Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

Abstract

Several attempts in recent decades have been devoted to investigating the genetic and phenotypic diversity harbored by the genus Capsicum. Particular efforts have been directed to old varieties or landraces. However, the genus is still under‐researched, and further investigations that accurately define the relationships among species and identify those geographic regions with greater variability are required. In the present work, 107 Capsicum landraces from Ecuador, Peru, and Bolivia were evaluated with a set of 16 microsatellite markers. In total, 187 alleles were detected in the Andean collection, and 49.7% of those were recorded as unique alleles. Indices of genetic diversity were high and very similar in the three evaluated countries, although the domesticated Capsicum species carrying the highest diversity varied among them: C. frutescens (L.) in Ecuador, C. chinense (Jacq.) in Peru, and C. annuum (L.) in Bolivia. Comparison of Andean accessions with others coming from diverse origins revealed intraspecific genetic differentiation in C. annuum, C. chinense, C. frutescens, C. baccatum (L.), and C. pubescens (Ruiz et Pav.), following a geographic pattern. Similarly, assessment of the genetic diversity currently maintained in Ecuadorian Capsicum species brought to light a dramatic decrease in the genetic variability of cultivated peppers when compared with those harbored by old landraces. Analysis of genetic relationships among Capsicum species was in agreement with previous taxonomic classifications: C. annuum, C. chinense, and C. frutescens were clustered as independent and highly related species; C. cardenasii (Heiser et Smith) and C. eximium (Hunz.) were indistinguishable as a single species; and C. chacoense (Hunz.) was placed between C. pubescens and C. annuum complexes.

Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

“…The phylogenetic analysis using rDNA-ITS almost agreed with previous studies using molecular markers [15,16,[18][19][20] and DNA barcoding [8] with sequences except rDNA-ITS in terms of the formation of species clades and phylogenetic relations, although rDNA-ITS could not differentiate between C. chinense and C. frutescens. The analysis using molecular markers or DNA barcoding except rDNA-ITS requires many Capsicum species for species identification, and thus takes a lot of effort.…”

“…In recent years, phylogenetic studies have been conducted to elucidate the relationship between Capsicum species based on molecular markers, including isozyme [16], random amplified polymorphic DNA [15], amplified fragment length polymorphism [17], simple sequence repeat [18,19], and single nucleotide polymorphism [20]. These studies analyzed the relationships between cultivated species, and indicated the species-specific clades formed; the species belonging to the C. annuum complex were genetically close to each other in phylogenetic trees.…”

Phytochemical Assessment of Native Ecuadorian Peppers (Capsicum spp.) and Correlation Analysis to Fruit Phenomics

“…C. frutescens accessions constituted the most homogenous group, except for PI224427. That accession was misclassified in a previous work that genetically placed it as more closely related to C. chinense [11]. Current data, based on fruit morphology and biochemical composition, confirmed that accession PI224427 should be ascribed to the C. chinense group.…”

“…For the sake of clarity, the accession PI585278 from the Galapagos Islands was considered within the Coastal region. This collection was previously characterized for genetic diversity and molecular markers linked to disease resistance and pungency-related traits [11,67]. The forty-eight landraces were cultivated during 2017 in an experimental field at the Technical University of Machala (Machala, El Oro, Ecuador) (03 • 16 S, 79 • 54 W).…”

“…Collections of native landraces have been widely investigated at the DNA level with molecular markers [ 10 , 11 , 12 ]. Nonetheless, highly precise phenotyping based on objective scales is much more limited.…”