Identification of candidate genes involved in wax deposition in Poa pratensis by RNA-seq.

Yu Ni,Qiuling Zhao,Na Guo,Yanjun Guo

doi:10.1186/s12864-016-2641-2

Abstract

BackgroundThe cuticular wax plays important roles in plant resistance to various biotic and abiotic stresses. Understanding the synthesis and secretion of cuticular waxes is necessary in utilizing cuticular waxes to improve crop productivity and plant ecological adaptation. Due to the lack of genomic resources, little genetic research on cuticular wax deposition has been focused on Poa pratensis, a perennial forage and turf grass species that is widely distributed under various habitats. In this study, we performed de novo transcriptome sequencing to explore differentially expressed genes between the leaf non-elongation zone (NEZm) and the emerged blade zone (EBZ) and to identify genes related to cuticular wax deposition.ResultsA total of 77,707,414 high quality reads were obtained from llumina HiSeq 2500 platform, which were then assembled into 106,766 unigenes. Among them, 6019 unigenes showed significant differences in expression between NEZm and EBZ. In our assembled sequences, 3087 SSRs molecular markers were discovered. All the unigenes were searched against the NR, Swissprot, GO, COG, and KEGG databases using BLAST program for functional annotation. From 3156 unigenes with more expression in NEZm compared to EBZ, a number of unigenes involved in very long chain fatty acids (VLCFAs) and cuticular wax biosynthesis, transportation and regulation were identified. Several unigenes related to defense response and epidermal patterning were also found. Twelve putative genes involved in VLCFAs and cuticular wax biosynthesis were further analyzed for their expressions using qRT-PCR.ConclusionsThe transcriptome of P. pratensis leaf was deep sequenced, de novo assembled and annotated, and the candidate genes potentially involved in VLCFAs and cuticular wax biosynthesis, secretion and regulation in P. pratensis were identified. This provides fundamental genetic resources in improving plant adaptation to abiotic and biotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2641-2) contains supplementary material, which is available to authorized users.

Highlights

The cuticular wax plays important roles in plant resistance to various biotic and abiotic stresses
CER6/KCS6 and CER10 have been identified for encoding ketoacyl-CoA synthase (KCS) and enoyl-CoA reductase (ECR) involved in very long chain fatty acids (VLCFAs) biosynthesis [12, 13]
Leaf cuticular wax Leaf three of P. pratensis was divided into mixed sample of non-elongation zone and elongation zone (NEZm) and emerged blade zone (EBZ) according to their positions (Fig. 1a)

Summary

Introduction

The cuticular wax plays important roles in plant resistance to various biotic and abiotic stresses. Ni et al BMC Genomics (2016) 17:314 performs a reiterative cycle of four reactions catalyzed by a β-ketoacyl-CoA synthase (KCS), a β-ketoacyl-CoA reductase (KCR), a β-hydroxyacyl-CoA dehydratase (HCD), and an enoyl-CoA reductase (ECR), to produce saturated VLCFAs with 24–36 carbon atoms. These VLCFAs are further modified to various wax molecules through two major pathways, the acyl-reduction and the decarbonylation pathways [10]. CER5/ABCG12 [19] and ABCG11 [20], which belong to ATP-binding cassette (ABC) transporters, were reported to be required for Arabidopsis wax export The identification of these wax-related genes helps understanding the production of cuticular wax and their functions

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