Comparative Transcriptomic Analysis of Gene Expression Inheritance Patterns Associated with Cabbage Head Heterosis

Shengjuan Li,Xingli Wang,Jia Guo,Enhui Zhang,Zhongmin Xu,Charitha P. A. Jayasinghege

doi:10.3390/plants10020275

Abstract

The molecular mechanism of heterosis or hybrid vigor, where F1 hybrids of genetically diverse parents show superior traits compared to their parents, is not well understood. Here, we studied the molecular regulation of heterosis in four F1 cabbage hybrids that showed heterosis for several horticultural traits, including head size and weight. To examine the molecular mechanisms, we performed a global transcriptome profiling in the hybrids and their parents by RNA sequencing. The proportion of genetic variations detected as single nucleotide polymorphisms and small insertion–deletions as well as the numbers of differentially expressed genes indicated a larger role of the female parent than the male parent in the genetic divergence of the hybrids. More than 86% of hybrid gene expressions were non-additive. More than 81% of the genes showing divergent expressions showed dominant inheritance, and more than 56% of these exhibited maternal expression dominance. Gene expression regulation by cis-regulatory mechanisms appears to mediate most of the gene expression divergence in the hybrids; however, trans-regulatory factors appear to have a higher effect compared to cis-regulatory factors on parental expression divergence. These observations bring new insights into the molecular mechanisms of heterosis during the cabbage head development.

Highlights

The phenomenon where offspring of genetically diverse parents show superior or beneficial alterations of agronomic traits, such as growth potentials, yield, fertility, or stress tolerance, compared to their parents, is known as heterosis or hybrid vigor [1]
The mid-parent heterosis (MPH) values were positive for all the traits in all the hybrids, which demonstrates improvements compared to the average of their parents
We further evaluated the differentially expressed genes (DEGs) between hybrids and parents as well as between male and female parents using Venn diagrams to identify common DEGs among hybrids (Figure 2)

Summary

Introduction

The phenomenon where offspring of genetically diverse parents show superior or beneficial alterations of agronomic traits, such as growth potentials, yield, fertility, or stress tolerance, compared to their parents, is known as heterosis or hybrid vigor [1]. Since most of the commercial cultivars of cabbage are F1 hybrids obtained by outcrossing, understanding the underlying mechanisms of heterosis can help increase cabbage breeding efficiencies and improve the market qualities of cabbage, such as head size and appearance. The overdominance model describes heterosis as a result of synergistic interactions between alleles at heterozygous loci of a hybrid. These models can only explain single-locus heterosis [5]. The data can be used to identify genetic variations, including single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels) as well as imbalanced contributions of the parental genomes in the hybrid gene expression [10,11]

Methods

Results

Conclusion