Comparative transcript profiling explores differentially expressed genes associated with sexual phenotype in kiwifruit.

Ping Tang,Qiong Zhang,Xiaohong Yao

doi:10.1371/journal.pone.0180542

Abstract

BackgroundKiwifruit is a perennial, deciduous and functionally dioecious plant. However, very little is known about the whole-genome molecular mechanisms contributing to distinct sexual phenotypes. To gain a global view of genes differentially expressed between male and female flowers, we analyzed genome-wide gene expression profiles in the flowers of male and female plants using high-throughput RNA sequencing.ResultsA total of 53.5 million reads were generated. Based on the alignments of unigenes to kiwifruit genome predicted genes, a total of 39,040 unique genes with a mean length of 970 bp were identified. There were 2,503 UniGenes differentially expressed between female and male flowers, with 1,793 up-regulated and 710 down-regulated in the female flowers. Moreover, the gene expression pattern of 17 out of 19 unigenes differentially expressed between male and female flowers revealed by RNA-Seq was confirmed by real-time quantitative PCR (qRT-PCR).ConclusionsHere, we obtained a large number of EST sequences from female and male flowers of kiwifruit. This comparative transcriptome analysis provides an invaluable resource for gene expression, genomics, and functional genomic studies in A. chinensis and its related species. This study also represents a first step toward the investigation of genes involved in kiwifruit sex determination.

Highlights

The genus Actinidia, commonly known as kiwifruit, contains 54 species and 21 botanical varieties, and most of these species are native to China [1,2]
The gene expression pattern of 17 out of 19 unigenes differentially expressed between male and female flowers revealed by RNA sequencing (RNA-Seq) was confirmed by real-time quantitative PCR
This comparative transcriptome analysis provides an invaluable resource for gene expression, genomics, and functional genomic studies in A. chinensis and its related species

Summary

Introduction

The genus Actinidia, commonly known as kiwifruit, contains 54 species and 21 botanical varieties, and most of these species are native to China [1,2]. Kiwifruit is an important horticultural crop with a short history of domestication (approximately 100 years), and was first cultivated in New Zealand and subsequently in other countries such as Chile, China and Italy [1]. According to data from the Food and Agriculture Organization, approximately 3.1 million metric tons of fresh kiwifruit were produced in 2014 (http://faostat.fao.org). In China, the current annual growing area is over 0.24 million hectares, with an annual production of 1.8 million metric tons [4]. To gain a global view of genes differentially expressed between male and female flowers, we analyzed genome-wide gene expression profiles in the flowers of male and female plants using high-throughput RNA sequencing

Methods

Results

Discussion

Conclusion