Transcriptome and DNA methylome reveal insights into yield heterosis in the curds of broccoli (Brassica oleracea L var. italic)

Hui Li,Zhanpin Han,Lihong Li,Chunguo Wang,Min Liu,Wenqin Song,Xue Han,Hanmin Jiang,Deling Sun,Jiye Yuan,Chengbin Chen,Mei Wu,Yinglan Jia

doi:10.1186/s12870-018-1384-4

Hui Li, Zhanpin Han + Show 11 more

Open Access

https://doi.org/10.1186/s12870-018-1384-4

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Abstract

BackgroundCurds are the main edible organs, which exhibit remarkable yield heterosis in F1 hybrid broccoli. However, the molecular basis underlying heterosis in broccoli remains elusive.ResultsIn the present study, transcriptome profiles revealed that the hybridization made most genes show additive expression patterns in hybrid broccoli. The differentially expressed genes including the non-additively expressed genes detected in the hybrid broccoli and its parents were mainly involved in light, hormone and hydrogen peroxide-mediated signaling pathways, responses to stresses, and regulation of floral development, which suggested that these biological processes should play crucial roles in the yield heterosis of broccoli. Among them, light and hydrogen peroxide-mediated signaling pathways represent two novel classes of regulatory processes that could function in yield or biomass heterosis of plants. Totally, 53 candidate genes closely involved in curd yield heterosis were identified. Methylome data indicated that the DNA methylation ratio of the hybrids was higher than that of their parents. However, the DNA methylation levels of most sites also displayed additive expression patterns. These sites with differential methylation levels were predominant in the intergenic regions. In most cases, the changes of DNA methylation levels in gene regions did not significantly affect their expression levels.ConclusionsThe differentially expressed genes, the regulatory processes and the possible roles of DNA methylation modification in the formation of curd yield heterotic trait were discovered. These findings provided comprehensive insights into the curd yield heterosis in broccoli, and were significant for breeding high-yield broccoli varieties.

Highlights

Curds are the main edible organs, which exhibit remarkable yield heterosis in F1 hybrid broccoli
Remarkable biomass heterosis in the hybrid broccoli Two hybrid combinations in which their F1 hybrids both showed obvious yield heterosis were analyzed in broccoli
Investigations involved in the heterosis produced by intraspecific hybridization in Arabidopsis, rice and other plant species confirmed that the majority of genes showed similar expression profiles in the hybrids and their parents, and that the expression levels of most genes were near the mid-parent value (MPV) [12, 21, 22]

Summary

Introduction

Curds are the main edible organs, which exhibit remarkable yield heterosis in F1 hybrid broccoli. The molecular basis underlying heterosis in broccoli remains elusive. Heterosis has been used extensively in breeding high yield corps. Heterosis has been successfully utilized in crop breeding practices, the molecular mechanism of heterosis remains poorly understood, and the explorations involved in how and why the F1 hybrids exhibit superior performance in plants never stopped since this phenomenon was discovered [4]. Previous studies have proposed three main genetic hypotheses, namely, dominance [5], over-dominance [6, 7] and epistasis [8], to explain the formation of heterosis in diverse plant species. The over-dominance hypothesis suggested that heterosis arises from the allelic interactions within each of many genetic loci.

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