Molecular phylogeny and DNA barcode regions efficacy for identification of the cultivar of Capsicum annuum L. in Thailand

Abstract

Capsicum annuum L. is an important hot chili species for commercial vegetable crop. This species has various cultivars that are cultivated in several localities in Thailand. The genetic diversity of C. annuum group in Thailand is poorly known. The aim of this study is to test the efficacy of DNA barcodes to identify the C. annuum group and to understand the genetic relationships among cultivars within this species. Seventeen samples were represented from 12 cultivars for molecular analysis. All samples were successfully amplified and generated DNA sequences from the internal transcribed spacer (ITS), the large subunit of ribulose bisphosphate carboxylase (rbcL) and Maturase K (matK) regions. Molecular phylogeny was analyzed based on the maximum likelihood (ML) and Bayesian inference (BI) methods with each of single DNA locus. The results showed that two DNA loci (rbcL and matK) did not distinguish between species level, while ITS region showed high genetic diversity within this species. The phylogenetic tree based on ITS region can delimit the C. annuum from other species (C. baccatum, C. chinense, C. frutescens and C. pubescens). Also, the phylogeny divided C. annuum species into three groups and revealed to these taxa as species complex. The morphological characters did not relate to molecular evidence, which shared between cultivars. In addition, C. annuum (Bang Chang) group demonstrated more genetic diversity than previously estimated, which separated into five subgroups with strong molecular data support. This study suggests that DNA barcode via ITS region is suitable for C. annuum identification into the species and cultivar level. However, further study needs to investigate the phylogenetic analysis from other DNA regions and more phenotypic characters such as chemotaxonomy to clarify the relationship of species complex within C. annuum species.