids may establish a plant structure able to support the higher yield.

Fine mapping of S31, a gene responsible for hybrid embryo-sac abortion in rice (Oryza sativa L.)

Partial abortion of female gametes and the resulting semi-sterility of indica x japonica inter-subspecific rice hybrids have been ascribed to an allelic interaction, which can be avoided by the use of wide compatibility varieties. To further understand the genetic mechanism of hybrid sterility, we have constructed two sets of hybrids, using as male parent either the typical japonica variety Asominori, or the wide compatibility variety 02428; and as female, a set of 66 chromosome segment substitution lines in which various chromosomal segments from the indica variety IR24 have been introduced into a common genetic background of Asominori. Spikelet semi-sterility was observed in hybrid between CSSL34 and Asominori, which is known to carry the sterility gene S31 (Zhao et al. in Euphytica 151:331-337, 2006). Cytological analysis revealed that the semi-sterility of the CSSL34 x Asominori hybrid was caused primarily by partial abortion of the embryo sac at the stage of the mitosis of the functional megaspore. A population of 1,630 progeny of the three-way cross (CSSL34 x 02428) x Asominori was developed to map S31. Based on the physical location of linked molecular markers, S31 was thereby delimited to a 54-kb region on rice chromsome 5. This fragment contains eight predicted open reading frames, four of which encode known proteins and four putative proteins. These results are relevant to the map-based cloning of S31, and the development of marker-assisted transfer of non-sterility allele inducing alleles to breeding germplasm, to allow for a more efficient exploitation of heterosis in hybrid rice.

Identification of AFLP Markers Favorable to Heterosis in Hybrid Rice.

In hybrid rice breeding programs, it is the most important to select donors for improving parental lines and to predict the hybrid performance. In this study, AFLP marker technology and a half-diallel method were used to address these related issues in hybrid rice. Based on the representative heterosis characters representing in the F1 generation, an innovative method was designed to identify the genetic diversity related to heterosis for yielding with the detected AFLP. The results showed that the genetic diversity among the parental lines was certainly related to F1 heterosis, and a few loci contributed to hybrid vigor. We discovered 11 favorable alleles with different genetic effects significantly contributing to the heterosis in grain yield among 85 AFLP markers, and 8 unfavorable alleles that significantly reduced heterosis. Based on the favorable and unfavorable alleles found, 42 accessions were evaluated for the exploitation potentials of heterosis, as reference for hybrid rice breeding. Moreover, some aspects related to heterosis formation are discussed in this paper.

Isozyme Divergence between Maintainers and Restorers in Hybrid Rice Breeding Programs in India

In hybrid rice breeding programs, genetic diversity between maintainers and restorers enhances heterosis. The objective was to measure the level of diversity between the two groups of rice (Oryza sativa L.) breeding lines or cultivars which were screened as potential maintainers or restorers by test-cross to WA (wild abortive)-cytoplasm. Allele frequencies at 15 isozyme loci were compared between 51 potential maintainers and 56 potential restorers. Differences between the two types were found at eight isozyme loci on chromosomes 4, 6, 7, 8, 11, and 12. The majority of the potential maintainers exhibited japonica type alleles, whereas most of the potential restorers exhibited indica type alleles. This pattern is considered to be due to retained associations between Rf (restorer)/rf (maintainer) genes and genetic markers on chromosomes other than those carrying Rflrf genes. The diversity as well as differentiation of indica and japonica type alleles between maintainers and restorers should contribute to enhanced heterosis in hybrid rice.

Molecular basis of heterosis in hybrid rice and hybrid maize revealed by mRNA amplification

Molecular basis of heterosis in hybrid rice and hybrid maize revealed by mRNA amplification