Identification of regulatory genes implicated in continuous flowering of longan (Dimocarpus longan L.).

Tianqi Jia,Andrew C Allan,Lihui Zeng,Danfeng Wei,Shan Meng,Manoj Prasad

doi:10.1371/journal.pone.0114568

Tianqi Jia, Andrew C Allan + Show 4 more

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https://doi.org/10.1371/journal.pone.0114568

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Abstract

Longan (Dimocarpus longan L.) is a tropical/subtropical fruit tree of significant economic importance in Southeast Asia. However, a lack of transcriptomic and genomic information hinders research on longan traits, such as the control of flowering. In this study, high-throughput RNA sequencing (RNA-Seq) was used to investigate differentially expressed genes between a unique longan cultivar ‘Sijimi’(S) which flowers throughout the year and a more typical cultivar ‘Lidongben’(L) which flowers only once in the season, with the aim of identifying candidate genes associated with continuous flowering. 36,527 and 40,982 unigenes were obtained by de novo assembly of the clean reads from cDNA libraries of L and S cultivars. Additionally 40,513 unigenes were assembled from combined reads of these libraries. A total of 32,475 unigenes were annotated by BLAST search to NCBI non-redundant protein (NR), Swiss-Prot, Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Of these, almost fifteen thousand unigenes were identified as significantly differentially expressed genes (DEGs) by using Reads Per kb per Million reads (RPKM) method. A total of 6,415 DEGs were mapped to 128 KEGG pathways, and 8,743 DEGs were assigned to 54 Gene Ontology categories. After blasting the DEGs to public sequence databases, 539 potential flowering-related DEGs were identified. In addition, 107 flowering-time genes were identified in longan, their expression levels between two longan samples were compared by RPKM method, of which the expression levels of 15 were confirmed by real-time quantitative PCR. Our results suggest longan homologues of SHORT VEGETATIVE PHASE (SVP), GIGANTEA (GI), F-BOX 1 (FKF1) and EARLY FLOWERING 4 (ELF4) may be involved this flowering trait and ELF4 may be a key gene. The identification of candidate genes related to continuous flowering will provide new insight into the molecular process of regulating flowering time in woody plants.

Highlights

Longan, Dimocarpus longan, is a member of the family Sapindaceae
We developed an algorithm to identify longan unigenes differentially expressed between L and S samples
Most of our knowledge about flower induction has arisen from studying flowering regulatory genes in Arabidopsis thaliana

Summary

Introduction

Dimocarpus longan, is a member of the family Sapindaceae. Longan trees are grown in many subtropical and tropical countries with majority of the production in Southeast Asia and Australia [1]. One cultivar of longan, ‘Sijimi’, originating from the China (Guangxi Province) and Vietnam border region [5], has a continuous blossoming trait due to a spontaneous mutation. ‘Sijimi’ was found to have a closer genetic relationship with longan cultivars of Guangxi Province by use of molecular marker analysis and is clustered with Chinese cultivar groups [6, 7] This cultivar blossoms and bears fruits throughout the year, under both tropical and subtropical conditions, with no requirement of environmental control. Both terminal and axillary buds of ‘Sijimi’ can differentiate into inflorescences. Based on the observation of specific flowering traits in ‘Sijimi’, we speculate that the mutation in ‘Sijimi’ gives mature shoots in mature trees or after grafting the capacity of continuous flowering

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