Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses
Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried o...
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BMC
2019-12-01
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| Series: | BMC Genetics |
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| Online Access: | https://doi.org/10.1186/s12863-019-0789-x |
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| author | Yuxia Li Lei Zhang Panpan Zhu Qinghe Cao Jian Sun Zongyun Li Tao Xu |
| author_facet | Yuxia Li Lei Zhang Panpan Zhu Qinghe Cao Jian Sun Zongyun Li Tao Xu |
| author_sort | Yuxia Li |
| collection | DOAJ |
| description | Abstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato. |
| first_indexed | 2024-12-10T12:25:55Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-12-10T12:25:55Z |
| publishDate | 2019-12-01 |
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| spelling | doaj.art-697ac81249584e88a0fe9f2c7da70cd82022-12-22T01:48:58ZengBMCBMC Genetics1471-21562019-12-0120111510.1186/s12863-019-0789-xGenome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stressesYuxia Li0Lei Zhang1Panpan Zhu2Qinghe Cao3Jian Sun4Zongyun Li5Tao Xu6Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityKey lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityDepartment of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National UniversityXuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAASKey lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityKey lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityKey lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal UniversityAbstract Background WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. Results A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. Conclusions In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.https://doi.org/10.1186/s12863-019-0789-xWRKYTranscription factorSweet potatoIpomoea trifidaAbiotic stress |
| spellingShingle | Yuxia Li Lei Zhang Panpan Zhu Qinghe Cao Jian Sun Zongyun Li Tao Xu Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses BMC Genetics WRKY Transcription factor Sweet potato Ipomoea trifida Abiotic stress |
| title | Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses |
| title_full | Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses |
| title_fullStr | Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses |
| title_full_unstemmed | Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses |
| title_short | Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses |
| title_sort | genome wide identification characterisation and functional evaluation of wrky genes in the sweet potato wild ancestor ipomoea trifida h b k g don under abiotic stresses |
| topic | WRKY Transcription factor Sweet potato Ipomoea trifida Abiotic stress |
| url | https://doi.org/10.1186/s12863-019-0789-x |
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