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

Background Heterosis has been exploited for decades in different crops for the dramatic increase in yield but less documented molecular evidences reported in cotton. Results An elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines was used to explore the source of its yield heterosis. A four years’ investigation of yield related traits showed that the boll number of the H318 was stable higher compare with its two parents whether in the climate suitable or unsuitable years. Besides, the hybrid H318 grows faster and showed higher fresh and dry weight than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differential expressed genes (DEGs) between H318 and its parental lines, and 945 extremely changed DEGs were screened out for later analysis. In which, most DEGs (931/945) were gathered between H318 and its paternal line (4–5), but only 78 DEGs were found between H318 and its maternal line (B0011), which implied that H318 display more similar gene action with its maternal parent. GO and KEGG analysis showed that these DEGs highly enriched in photosynthesis and carbohydrate metabolic processes, the expression level of these DEGs was significantly higher in the H318 relative to its parental lines, which implies that sucrose and starch biosynthesis were enhanced in H318. Conclusion The enhanced photosynthesis and carbohydrate metabolic capability contributes to the heterosis of H318 at seedling stage, and establish the material foundation for later higher boll setting rates in the complex field environments.