Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting
Response regulator (RR) is the core component of cytokinin (CK) signaling, and it regulates the expression of numerous downstream CK-responsive genes. However, the knowledge regarding the pecan <i>RR</i> (<i>CiRR</i>) gene family is still limited. In this study, we first moni...
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MDPI AG
2024-03-01
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| Online Access: | https://www.mdpi.com/1999-4907/15/3/473 |
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| author | Yan Zhang Zhanhui Jia Guoming Wang Mengxin Hou Min Zhai Longjiao Hu Jiping Xuan Zhenghai Mo |
| author_facet | Yan Zhang Zhanhui Jia Guoming Wang Mengxin Hou Min Zhai Longjiao Hu Jiping Xuan Zhenghai Mo |
| author_sort | Yan Zhang |
| collection | DOAJ |
| description | Response regulator (RR) is the core component of cytokinin (CK) signaling, and it regulates the expression of numerous downstream CK-responsive genes. However, the knowledge regarding the pecan <i>RR</i> (<i>CiRR</i>) gene family is still limited. In this study, we first monitored trans-zeatin riboside (tZR) content in the graft union 0, 7, 14, and 32 days after grafting and then conducted genome-wide analysis and expression profiling of the <i>CiRR</i> gene family using an available genome sequence and RNA-seq dataset, aiming to better understand the roles of CK during pecan grafting. The dynamic contents of tZR showed an increased trend during the specific period for both the scion and rootstock. There were 20 <i>CiRRs</i> in the pecan genome, including 12 type A <i>CiRRs</i>, 5 type B members, and 3 type C genes. All members contained a receiver domain and type B <i>CiRRs</i> possessed an additional Myb-like DNA-binding domain. Promoter analysis showed that the <i>CiRR</i> gene family contained <i>cis</i>-elements associated with growth and development, hormones, and stress. A total of 10 genes, including <i>CiRR18/9/4a/14a/12c/5/12b/14b/2b/2a</i>, were abundantly expressed in the samples of different tissues, drought stress, and kernel development. There were 12 genes (<i>CiRR5/18/4a/12b/2b/12c/14b/2a/14a/4b/9/11a</i>) showing active expressions during grafting, and weighted gene co-expression network analysis (WGCNA) grouped them into six modules. Among them, <i>CiRR14a</i> and <i>CiRR12b</i> were the hub genes for the turquoise and brown modules, respectively. Functional annotation indicated that the turquoise module was associated with gene transcription and translation, while the brown module was related to cell proliferation. Our results suggest that the <i>CiRR</i> gene family central to CK signaling is probably involved in callus formation during pecan grafting. |
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| issn | 1999-4907 |
| language | English |
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| spelling | doaj.art-35a1c0cfe0af439b9b8167b1b9bf689a2024-03-27T13:41:42ZengMDPI AGForests1999-49072024-03-0115347310.3390/f15030473Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during GraftingYan Zhang0Zhanhui Jia1Guoming Wang2Mengxin Hou3Min Zhai4Longjiao Hu5Jiping Xuan6Zhenghai Mo7Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaResponse regulator (RR) is the core component of cytokinin (CK) signaling, and it regulates the expression of numerous downstream CK-responsive genes. However, the knowledge regarding the pecan <i>RR</i> (<i>CiRR</i>) gene family is still limited. In this study, we first monitored trans-zeatin riboside (tZR) content in the graft union 0, 7, 14, and 32 days after grafting and then conducted genome-wide analysis and expression profiling of the <i>CiRR</i> gene family using an available genome sequence and RNA-seq dataset, aiming to better understand the roles of CK during pecan grafting. The dynamic contents of tZR showed an increased trend during the specific period for both the scion and rootstock. There were 20 <i>CiRRs</i> in the pecan genome, including 12 type A <i>CiRRs</i>, 5 type B members, and 3 type C genes. All members contained a receiver domain and type B <i>CiRRs</i> possessed an additional Myb-like DNA-binding domain. Promoter analysis showed that the <i>CiRR</i> gene family contained <i>cis</i>-elements associated with growth and development, hormones, and stress. A total of 10 genes, including <i>CiRR18/9/4a/14a/12c/5/12b/14b/2b/2a</i>, were abundantly expressed in the samples of different tissues, drought stress, and kernel development. There were 12 genes (<i>CiRR5/18/4a/12b/2b/12c/14b/2a/14a/4b/9/11a</i>) showing active expressions during grafting, and weighted gene co-expression network analysis (WGCNA) grouped them into six modules. Among them, <i>CiRR14a</i> and <i>CiRR12b</i> were the hub genes for the turquoise and brown modules, respectively. Functional annotation indicated that the turquoise module was associated with gene transcription and translation, while the brown module was related to cell proliferation. Our results suggest that the <i>CiRR</i> gene family central to CK signaling is probably involved in callus formation during pecan grafting.https://www.mdpi.com/1999-4907/15/3/473pecancytokinin signalinggene family identificationresponse regulatorweighted gene co-expression network analysisgrafting |
| spellingShingle | Yan Zhang Zhanhui Jia Guoming Wang Mengxin Hou Min Zhai Longjiao Hu Jiping Xuan Zhenghai Mo Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting Forests pecan cytokinin signaling gene family identification response regulator weighted gene co-expression network analysis grafting |
| title | Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting |
| title_full | Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting |
| title_fullStr | Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting |
| title_full_unstemmed | Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting |
| title_short | Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting |
| title_sort | genome wide identification and expression profiling of the response regulator rr gene family in pecan reveals its possible association with callus formation during grafting |
| topic | pecan cytokinin signaling gene family identification response regulator weighted gene co-expression network analysis grafting |
| url | https://www.mdpi.com/1999-4907/15/3/473 |
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