Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton

Xu, Jingying; Xu, Xiaoyang; Tian, Lei; Wang, Guilin; Zhang, Xueying; Wang, Xinyu; Guo, Wenshan

doi:10.1038/srep29022

Cited by 46 publications

(48 citation statements)

References 67 publications

(119 reference statements)

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“…Gene structure analysis showed that Gh4CL genes of the same class share a similar intron-exon structure (Fig. 2b), similar to the observations made in other gene families [40,41].…”

Section: Discussionsupporting

confidence: 85%

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Sun

Xiong

Zhang

et al. 2019

Preprint

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Background The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses have been studied in plants, however, limite is known about the upland cotton 4CL genes and their roles in response to drought stress. ResultsIn this study, we performed genome-wide identification of the 4CL genes in G. hirsutum and investigated the expression profiles of the identified genes in various cotton tissues and in response to stress conditions with an aim to identify 4CL gene(s) associated with drought tolerance. We identified 34 putative 4CL genes in G. hirsutum that were clustered into three classes. Genes of the same class usually share a similar gene structure and motif composition. Many cis -elements related to stress and phytohormone responses were found in the promoters of the Gh4CL genes. Of the 34 Gh4CL genes, 26 were induced by at least one abiotic stress and 10 were up-regulated under the PEG simulated drought stress conditions, including Gh4CL7 . Virus-induced gene silencing (VIGS) in cotton and overexpression (OE) in Arabidopsis thaliana were applied to investigate the biological function of Gh4CL7 in drought tolerance. The Gh4CL7 -silencing cotton plants showed more sensitive to drought stress, probably due to decreased relative water content (RWC), chlorophyll content and antioxidative enzyme activity, increased stomatal aperture, and the contents of malondialdehyde (MDA) and hydrogen peroxide (H 2 O 2 ). Arabidopsis lines overexpressing Gh4CL7 , however, were more tolerant to drought treatment, which was associated with improved antioxidative enzyme activity, reduced accumulation of MDA and H 2 O 2 and up-regulated stress-related genes under the drought stress conditions. In addition, compared to their respective controls, the Gh4CL7 -silencing cotton plants and the Gh4CL7-overexpressing Arabidopsis lines had a lower and higher lignin content, respectively. Taken together, these results demonstrated that Gh4CL7 could positively respond to drought stress and therefore might be a candidate gene for improvement of drought tolerance in cotton.Conclusion We comprehensively identified 4CL family genes in upland cotton and provide valuable information on the evolutionary relationship. Gh4CL7 gene is involved in lignin biosynthesis and play a positively role in reponsing drought stress.

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“…Gene structure analysis showed that Gh4CL genes of the same class share a similar intron-exon structure (Fig. 2b), similar to the observations made in other gene families [40,41].…”

Section: Discussionsupporting

confidence: 85%

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Sun

Xiong

Zhang

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…Gene structure analysis showed that Gh4CL genes of the same class share a similar intron-exon structure (Fig. 2b), similar to the observations made in other gene families [30][31][32].…”

Section: Discussionsupporting

confidence: 84%

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Sun

Xiong

Zhang

et al. 2020

Preprint

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Background: The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses has been studied in plants, however, limited is known about the 4CL genes in cotton (G. hirsutum L.) and their roles in response to drought stress.Results: We performed genome-wide identification of the 4CL genes in G. hirsutum and investigated the expression profiles of the identified genes in various cotton tissues and in response to stress conditions with an aim to identify 4CL gene(s) associated with drought tolerance. We identified 34 putative 4CL genes in G. hirsutum that were clustered into three classes. Genes of the same class usually share a similar gene structure and motif composition. Many cis-elements related to stress and phytohormone responses were found in the promoters of the Gh4CL genes. Of the 34 Gh4CL genes, 26 were induced by at least one abiotic stress and 10 (including Gh4CL7) were up-regulated under the polyethylene glycol (PEG) simulated drought stress conditions. Virus-induced gene silencing (VIGS) in cotton and overexpression (OE) in Arabidopsis thaliana were applied to investigate the biological function of Gh4CL7 in drought tolerance. The Gh4CL7-silencing cotton plants showed more sensitive to drought stress, probably due to decreased relative water content (RWC), chlorophyll content and antioxidative enzyme activity, increased stomatal aperture, and the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Arabidopsis lines overexpressing Gh4CL7, however, were more tolerant to drought treatment, which was associated with improved antioxidative enzyme activity, reduced accumulation of MDA and H2O2 and up-regulated stress-related genes under the drought stress conditions. In addition, compared to their respective controls, the Gh4CL7-silencing cotton plants and the Gh4CL7-overexpressing Arabidopsis lines had a ~20% reduction and a ~10% increase in lignin content, respectively. The expression levels of genes related to lignin biosynthesis, including PAL, CCoAOMT, COMT, CCR and CAD, were lower in Gh4CL7-silencing plants than in controls. Taken together, these results demonstrated that Gh4CL7 could positively respond to drought stress and therefore might be a candidate gene for improvement of drought tolerance in cotton.Conclusion: We characterized the 4CL gene family in upland cotton and revealed a role of Gh4CL7 in lignin biosynthesis and drought tolerance.

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“…Analysis method of data model expression as follows: if the value of log 2 FPKM is more than 1, we consider it to be expressed and if the value of log 2 FPKM is less than or equal to 1, we consider it not to be expressed (Xu et al 2016a, b). …”

Section: Methodsmentioning

confidence: 99%

Genome-wide characterization of the Rab gene family in Gossypium by comparative analysis

Guo

2017

Bot Stud

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Background Rab protein family is the largest subfamily of small G protein family. As one of the most important families in plant, Rab family plays an important role in the process of plant growth and development. So far, the identification of 57 members of the Rab family in Arabidopsis has been completed. In cotton, the relevant family has not been reported.ResultsHere, we identified 87, 169, 136, 80 Rabs in the four sequenced cotton species, G. raimondii (D5), G. hirsutum acc. TM-1 (AD1), G. barbadense acc. 3-79 (AD2) and G. arboreum (A2), respectively. Biological information analysis showed that the number of amino acid is 200–300 aa among Rab family members in G. raimondii and the protein molecular weight is between 20 and 30 kDa, which is consistent with the characterization of the Rab protein itself. 87 GrRabs in G. raimondii are divided into eight groups. In each group, intron numbers and subcellular localization of Rab protein are basically the same. We mapped the distribution of GrRab genes on 13 chromosomes of G. raimondii except two genes. Among the 87 GrRabs in G. raimondii, we identified 60 pairs of GrRabs formed in whole genome duplication. Among all the gene pairs, the Ka/Ks values were less than 1. This indicates that it is the results of the purification selection and will help maintain the conservation of gene in structure and function. Further, 4 of the 87 GrRabs showed tandem duplication. They were GrRabA2a vs GrRabD1a and GrRabA2h vs GrRabD1b respectively. Expression patterns analysis of 169 GhRabs in G. hirsutum acc. TM-1 indicates that most Rab family members play a certain role in different tissues/organs and different growth stages of cotton, implying their potential function in the polar growth of pollen tube, root hair and fiber cell, as well as improving stress and disease tolerance.ConclusionThe systematic investigation of Rab genes in cotton will lay a foundation for understanding the functional roles of different Rab members in the polar growth and stress tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-017-0181-y) contains supplementary material, which is available to authorized users.

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Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton

Cited by 46 publications

References 67 publications

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance

Genome-wide characterization of the Rab gene family in Gossypium by comparative analysis

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