scholarly journals Rootstock-Mediated Transcriptional Changes Associated with Cold Tolerance in Prunus mume Leaves

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 572
Author(s):  
Faisal Hayat ◽  
Chengdong Ma ◽  
Shahid Iqbal ◽  
Xiao Huang ◽  
Ouma Kenneth Omondi ◽  
...  
Keyword(s):  
Oxidative Damage ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Cold Tolerant ◽  
Cold Sensitive

Japanese apricot (Prunus mume) is remarkably valuable for its high ornamental and economic importance due to its distinctive features. Low temperature is a serious environmental constraint for this species, restricting its cultivation and dispersal in the north of China. To address this issue, breeding requires an understanding of the molecular mechanisms underlying responses to cold stress. We examined the leaf physiological and transcriptome profile by RNA sequencing in ‘Bungo’ scion cultivar grafted onto Prunus mume (cold-sensitive) and Prunus armeniaca (cold-tolerant) rootstocks at 4 °C for 0, 6, and 24 h. Our results revealed that the increased MDA concentration in the leaves of P. mume cultivar (cold-sensitive) suggests that cold stress might cause oxidative damage and increased sensitivity. Moreover, the cold-tolerant cultivar (P. armeniaca) considerably enhances the enzyme activities (i.e., SOD, POD, and CAT), as well as osmo-protectants (soluble sugars and proline) compared with sensitive cultivar, which helps plants to withstand oxidative damage caused by cold stress. Additionally, differentially expressed genes were shown to be enriched in plant hormone signal transduction, ribosome, MAPK signaling, and circadian rhythm pathway. After 24 h of cold stress, genes related to PYL4, histidine kinase 1, SAUR36, bHLH130, bHLH123, TIFY 6B-like, WRKY 40, WRKY 57, and 60S acidic ribosomal protein P1 were differentially expressed, implying that these DEGs involved in multiple pathways are involved in cold tolerance in Japanese apricot. This study improved our current understanding of the mechanism of cold tolerance in Japanese apricot, and the findings could be utilized for other related fruit species.

scholarly journals Transcriptome sequencing and iTRAQ of different rice cultivars provide insight into molecular mechanisms of cold-tolerance response in japonica rice

2020 ◽  
Author(s):  
Yan Jia ◽  
Hualong Liu ◽  
Zhaojun Qu ◽  
Jin Wang ◽  
Xinpeng Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Nitrogen Metabolism ◽  
N Uptake ◽  
Differentially Expressed ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Gene And Protein Expression ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background: Rice ( Oryza sativa L.), one of the most important crops cultivated in both tropical and temperate regions, has a high sensitivity to cold stress. Chilling stress limits N uptake and nitrogen metabolism in rice. To identify the genes and pathways involved in cold tolerance, specifically within the nitrogen metabolism pathway, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ). Results: Using isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5,549 genes and 450 proteins in DN and 6,145 genes and 790 proteins in SJ, that were differentially expressed during low water temperature (T w ) treatment. There were 354 transcription factor (TF) genes (212 down, 142 up), and 366 TF genes (220 down, 146 up), including 47 gene families, differentially expressed in the DN under control (CKDN) vs. DN under low-T w (D15DN) and CKSJ vs. D15SJ, respectively. Genes related to rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling pathway, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) related to rice cold-related biosynthesis pathways and particularly glutathione metabolism were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated. Conclusion: Under cold stress conditions during reproductive growth, genes and proteins related to the biosynthesis pathways of cold stress were significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified a number of putative new cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-T w treatments affected N uptake and N metabolism in rice, and promoted Glu metabolism, and the synthesis of ornithine and proline in cold-sensitive SJ.

scholarly journals An association between the nitrogen metabolism pathway and cold tolerance in rice was identified using comparative transcriptome and proteome profiling

