Genome-wide identification and characterization of HD-ZIP genes in potato

Wan, Li; Dong, Jieya; Cao, Minxuan; Gao, Xianxian; Wang, Dongdong; Liu, Bailin; Chen, Qin

doi:10.1016/j.gene.2019.02.024

Cited by 54 publications

(58 citation statements)

References 76 publications

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“…However, there is little evidence about the potential function of these WRKY genes as regulator in heat stress response. We also found heat stress repressed the expression of three bZIP genes, and the potato bZIP gene family has been characterized in response to several abiotic stresses including heat [24]. Some of other TF family members, such as PHOR1, ARR, C2H2 zinc finger family and MYB showed decreased expression after heat treatment, providing the evidence that whether these TFs may function as general repressors of heat responses.…”

Section: Short and Prolonged Heat Stress Repressed Transcription Factsupporting

confidence: 55%

WITHDRAWN: Physiological and molecular changes to short and prolonged heat in highlands China potato genotype

Liu

Cao

Kong

et al. 2020

Preprint

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Background: Potato is the fourth world's most important crops. Global warming has heavily constrained potato production. Although some work has been undertaken regarding the response of potato to moderately increased temperature (25-30°C), few studies have examined the extreme high temperature above 35°C and sustaining high temperature impact on physiological, biochemical and molecular responses of potato. Methods: Potato plants were subjected to high temperature (35°C/33 °C day/night) treatments for 6 h (short) and 3 days (long), physiological and biochemical response of electrolyte leakage and photosynthetic performance were measured, transcriptome and metabolome profiles of leaves were examined. Expression profiles of 20 DEGs were verified by RT–qPCR, heat induced conserved genes were transient expressed in Nicotiana benthamiana.Results: Growth at short heat stress induced stomata open and lower membrane stability. Prolonged heat stress decreased the photosynthetic parameters and increased photosynthetic pigments. Integration of transcriptomics and metabolomics methods demonstrated that 448 heat upregulated and 918 heat downregulated genes as well as 325 and 219 compounds in the positive and negative ionization modes, respectively, that were up- or down-regulated in leaves detected in responsive to short and prolonged heat stress. Global transcripts changes were mainly induced by short heat stress, where metabolites changes were mainly activated by prolonged heat stress. General responses to heat stress in gene expression and metabolite accumulation enriched in amino acid metabolism and secondary metabolism pathway. Metabolite and transcript abundances for the up-regulation of flavone and flavonol biosynthesis under the prolonged heat stress were closely correlated. Both conserved and heat- and potato-specific stress responsive genes were identified by comparing heat and drought stress in potato as well as heat stress in potato and Arabidopsis shoots, transient expression of four heat induced genes in Nicotiana benthamiana exhibited heat tolerance to higher temperature.Conclusions: A new potato leaf transcriptomes and metabolomes revealed a widely adaptive response to high temperature by mainly generation and accumulation of heat shock proteins.

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Section: Short and Prolonged Heat Stress Repressed Transcription Factsupporting

confidence: 55%

WITHDRAWN: Physiological and molecular changes to short and prolonged heat in highlands China potato genotype

Liu

Cao

Kong

et al. 2020

Preprint

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“…StCBF6 and StCBF7 were distributed in the tuber peel, and the expression of StCBF7 was detected in the mature tubers. The plants were treated with 10 different conditions, including phytohormone treatments (6-benzylaminopurine, BAP; indole-3-acetic acid, IAA; abscisic acid, ABA; gibberellic acid, GA3); abiotic stress (heat, drought, and salinity); and biotic stress (pathogen; DL-β-amino-n-butyric acid, BABA; acibenzolar-S-methyl, BTH) [ 45 ]. Under the 10 different treatments, most genes showed downregulated expression or little change in expression.…”

Section: Resultsmentioning

confidence: 99%

“…On the basis of the data obtained from the PGSC database, we measured and analysed the expression levels of the 8 CBF/DREB1 genes at different stages of potato development and under various stresses [ 59 ]. The data related to the CBF/DREB1 genes from the PGSC database were analysed in double haploid potato material (DM) or heterozygous diploid material (RH) [ 45 ]. The change in the expression levels of the CBF/DREB1 proteins in potato under abiotic stress was different from the results of other studies on CBF/DREB1 genes [ 43 , 49 , 50 , 57 , 58 ].…”

