Genetic Diversity of Olive ( Olea europaea L.) Cultivars Assessed by Genotyping-by-Sequencing in Southern Peru

Martín Eloy Casilla García (), Rina Alvarez Becerra, José Cotrado Cotrado, Juan Iván Casilla Rondán, Janet Libertad Huatuco Coaquira and Edgar Virgilio Bedoya Justo
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Martín Eloy Casilla García: Faculty of Agricultural Sciences, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
Rina Alvarez Becerra: Faculty of Health Sciences, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
José Cotrado Cotrado: Faculty of Agricultural Sciences, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
Juan Iván Casilla Rondán: Faculty of Agricultural Sciences, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
Janet Libertad Huatuco Coaquira: Faculty of Agricultural Sciences, Universidad Nacional Jorge Basadre Grohmann, Tacna 23000, Peru
Edgar Virgilio Bedoya Justo: Faculty of Engineering, Universidad Nacional de Moquegua, Moquegua 18001, Peru

Agriculture, 2025, vol. 15, issue 12, 1-20

Abstract: The genetic diversity of the olive tree ( Olea europaea L.) is critical for enhancing crop resilience and productivity under changing climatic conditions. Peru’s southern region, particularly Tacna, hosts over 30 olive cultivars, yet their genetic structure remains poorly characterized. This study aimed to evaluate the morphological and genomic diversity of ten economically important olive varieties cultivated in 15 sectors across Tacna and Jorge Basadre provinces. A total of 92 mother plants were selected for morphological assessment using 25 standardized descriptors. Additionally, genomic DNA was extracted from 30 samples and subjected to genotyping-by-sequencing (GBS). Quality metrics confirmed the efficiency of a modified 6h-DNA extraction protocol. Bioinformatic analysis identified hundreds of thousands of SNPs per variety, with a high transition/transversion ratio (∼2.1), indicating reliable variant calls. Phylogenetic clustering revealed three diversity groups, with the olive cultivars Ascolana and Frantoio exhibiting high genetic variability, and Arbequina and Leccino—also olive cultivars—showing reduced diversity. The integration of phenotypic and genomic data highlights hidden variability and supports informed selection and conservation strategies. These findings provide a genomic baseline for breeding programs and genetic resource management in emerging olive-growing regions such as southern Peru.

Keywords: olive ( Olea europaea ); genotyping-by-sequencing (GBS); single nucleotide polymorphisms (SNPs); genetic diversity; Peruvian olive cultivars; phylogenetic clustering; morphological characterization; germplasm conservation (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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