2020 ◽  
Author(s):  
Jia Yan ◽  
Liu Hualong ◽  
Qu Zhaojun ◽  
Wang Jin ◽  
Wang Xinpeng ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Nitrogen Metabolism ◽  
N Uptake ◽  
Differentially Expressed ◽  
Rice Cultivars ◽  
Metabolism Pathway ◽  
Gene And Protein Expression ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract BackgroundRice (Oryza sativa L.), one of the most important crops cultivated in both tropical and temperate regions, has a high sensitivity to cold stress. Chilling stress limits the N uptake and nitrogen metabolism in rice. To identify the genes and pathways involved in cold tolerance, and specifically associations with the nitrogen metabolism pathway, we have compared the gene and protein expression changes between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10(SJ).ResultsUsing absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5,549 genes and 450 proteins in DN and 6,145 genes and 790 proteins in SJ, that were differentially expressed during low- water temperature (Tw) treatment. There were 354 transcription factor (TF) genes (212down, 142 up), 366 TF genes (220 down, 146 up), including 47 gene families, differentially expressed in the DN under control (CKDN) vs. DN under low-Tw (D15DN) and CKSJ vs. D15SJ, respectively. These results indicated that TF genes play a major role in post-translational regulations. Genes related to rice cold-related biosynthesis pathways, particularly the MAPK signaling pathway, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) related to rice cold-related biosynthesis pathways and particularly glutathione metabolism were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins were down-regulated that participated in γ-aminobutyric acid (GABA) and glutamine synthesis. ConclusionUnder cold stress conditions during reproductive growth, genes and proteins related to the biosynthesis pathways of cold stress, were significantly differentially expressed in the DN and SJ. The present study confirmed the known cold stress-associated genes and identified a number of putative new cold-responsive genes. It has also revealed that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Tw treatments affect the N uptake and N metabolism in rice, and promote Glu metabolism, and the synthesis of ornithine and proline in cold-sensitive SJ.

scholarly journals Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

2020 ◽  
Author(s):  
Changbing Huang ◽  
Chun Jiang ◽  
limin Jin ◽  
Huanchao Zhang
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Low Temperature Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

scholarly journals Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

2020 ◽  
Vol 21 (6) ◽  
pp. 1921 ◽  
Author(s):  
Chunji Jiang ◽  
He Zhang ◽  
Jingyao Ren ◽  
Jiale Dong ◽  
Xinhua Zhao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Expression Profiling ◽  
Gene Networks ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Evolutionary Analysis ◽  
Comparative Transcriptome ◽  
Cold Tolerant

Plants tolerate cold stress by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. Identifying TFs related to cold tolerance contributes to cold-tolerant crop breeding. In this study, a comparative transcriptome analysis was carried out to investigate global gene expression of entire TFs in two peanut varieties with different cold-tolerant abilities. A total of 87 TF families including 2328 TF genes were identified. Among them, 445 TF genes were significantly differentially expressed in two peanut varieties under cold stress. The TF families represented by the largest numbers of differentially expressed members were bHLH (basic helix—loop—helix protein), C2H2 (Cys2/His2 zinc finger protein), ERF (ethylene-responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), NAC (NAM, ATAF1/2, CUC2) and WRKY TFs. Phylogenetic evolutionary analysis, temporal expression profiling, protein–protein interaction (PPI) network, and functional enrichment of differentially expressed TFs revealed the importance of plant hormone signal transduction and plant-pathogen interaction pathways and their possible mechanism in peanut cold tolerance. This study contributes to a better understanding of the complex mechanism of TFs in response to cold stress in peanut and provides valuable resources for the investigation of evolutionary history and biological functions of peanut TFs genes involved in cold tolerance.

scholarly journals Relationship Between Cold Tolerance during Seed Germination and Vegetative Growth in Tomato: Analysis of Response and Correlated Response to Selection

2001 ◽  
Vol 126 (2) ◽  
pp. 216-220 ◽  
Author(s):  
M.R. Foolad ◽  
G.Y. Lin
Keyword(s):  
Seed Germination ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Vegetative Growth ◽  
Developmental Stages ◽  
Correlated Response ◽  
Significant Difference ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Selection For

The genetic relationship between cold tolerance (CT) during seed germination and vegetative growth in tomato (Lycopersicon esculentum Mill.) was determined. An F2 population of a cross between accession PI120256 (cold tolerant during both seed germination and vegetative growth) and UCT5 (cold sensitive during both stages) was evaluated for germination under cold stress and the most cold tolerant progeny (the first 5% germinated) were selected. Selected progeny were grown to maturity and self-fertilized to produce F3 families (referred to as the selected F3 population). The selected F3 population was evaluated for CT separately during seed germination and vegetative growth and its performance was compared with that of a nonselected F3 population of the same cross. Results indicated that selection for CT during seed germination significantly improved CT of the progeny during germination; a realized heritability of 0.75 was obtained for CT during seed germination. However, selection for CT during germination did not affect plant CT during vegetative growth; there was no significant difference between the selected and nonselected F3 populations in either absolute CT [defined as shoot fresh weight (FW) under cold stress] or relative CT (defined as shoot FW under cold as a percentage of control). Results indicated that, in PI120256, CT during seed germination was genetically independent of CT during vegetative growth. Thus, to develop tomato cultivars with improved CT during different developmental stages, selection protocols that include all critical stages are necessary.

scholarly journals BSR-Seq Analysis Provides Insights into Cold Stress in Actinidia Arguta F1 Populations

