**Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (***Capsicum annuum* **L.) and Transcriptional Regulation to** *Phytophthora capsici***, Abiotic Stresses and Hormonal Applications**

#### **Muhammad Ali <sup>1</sup> ID , De-Xu Luo <sup>2</sup> , Abid Khan <sup>1</sup> , Saeed ul Haq <sup>1</sup> , Wen-Xian Gai <sup>1</sup> , Huai-Xia Zhang <sup>1</sup> , Guo-Xin Cheng <sup>1</sup> , Izhar Muhammad <sup>3</sup> and Zhen-Hui Gong 1,\***


Received: 29 June 2018; Accepted: 26 July 2018; Published: 29 July 2018

**Abstract:** Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (*Capsicum annuum* L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. *Phytophthora capsici* post inoculation, most of the CaChi (*CaChiI3*, *CaChiIII1*, *CaChiIII2*, *CaChiIII4*, *CaChiIII6*, *CaChiIII7*, *CaChiIV1*, *CaChiVI1* and *CaChiVI2*) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the *CaChiIII2*, *CaChiIII7*, *CaChiVI1* and *CaChiVI2* were upregulated by abiotic stress, while *CaChiI1*, *CaChiIII7*, *CaChiIV1* and *CaChiIV2* responded to hormonal treatments. Furthermore, *CaChiIV1*-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.

**Keywords:** chitin-binding protein; chitinase; pepper; expression; biotic stress; abiotic stress
