Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq.

Chunbao Zhang,Weilong Zhang,Xiaoyang Ding,Xiaofang Zhong,Bao Peng,Limei Zhao,Chunjing Lin,Pengnian Wang,Jingyong Zhang,Hao Yan,Fuyou Fu,Wei Zhang

doi:10.1371/journal.pone.0181061

Chunbao Zhang, Weilong Zhang + Show 10 more

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https://doi.org/10.1371/journal.pone.0181061

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Abstract

Heterosis has been widely exploited as an approach to enhance crop traits during breeding. However, its underlying molecular genetic mechanisms remain unclear. Recent advances in RNA sequencing technology (RNA-seq) have provided an opportunity to conduct transcriptome profiling for heterosis studies. We used RNA-seq to analyze the flower transcriptomes of two F1 hybrid soybeans (HYBSOY-1 and HYBSOY-5) and their parents. More than 385 million high-quality reads were generated and aligned against the soybean reference genome. A total of 681 and 899 genes were identified as being differentially expressed between HYBSOY-1 and HYBSOY-5 and their parents, respectively. These differentially expressed genes (DEGs) were categorized into four major expression categories with 12 expression patterns. Furthermore, gene ontology (GO) term analysis showed that the DEGs were enriched in the categories metabolic process and catalytic activity, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found that metabolic pathway and biosynthesis of secondary metabolites were enriched in the two F1 hybrids. Comparing the DEGs of the two F1 hybrids by GO term and KEGG pathway analyses identified 26 common DEGs that showed transgressive up-regulation, and which could be considered potential candidate genes for heterosis in soybean F1 hybrids. This identification of an extensive transcriptome dataset gives a comprehensive overview of the flower transcriptomes in two F1 hybrids, and provides useful information for soybean hybrid breeding. These findings lay the foundation for future studies on molecular mechanisms underlying soybean heterosis.

Highlights

We did not detect significant heterosis in plant height (PH), PC, or OC; significant heterosis was identified in four agronomic traits: nodes of the main stem (NNS), NPS, number of seeds per plant (NSP), and HSW (Fig 1 and Table 1)
Mid-parent heterosis (MPH) and heterosis (MPH) and best-parent heterosis (HPH) were calculated to measure the heterosis of HYBSOY-1 and HYBSOY-5
The degree of heterosis for these traits was greater in HYBSOY-5 than in HYBSOY-1, with the MPH ranging from 23.18% to 57.25%

Summary

Introduction

Heterosis has been widely used for the increase and exhibition of superior phenotypes in crop breeding, such as enhanced biomass production, development rate, grain yield, and stress. With the development of functional genomics, large-scale transcriptome analysis has been used to investigate heterosis in Arabidopsis [6, 7], maize [8], and rice [9,10,11] These studies partially unveiled the molecular basis of heterosis at the transcriptional level [12, 13]. The first soybean CMS three-line system, comprising a male-sterile line, a maintainer line, and a restorer line, was developed by Sun et al in 1994 [23] This achievement showed that it is possible to utilize soybean heterosis for hybrid soybean breeding. We focused our heterosis research on two F1 soybean hybrids varieties, HYBSOY-1 and HYBSOY-5 These were developed by the soybean CMS three-line system, using a restorer line crossed with different two male-sterile lines. Heterosis analysis of soybean hybrids by RNA-seq starting point for understanding the causative mechanism of altered gene expression in hybrids and the molecular mechanisms underlying soybean heterosis

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