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

The response regulator (RR) genes play a crucial function in the cytokinin signaling pathway and in activating the downstream genes to respond to cytokinin in the two-component system. However, the characteristics and expression patterns of RR genes in Chinese hickory (Carya cathayensis) are still less studied. In this study, 17 CcRR genes were identified from Chinese hickory, including 8 type-A CcRRs, 8 type-B CcRRs, and 1 type-C CcRR. All type-B and some type-A CcRRs (CcRR5/9a/9b) were nucleus-localized, whereas the other type-A CcRRs (CcRR3/4/8/16/17) and type-C CcRRs (CcRR22) were nucleus- and cytomembrane-localized. All CcRRs encoded hydrophilic proteins with receptor domain. Numerous phytohormone-related cis-regulatory elements were detected on the promoter sequences of CcRRs, and qRT-PCR data verified that the majority of CcRR genes showed a noticeable responsiveness to various hormones, particularly CcRR1, CcRR3, and CcRR8. The tissue-specific expression analysis revealed that the majority of genes were expressed in all tissues, but a few were tissue-specific, such as CcRR4 in the embryo, CcRR10 in the roots, CcRR14b in the pericarps, and CcRR22 in the testae. Expression profiles of CcRRs during the critical periods of grafting success showed that two CcRRs (CcRR4 and CcRR22) were significantly down-regulated to less than 10% of the original, indicating that these genes might function as negative regulators in the grafting process. In contrast, the expression levels of some genes were up-regulated by 2–10 times at various stages of the grafting, implying that they might play a positive role in the grafting process. Results from this study will provide the basis for further understanding the mechanisms of cytokinin in regulating the grafting process of Chinese hickory.