Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools

A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant gen...

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Bibliographic Details
Published in:Plants (Basel) 2022-08, Vol.11 (16), p.2151
Main Authors: Carrasco, Basilio, Arévalo, Bárbara, Perez-Diaz, Ricardo, Rodríguez-Alvarez, Yohaily, Gebauer, Marlene, Maldonado, Jonathan E., García-Gonzáles, Rolando, Chong-Pérez, Borys, Pico-Mendoza, José, Meisel, Lee A., Ming, Ray, Silva, Herman
Format: Article
Language:English
Subjects:
Animal behavior
Biological diversity
Breeding
Comparative analysis
Differentiation
DNA sequencing
Domestication
Flowers & plants
Fruits
GBS
Genes
Genetic aspects
Genetic diversity
Genetic drift
Genetic research
Genomes
Genomic analysis
Genomics
Genotyping
Identification and classification
National parks
Natural selection
Nematodes
Nucleotide sequencing
Orchards
Papaya
Papayas
Physiological aspects
Plant breeding
Population genetics
Seeds
Single nucleotide polymorphisms
Single-nucleotide polymorphism
SNPs/INDELs
Vasconcellea
Vasconcellea chilensis
Vasconcellea pubescens
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Summary:A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants11162151