Phylogenetic Analysis and Molecular Diversity of <i>Capsicum</i> Based on rDNA-ITS Region

• Main Authors: Kumpei Shiragaki, Shuji Yokoi, Takahiro Tezuka
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Horticulturae
• Subjects: <i>Capsicum</i>; rDNA-ITS; phylogeny; genetic diversity; morphological traits
• Online Access: https://www.mdpi.com/2311-7524/6/4/87

The genus <i>Capsicum</i> is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in <i>Capsicum</i>. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 <i>Capsicum</i> accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in <i>Capsicum</i> accessions. Specific morphological characteristics were found in <i>C. annuum</i>, <i>C. baccatum,</i> and <i>C.</i><i>pubescens</i>. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding <i>C. annuum</i>, suggesting that incomplete concerted evolution occurred in rDNA-ITS of <i>Capsicum</i>. The genetic diversity was evaluated using nucleotide polymorphism and diversity. <i>C. annuum</i> had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for <i>C. annuum</i>, <i>C. baccatum</i>, and <i>C. pubescens</i>. The <i>C. chinense</i> clade existed in the <i>C. frutescens</i> clade, implying that it was a cultivated variant of <i>C. frutescens</i>. <i>C. chacoense</i> likely belonged to the <i>C. baccatum</i> complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated <i>Capsicum</i> species.