Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume.

Xiaokang Zhuo,Zhiyong Zhang,Lidan Sun,Qixiang Zhang,Jia Wang,Tangren Cheng,Liangbao Jiang,Yichi Zhang,Tangchun Zheng,Sagheer Ahmad

doi:10.3390/genes9100494

Abstract

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

Highlights

Transcription factors (TFs) act as vital molecular control systems of gene expression via their specific cis-regulatory element
A total of 113 highly confident NAC genes of P. mume were obtained by HMMER and SMART
Search (Table S2), and these genes were designated as PmNAC1–PmNAC113 based on the coordinate order on chromosome information following the rules for potato [66]

Summary

Introduction

Transcription factors (TFs) act as vital molecular control systems of gene expression via their specific cis-regulatory element. They can activate or repress transcriptional frequencies of their targeted genes by binding to specific promoter elements [1,2]. NAC (No apical meristem (NAM), Arabidopsis transcription activation factor (ATAF), Cup-shape cotyledon (CUC)) consists of a large and complex family of transcription factors. It is involved in multiple biological processes in plants, including perception of biotic/abiotic stress, signal transduction, transcription control and gene activation [1]. The NAC domain is composed of five sub-domains (A–E)

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Conclusion