Knowledge on the structure and distribution of genetic diversity is a key aspect to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1,765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the Neotropics and used as a food source by pre-Columbian cultures, was collected from six different countries across the American continent and amplified with nine highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops.

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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 Curaao, 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.

The diversity of 42 Xylella fastidiosa strains from Costa Rica, São Paulo, Brazil, and the United States were analyzed using the sequence of the 16S rRNA gene by variable number of tandem repeat (VNTR) fragment analysis and by restriction fragment length polymorphisms (RFLP) of a specific polymerase chain reaction (PCR)-amplification product using enzyme CfoI. Limited variability in the sequence of the 16S rRNA gene was observed and, although the separation was not absolute, most strains from Costa Rica clustered with strains from the United States and not with strains from São Paulo. The PCR-RFLP produced different patterns of DNA bands. The same pattern was shared by strains from Costa Rica, the United States, and two coffee strains from São Paulo, but a different pattern was observed in six coffee and orange strains from Brazil. In all, 32 amplification products were scored in the VNTR fragment analysis. The total variation observed among the X. fastidiosa strains had significant (P < 0.001) contributions from both geography and host origin as inferred by Nei's values of genetic diversity and WINAMOVA statistics. The strains from Costa Rica were isolated from diseased grapevines, coffee, and sweet orange and these strains grouped together and could be distinguished from strains from grapevine from the United States or from either coffee or sweet orange from São Paulo. The strains tested from Costa Rica are most likely of local origin, although the possibility that they have been introduced along with horticultural crops cannot be excluded. In either case, they are examples of independent selection of strains of X. fastidiosa affecting coffee and sweet orange. Greater genetic similarity was observed between strains from Costa Rica and the United States than with those from São Paulo.

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