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

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.

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

“…We obtained the expression data of CabHLH genes from previous research ( Liu et al, 2017 ) and removed 22 CabHLH genes with FPKM values of less than one in all tissues ( Zhuo et al, 2018 ). An expression heatmap was created using the remaining 100 genes ( Figure 5 , Supplementary Table S5 ).…”

Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to Water Stressed Environments

“…Interestingly, NAC (close to CPSCT024) was also related to cold-stress responses in P. mume [53], and to the metabolic pathway of anthocyanins responsible for fruit color in different plants such as peach, plum, and Arabidopsis [54][55][56].…”

Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida

“…For example, miR156 was a key component of the aging pathway through directly regulating its targets SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) at a posttranscriptional level [45]. miRNA164 is involved in plant growth and abiotic stress responses through guiding the cleavage of the mRNAs of NAC genes [54]. The miR172 regulated flowering time and vegetative phase change through clearing the mRNA of AP2 and AP2-like genes [45].…”