The transcriptomic basis of heterosis in rice

Abstract

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).