Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economica...
| Main Authors: | , , , , , , |
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PeerJ Inc.
2022-07-01
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| author | Zhenfan Yu Dongdong Zhang Bin Zeng Xingyue Liu Jiahui Yang Wenwen Gao Xintong Ma |
| author_facet | Zhenfan Yu Dongdong Zhang Bin Zeng Xingyue Liu Jiahui Yang Wenwen Gao Xintong Ma |
| author_sort | Zhenfan Yu |
| collection | DOAJ |
| description | Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding. |
| first_indexed | 2024-03-09T07:11:28Z |
| format | Article |
| id | doaj.art-83f1b5f63d1644589dc4b8993895af46 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:11:28Z |
| publishDate | 2022-07-01 |
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| spelling | doaj.art-83f1b5f63d1644589dc4b8993895af462023-12-03T09:07:00ZengPeerJ Inc.PeerJ2167-83592022-07-0110e1349110.7717/peerj.13491Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)Zhenfan Yu0Dongdong Zhang1Bin Zeng2Xingyue Liu3Jiahui Yang4Wenwen Gao5Xintong Ma6College of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaCollege of Horticulture, Xinjiang Agriculture University, Urumqi, ChinaBackground WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.https://peerj.com/articles/13491.pdfAlmond (Prunus dulcis)WRKY transcription factorsGenome-wideEvolutionary analysesExpression patternsAbiotic stress |
| spellingShingle | Zhenfan Yu Dongdong Zhang Bin Zeng Xingyue Liu Jiahui Yang Wenwen Gao Xintong Ma Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) PeerJ Almond (Prunus dulcis) WRKY transcription factors Genome-wide Evolutionary analyses Expression patterns Abiotic stress |
| title | Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) |
| title_full | Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) |
| title_fullStr | Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) |
| title_full_unstemmed | Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) |
| title_short | Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis) |
| title_sort | characterization of the wrky gene family reveals its contribution to the adaptability of almond prunus dulcis |
| topic | Almond (Prunus dulcis) WRKY transcription factors Genome-wide Evolutionary analyses Expression patterns Abiotic stress |
| url | https://peerj.com/articles/13491.pdf |
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