Section: Discussionmentioning

confidence: 99%

Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum

Wan

Chen

et al. 2020

BMC Evol Biol

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Background Plants are easily affected by temperature variations, and high temperature (heat stress) and low temperature (cold stress) will lead to poor plant development and reduce crop yields. Therefore, it is very important to identify resistance genes for improving the ability of plants to resist heat stress or cold stress by using modern biotechnology. Members of the C-repeat binding factor/Dehydration responsive element-binding 1 (CBF/DREB1) protein family are related to the stress resistance of many plant species. These proteins affect the growth and development of plants and play vital roles during environmental stress (cold, heat, drought, salt, etc.). In this study, we identified CBF/DREB1 genes from 43 plant species (including algae, moss, ferns, gymnosperms, angiosperms) by using bioinformatic methods to clarify the characteristics of the CBF/DREB1 protein family members and their functions in potato under heat and cold stresses. Results In this study, we identified 292 CBF/DREB1 proteins from 43 plant species. However, no CBF/DREB1 protein was found in algae, moss, ferns, or gymnosperms; members of this protein family exist only in angiosperms. Phylogenetic analysis of all the CBF/DREB1 proteins revealed five independent groups. Among them, the genes of group I do not exist in eudicots and are found only in monocots, indicating that these genes have a special effect on monocots. The analysis of motifs, gene duplication events, and the expression data from the PGSC website revealed the gene structures, evolutionary relationships, and expression patterns of the CBF/DREB1 proteins. In addition, analysis of the transcript levels of the 8 CBF/DREB1 genes in potato (Solanum tuberosum) under low-temperature and high-temperature stresses showed that these genes were related to temperature stresses. In particular, the expression levels of StCBF3 and StCBF4 in the leaves, stems, and roots significantly increased under high-temperature conditions, which suggested that StCBF3 and StCBF4 may be closely related to heat tolerance in potato. Conclusion Overall, members of the CBF/DREB1 protein family exist only in angiosperms and plays an important role in the growth and development of plants. In addition, the CBF/DREB1 protein family is related to the heat and cold resistance of potato. Our research revealed the evolution of the CBF/DREB1 family, and is useful for studying the precise functions of the CBF/DREB1 proteins when the plants are developing and are under temperature stress.

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“…We predicted 97 RAVs (Additional le 6) which had no transmembrane domain and signal peptide (same as other transcription factors) [39] and analyzed B3 and AP2 domains in each protein. Each protein had and only had both B3 and AP2 domains, except CbRAV4 which had an extra domain: MetAP1.…”

Section: Analysis Of Ravsmentioning

confidence: 99%

“…The same class probably means similar characteristic of RAV family. Therefore, we can speculate the function of a RAV gene in any species based on the existing research results, thus providing effective ideas and directions for further research [39].…”

Section: Evolution Of Ravsmentioning

confidence: 99%

Evolutionary Significance of RAV Family in 25 Plants from Chlorophyta to Angiospermae

Wan¹,

Minghui²,

Wang³

et al. 2020

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Background: Plants are easily affected by various environmental factors such as temperature, high salinity, and drought which will cause poor plant development and reduce crop yield. Transcription factors (TFs) are related to the stress resistance found in many plant species and play vital roles in the growth and development of plants. Among them, the RAV (related to ABI3/VP1) gene family, which is a plant-specific type of transcription factor containing AP2 (APETALA2) DNA binding domain and B3 DNA binding domain, is the focus in this research.Results: There more RAV genes/proteins (RAVs) were present in Gymnospermae and Angiosperm, a few RAVs in Bryophyta and Lycophyte, and no RAV gene was predicted in Chlorophyta. RAVs could be defined as three main groups, based on our phylogenetic analysis. The members of clade I included all plant stages from Chlorophyta to Angiosperm except Monocots. Clade II only contained eudicots plant species. Clade III, as a branch consisting of monocots plant species and Marchantia polymorpha, may help us explore the evolutionary relationship of RAVs between Bryophyta and Monocots. According to our results, it is shown that RAVs first appeared in bryophytes. While the vasculature continues to develop and evolve, RAV gene family also has functional differentiation and has formed new functions due to the existence of gene replication events.Conclusions: Our findings indicate that the RAVs originated from Bryophytes, and RAVs of these plant species had obvious divisions in the evolutionary tree, which revealed the evolution of RAVs. These results have guiding significance for further research.

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Genome-wide identification and characterization of HD-ZIP genes in potato

Cited by 54 publications

References 76 publications

WITHDRAWN: Physiological and molecular changes to short and prolonged heat in highlands China potato genotype

WITHDRAWN: Physiological and molecular changes to short and prolonged heat in highlands China potato genotype

Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum

Evolutionary Significance of RAV Family in 25 Plants from Chlorophyta to Angiospermae

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