Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Bao, Fei; Ding, Anqi; Cheng, Tangren; Wang, Jia; Zhang, Qixiang

doi:10.3390/genes10110911

Cited by 31 publications

(31 citation statements)

References 42 publications

(62 reference statements)

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“…The rate of gene duplication in this study was lower than in other plants, suggesting gene duplication was the secondary formation in PmbHLH gene expansion or PmbHLHs, and that loss-functions or redundancies may be lost during evolution. This conclusion was similar to the PmWRKY genes family (Bao et al, 2019).…”

Section: Discussionsupporting

confidence: 84%

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Ding

et al. 2021

Front. Genet.

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Prunus mume is an illustrious ornamental woody plant with colorful flowers, delicate fragrances, and graceful tree forms. Low temperature limits its geographical distribution. The basic helix-loop-helix (bHLH) proteins exist in most eukaryotes as a transcription factor superfamily, which play a crucial role in metabolism, physiology, development, and response to various stresses of higher organisms. However, the characteristics of the bHLH gene family and low-temperature response remain unknown in P. mume. In the present study, we distinguished 95 PmbHLH genes in the P. mume whole-genome and analyzed their features. PmbHLHs were divided into 23 subfamilies and one orphan by phylogenetic analysis. Similar gene structures and conserved motifs appeared in the same subfamily. These genes were situated in eight chromosomes and scaffolds. Gene duplication events performed a close relationship to P. mume, P. persica, and P. avium. Tandem duplications probably promoted the expansion of PmbHLHs. According to predicted binding activities, the PmbHLHs were defined as the Non-DNA-binding proteins and DNA-binding proteins. Furthermore, PmbHLHs exhibited tissue-specific and low-temperature induced expression patterns. By analyzing transcriptome data, 10 PmbHLHs which are responsive to low-temperature stress were selected. The qRT-PCR results showed that the ten PmbHLH genes could respond to low-temperature stress at different degrees. There were differences in multiple variations among different varieties. This study provides a basis to research the evolution and low-temperature tolerance of PmbHLHs, and might enhance breeding programs of P. mume by improving low-temperature tolerance.

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Section: Discussionsupporting

confidence: 84%

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Ding

et al. 2021

Front. Genet.

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“…Based on our study and similar work in other croppathogen systems, we predict that these GbCNL genes in cotton may provide resistance to various pathogens, including V. dahliae. Transcriptome analysis has also been used to identify candidate genes involved in disease resistance of several species, including G. barbadense Bao et al, 2019). Our transcriptome analysis showed that ten GbCNL genes, including six GbCNLs from two largest clusters (GC11 and GC12), are significantly upregulated after V. dahliae inoculation, supported by RT-qPCR analysis of multiple candidate genes.…”

Section: Discussionmentioning

confidence: 61%

“…Transcriptome analysis has also been used to identify candidate genes involved in disease resistance of several species, including G. barbadense ( Yang and Wang, 2016 ; Bao et al, 2019 ). Our transcriptome analysis showed that ten GbCNL genes, including six GbCNL s from two largest clusters (GC11 and GC12), are significantly upregulated after V. dahliae inoculation, supported by RT-qPCR analysis of multiple candidate genes.…”

Section: Discussionmentioning

confidence: 99%

Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species

Zhang

Jiang

et al. 2021

Front. Plant Sci.

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Verticillium wilt (VW) is a destructive disease in cotton caused by Verticillium dahliae and has a significant impact on yield and quality. In the absence of safe and effective chemical control, VW is difficult to manage. Thus, at present, developing resistant varieties is the most economical and effective method of controlling Verticillium wilt of cotton. The CC-NBS-LRR (CNL) gene family is an important class of plant genes involved in disease resistance. This study identified 141 GbCNLs in Gossypium barbadense genome, with 37.5% (53 genes) GbCNLs enriched in 12 gene clusters (GC01–GC12) based on gene distribution in the chromosomes. Especially, seven GbCNLs from two largest clusters (GC11 and GC12) were significantly upregulated in the resistant cultivar (Hai No. 7124) and the susceptible (Giza No. 57). Virus-induced gene silencing of GbCNL130 in G. barbadense, one typical gene in the gene cluster 12 (GC12), significantly altered the response to VW, compromising plant resistance to V. dahliae. In contrast, GbCNL130 overexpression significantly increased the resistance to VW in the wild-type Arabidopsis thaliana. Based on our research findings presented here, we conclude that GbCNL130 promotes resistance to VW by activating the salicylic acid (SA)-dependent defense response pathway resulting in strong accumulation of reactive oxygen species and upregulation of pathogenesis-related (PR) genes. In conclusion, our study resulted in the discovery of a new CNL resistance gene in cotton, GbCNL130, that confers resistance to VW across different hosts.

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“…Interestingly, MYB and TCP TFs were found to express more and earlier in the cold-sensitive sugarcane varieties compared to the cold-tolerant varieties [ 32 ]. WRKY TFs were significantly changed in multiple tissues and identified to regulate cold resistance in Prunus mume [ 33 ]. In the present study, we observed that 4 TF subtypes (e.g., HSF domain class, WRKY, ethylene-responsive, and TCP4) were regulated by 5 miRNAs (Supplementary Table S4 ), including miR1886, miR2084, miR6135, miR8036, and gma-miR1520o-3p.…”

Section: Discussionmentioning

confidence: 99%

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress

Wan

Song

et al. 2021

BioMed Research International

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Taxillus chinensis (DC.) Danser, a parasitic plant that belongs to the Loranthaceae family, has a long history of being used in the Chinese medicine. We observed that the loranthus seeds were sensitive to temperature and could lose viability below 0°C quickly. Thus, we performed small RNA sequencing to study the microRNA (miRNA) regulation in the loranthus seeds under cold stress. In total, we identified 600 miRNAs, for the first time, in the loranthus seeds under cold stress. Then, we detected 224, 229, and 223 miRNAs ( TPM > 1 ) in A0 (control), A1 (cold treatment for 12 h at 0°C), and A2 (cold treatment for 36 h at 0°C), respectively. We next identified 103 differentially expressed miRNAs (DEmiRs) in the loranthus seeds in response to cold. Notably, miR408 was upregulated during the cold treatment, which can regulate genes encoding phytocyanin family proteins and phytophenol oxidases. Some DEmiRs were specific to A1 and may function in early response to cold, such as gma-miR393b-3p, miR946, ath-miR779.2-3p, miR398, and miR9662. It is interesting that ICE3, IAA13, and multiple transcription factors (e.g., WRKY and CRF4 and TCP4) regulated by the DEmiRs have been reported to respond cold in other plants. We further identified 4, 3, and 4 DEmiRs involved in the pathways “responding to cold,” “responding to abiotic stimulus,” and “seed development/germination,” respectively. qRT-PCR was used to confirm the expression changes of DEmiRs and their targets in the loranthus seeds during the cold treatment. This is the first time to study cold-responsive miRNAs in loranthus, and our findings provide a valuable resource for future studies.

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Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Cited by 31 publications

References 42 publications

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Genome-Wide Identification and Low-Temperature Expression Analysis of bHLH Genes in Prunus mume

Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress

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