Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

Abstract

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

Grain Yield Performance of Hybrid Rice in Multi-Environment Tests for Thirty-two Years in India

“…The molecular mechanism of heterosis still remains mysterious despite research on heterosis for more than a century. Unfolding research ndings indicate the potential to improve heterosis by exploiting inter-speci c heterosis between African rice and Asian rice 45 , differential expression of genes 46 , divergent selection and genetic introgression 47 , genomic hybrid breeding using whole genome markers 48 , epistasis interactions between select parents 49 , chromosome-segment substitution lines 47 , heterotic loci from wild Oryza longistaminata for yield heterosis 50 , wide compatible neo-tetraploid rice line with long panicles 51 and genome wide transcriptome pro ling of O. ru pogon 52 .…”

Genetic basis of negative heterosis for growth traits in chickens revealed by genome-wide gene expression pattern analysis

“…In particular, the gene expression patterns involved in some metabolic pathways are obviously correlated with heterotic phenotypes. For example, several studies on heterosis in rice revealed that differentially expressed genes between hybrids and their parents were involved in energy metabolism, which contributed in a significant way to the increased yield of hybrids [ 11 , 12 ]. Fujimoto et al [ 13 ] demonstrated that the higher photosynthetic efficiency of Arabidopsis hybrids was obviously associated with the early increase in the activity of genes involved in chlorophyll biosynthesis and photosynthesis, which contributed to increased heterotic biomass.…”

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 past years, many transcriptome studies have provided insights into the molecular basis of heterosis in different species, such as rice [ 8 , 12 ], Arabidopsis [ 13 , 14 ] and maize [ 15 , 16 ]. In these studies, an extremely high number of differentially expressed genes (DEGs) associated with different biochemical pathways have been found to be related to heterosis.…”