Analysis of genetic diversity of Cucurbita moschata (D.) germplasm accessions from Mesoamerica revealed by PCR SSCP and chloroplast sequence data

The aim of this research was the genetic characterization of 218 accessions of Cucurbita moschata Duchesne, a squash, and its relationship with morphological characteristics of agronomic interest, which are part of the international collection conserved at Tropical Agricultural Research and Higher Education Center (CATIE), Costa Rica. The majority of the accessions came from Mexico and Central America; single genotypes from Curaζao, Colombia, Peru and the Russian Federation were also included. The polymerase chain reaction (PCR) and single strand conformation polymorphism analysis (SSCP) were used for the analysis of the regions amplified with ITS1–ITS2 nuclear primers and tRNL–F chloroplast primers. Haplotypes were constructed according to band patterns in SSCP gels. Twenty-five haplotypes were found using the ITS1–ITS2 markers, and 24 haplotypes were found with the tRNL–F markers. Unique haplotypes were found with both markers. Two individuals of each tRNL–F haplotype were sequenced. The results indicated a high level of genetic diversity in CATIE squash collection. Using ITS1–ITS2 primers, it was found that the number of haplotypes was independent of the geographical source of the accession, and haplotypes were distributed randomly throughout the study area. Mexico had the highest values of total heterozygosity (HE), genetic diversity (H) and Shannon index (I) while Panama showed the lowest values. Sequences obtained from tRNL–F intergenic marker showed the highest diversity index values were present in the group of additional sequences and Mexico, and lower values were observed for Nicaragua, Guatemala and Panama. PCoA based on morphological data showed three groups and by ANOSIM (R) all group differences were significant. Results obtained in this study suggest that high diversity is a characteristic of C. moschata from Mesoamerica.

► DNA molecular markers SSCP ITS region and tRNL–F intergenic chloroplast region agree in clustering different squash accessions.
► tRNL–F DNA sequences identify 29 haplotypes.
► Morphological and molecular data were compared.
► Mesoamerican Cucurbita moschata germplasm shows great genetic diversity.