2020 ◽  
Author(s):  
Miao miao Lin ◽  
Shihang Sun ◽  
Jinbao Fang ◽  
Xiujuan Qi ◽  
Leiming Sun ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Single Molecule ◽  
Cold Hardiness ◽  
Molecular Mechanisms ◽  
Cold Resistance ◽  
Differentially Expressed ◽  
Freezing Injury ◽  
Actinidia Arguta ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract BackgroundThe freezing injury, which is one of the important abiotic stresses in horticultural crops, can influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Actinidia arguta has excellent cold resistance in Actinidia species, but knowledge relevant to molecular mechanisms is still limited so far. Understanding the mechanism of cold resistance in kiwifruit is important for cold-resistant breeding. ResultsIn our study, a cross of ‘Ruby-3’בKuilv’ male was built for the A. arguta hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to LT50. Then, we performed Bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes with cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold tolerant population pool than in the cold sensitive population pool. Upon -30°C low temperature treatment, 126 differentially expressed genes were found, and 59 genes were upregulated and 67 genes were downregulated when comparing the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs mainly belonged to starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. There were main 10 key enzyme encoding genes and two regulatory genes were up regulated in tolerant pool, regulated genes of CBF pathway were found to be different expressed, especially, 14-3-3 gene was down regulated and EBF gene was up regulated. To validate the BSR-Seq results, 24 DEGs were determined by qRT-PCR, and the results were consistent with BSR-Seq.ConclusionOur research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Oryza Rufipogon ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background: Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance for many abiotic stresses including cold stress, but little is known about the mechanism underlying its resistance to cold. Low temperature is one of the most prevalent factors that limit rice productivity and geographical distribution.Results: This study aimed to elucidate the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29128 and 30131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in cold-tolerant genotypes than in cold-sensitive genotypes at four stages under cold stress. Gene ontology enrichment analyses indicated more upregulated genes than downregulated ones in cold-tolerant genotypes based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity. To confirm the RNA Sequencing (RNA-seq) data, Quantitative real time polymerase chain reaction (qRT-PCR) was performed on seven randomly selected DEGs. These genes showed similar expression patterns corresponding with the RNA-Seq method. We also explored a gene for cold tolerance LTG5 , encoding a UDP-glucosyltransferase. The overexpression of LTG5 gene conferred cold tolerance to indica rice.Conclusion: Overall, our results suggested that gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crop plants.

scholarly journals BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Miaomiao Lin ◽  
Shihang Sun ◽  
Jinbao Fang ◽  
Xiujuan Qi ◽  
Leiming Sun ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Cold Hardiness ◽  
Molecular Mechanisms ◽  
Cold Resistance ◽  
Regulatory Genes ◽  
Differentially Expressed ◽  
Freezing Injury ◽  
Actinidia Arguta ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia arguta has excellent cold resistance, but knowledge relevant to molecular mechanisms is still limited. Understanding the mechanism underlying cold resistance in kiwifruit is important for breeding cold resistance. Results In our study, a population resulting from the cross of A. arguta ‘Ruby-3’ × ‘Kuilv’ male was generated for kiwifruit hardiness study, and 20 cold-tolerant and 20 cold-sensitive populations were selected from 492 populations according to their LT50. Then, we performed bulked segregant RNA-seq combined with single-molecule real-time sequencing to identify differentially expressed genes that provide cold hardiness. We found that the content of soluble sucrose and the activity of β-amylase were higher in the cold-tolerant population than in the cold-sensitive population. Upon − 30 °C low-temperature treatment, 126 differentially expressed genes were identify; the expression of 59 genes was up-regulated and that of 67 genes was down-regulated between the tolerant and sensitive pools, respectively. KEGG pathway analysis showed that the DEGs were primarily related to starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Ten major key enzyme-encoding genes and two regulatory genes were up-regulated in the tolerant pool, and regulatory genes of the CBF pathway were found to be differentially expressed. In particular, a 14–3-3 gene was down-regulated and an EBF gene was up-regulated. To validate the BSR-Seq results, 24 DEGs were assessed via qRT-PCR, and the results were consistent with those obtained by BSR-Seq. Conclusion Our research provides valuable insights into the mechanism related to cold resistance in Actinidia and identified potential genes that are important for cold resistance in kiwifruit.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
Yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Sensitive Genotype ◽  
Tolerant Genotype

Abstract Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29 128 and 30 131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis（WGCNA）revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

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

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 494 ◽  
Author(s):  
Xiaokang Zhuo ◽  
Tangchun Zheng ◽  
Zhiyong Zhang ◽  
Yichi Zhang ◽  
Liangbao Jiang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Freezing Stress ◽  
Prunus Mume ◽  
Flower Bud ◽  
Freezing Resistance

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.

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