Nucleotide sequence diversities of Chitinase and PR1 genes from Theobroma cacao cv. MCC 02 and Sulawesi 1

Abstract. Setiowati A, Ardie SW, Santoso TJ, Sudarsono. 2024. Nucleotide sequence diversities of Chitinase and PR1 genes from Theobroma cacao cv. MCC 02 and Sulawesi 1. Biodiversitas 25: 1-13. Cocoa (Theobroma cacao) faces vascular streak dieback (VSD) disease caused by Ceratobasidium theobromae, so disease control strategies are necessary, such as developing disease-resistant cocoa cultivars. Characterization of Chitinase (Chi) and Pathogenesis Related Protein 1 (PR1) could be the starting point for such purposes. This research aimed to characterize Chi-like and PR1-like genes from cocoa cv. MCC 02 (VSD resistant) and Sulawesi 1 (SUL 1, susceptible). The Chi-like and PR1-like amplicons were generated from cocoa cultivars, and sequencing of the amplicons generated 858 bp (Chi-like) and 569 bp (PR1-like). The multiple sequence alignment (MSA) of seven Chi-like fragments from two cocoa clones identifies four non-synonymous and two synonymous SNPs. The MSA of seven PR1-like fragments from two cocoa clones identifies three non-synonymous and two synonymous SNPs in the PR1-like coding and two SNPs in the 3’-non-coding regions. Phylogenetic tree construction among four TcChi-like accessions and 36 accessions from the NCBI Database indicates that all cocoa Chi-like genes are clustered in Clade II, separated from Chi-like of other species that belong to Clade I or Clade III. Phylogenetic tree construction among 24 accessions of PR1-like sequences from various plant species indicates that the cocoa PR1-like gene sequences are more closely related to Herrania umbratica and Theobroma grandiflorum.