Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

Abstract

Background: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood.

Results: Three stable performing F₁ hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results.

Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

Keywords: Biomass vigor; Circadian rhythm; DEGs; Heterosis; Hybrid cotton; Overdominant; Transcriptome.

Fig. 1

Phenotypic heterosis observed in F₁ hybrids at 30 days after emergence of seedling (DAE). a Fresh biomass observed in hybrids relative to their mid-parent value (MPV). Here ** is used for significant difference at p < 0.01 and * at p < 0.05. b Dry biomass observed in hybrids compared with their MPV

Fig. 2

Total DEGs and their distribution in root and leaf of each hybrid parent triad. a shows total number of up and down regulated DEGs. Here, R: root, L: leaf, A: maternal parent, and B, C, D represents three paternal parents of high (H), medium (M), and low (L) hybrids, respectively. b in root c in leaf represents distribution of unique and common DEGs in high hybrid parent triad. Similarly, d in root e in leaf shows distribution of unique and common DEGs in medium hybrid parent triad. f in root g in leaf represents unique and common DEGs distribution in low hybrid parent triad

Fig. 3

The 12 possible gene expression patterns in F₁ hybrids compared to their parents in root and leaf. a Expression patterns of 12 groups, M: male parent, F₁: hybrid, and F: female parent. b Total number of genes in each group in root and leaf of high (H) hybrid. c Total number of genes in each group in root and leaf of medium (M) hybrid. d Total number of genes in each group in root and leaf of low (L) hybrid

Fig. 4

Enriched pathways of overdominant DEGs in root and leaf of F₁ hybrids. H: High, M: Medium, and L: Low a Pathways of upregulated overdominant DEGs. b Pathways of downregulated overdominant DEGs

Fig. 5

Expression heatmap of all common overdominance genes of F₁ hybrids. H: High, M: Medium, L: Low, A, B, C, and D represent four inbred parents

Fig. 6

qRT-PCR of 12 DEGs involved in the circadian rhythm pathway and showed overdominance performance in all hybrids relative to their parents. In each figure, H: High, M: Medium, L: Low and A, B, C, and D represents four inbred parents. First five genes represent expression in root, while later genes represent expression in leaf