Genome-Wide Identification and Expression Analysis of Response Regulators Family Genes in Chinese Hickory (Carya cathayensis) Suggests Their Potential Roles during Grafting

Tao, Shenchen; Zhao, Lu; Mei, Jiaqi; Abbas, Farhat; Xie, Xiaoting; Yang, Ying; Huang, Qiaoyu; Wang, Jiayan; Yuan, Huwei; Sharma, Anket; He, Yi; Zheng, Bingsong; Wang, Xiaofei

doi:10.1007/s00344-022-10898-6

Cited by 4 publications

(6 citation statements)

References 76 publications

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“…For the RR gene family, a total of 20 members were detected in pecan. This number was less than that of Rhododendron delavayi (33) [38], Malus domestica (34) [39], and Citrus clementina (29) [40] and closely equivalent to the size in Fragaria vesca (18) [41], Jatropha curcas (14) [42], and hickory (17) [18]. The RR gene family has been reported to be expanded greatly by duplication events [43].…”

Section: Discussionmentioning

confidence: 90%

“…HK binds to cytokinin free bases, and this induces their auto-phosphorylation; HP senses the phosphoryl group from HK and transfers it to RR; phosphorylated RR regulates the transcriptional activation of downstream cytokinin-responsive genes, among which, many are transcription factors [15]. Given its pivotal role in cytokinin signaling, the RR gene family has been systematically explored in different kinds of plants, such as Arabidopsis thaliana [16], Populus trichocarpa [17], and hickory (Carya cathayensis) [18].…”

Section: Introductionmentioning

confidence: 99%

“…The bioinformatics, structural, and genetic analyses for the model plant of Arabidopsis have provided relatively detailed information regarding the RR gene family. According to their sequence and domain structure, the 24 Arabidopsis RR members (ARRs) can be divided into three types: type A (10 genes: ARR3-9, 15-17), type B (12 genes: ARR1-2, 10-14, [18][19][20][21]23), and type C (2 genes: ARR22, 24) [19,20]. Type A RRs consist of a receiver domain and a short variable extension at the C-terminus, and these members are probably the primary targets for cytokinin [19].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting

Zhang,

Jia,

Wang

et al. 2024

Forests

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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 RR (CiRR) 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 CiRR 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 CiRRs in the pecan genome, including 12 type A CiRRs, 5 type B members, and 3 type C genes. All members contained a receiver domain and type B CiRRs possessed an additional Myb-like DNA-binding domain. Promoter analysis showed that the CiRR gene family contained cis-elements associated with growth and development, hormones, and stress. A total of 10 genes, including CiRR18/9/4a/14a/12c/5/12b/14b/2b/2a, were abundantly expressed in the samples of different tissues, drought stress, and kernel development. There were 12 genes (CiRR5/18/4a/12b/2b/12c/14b/2a/14a/4b/9/11a) showing active expressions during grafting, and weighted gene co-expression network analysis (WGCNA) grouped them into six modules. Among them, CiRR14a and CiRR12b 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 CiRR gene family central to CK signaling is probably involved in callus formation during pecan grafting.

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Section: Discussionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting

Zhang,

Jia,

Wang

et al. 2024

Forests

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“…Phytohormones, being involved in various signal transduction, exert meaningful roles in plant growth and development. Previous reportes indicated that tomato B-type SlARR genes and CcRR genes exhibited different expressions patterns in response to different phytohormones ( Wang et al., 2020 ; Tao et al., 2023 ). In addition, BuARRs in B. napus were found to respond to ABA treatment ( Jiang et al., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…GuARR2 and GuARR12 were markedly induced by ABA and MeJA treatment and GuARR1 was up-regulated after MeJA treatment for 6 h. It was reported that the SlARR-B1/2/12 in tomato reached the highest expression after treating with MeJA for 6 h ( Wang et al., 2020 ). CcRR1/2/12a were up-regulated upon MeJA treatment and CcRR2 was induced by ABA ( Tao et al., 2023 ). These analyses indicated the essential function of these GuARRs in licorice phytohormone responses.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice

Shi,

Ding,

Shen

et al. 2024

Front. Plant Sci.

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IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.

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Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR

Hui,

Wu,

Zheng

et al. 2024

Plant Physiology and Biochemistry

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Genome-Wide Identification and Expression Analysis of Response Regulators Family Genes in Chinese Hickory (Carya cathayensis) Suggests Their Potential Roles during Grafting

Cited by 4 publications

References 76 publications

Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting

Genome-Wide Identification and Expression Profiling of the Response Regulator (RR) Gene Family in Pecan Reveals Its Possible Association with Callus Formation during Grafting

Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice

Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR

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