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Article

Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

1
Dipartimento di Bioscienze, Università degli Studi di Milano, 20122 Milan, Italy
2
Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), CSIC, Universitat Politecnica de Valencia, 46011 Valencia, Spain
3
Departamento de Didáctica de las Matemáticas y las Ciencias Experimentales, Facultad de Educación, Universidad Internacional de la Rioja (UNIR), 26006 Logroño, Spain
4
Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, 23071 Jaén, Spain
5
Departamento de Biología Animal, Biologia Vegetal y Ecología, Facultad de Ciencias Experimentales, Campus de Las Lagunillas s/n, Universidad de Jaén UJA, 23071 Jaén, Spain
*
Author to whom correspondence should be addressed.
Academic Editors: Luis Rallo, Fernando Pliego Alfaro, Pilar Rallo, Concepción Muñoz Díez and Carlos Trapero
Plants 2021, 10(11), 2514; https://doi.org/10.3390/plants10112514
Received: 6 August 2021 / Revised: 27 October 2021 / Accepted: 11 November 2021 / Published: 19 November 2021
(This article belongs to the Special Issue 10th Anniversary of Plants—Recent Advances and Perspectives)
Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data. View Full-Text
Keywords: Olea europaea L.; olive; genotype by sequencing (GBS); single-nucleotide polymorphism (SNP); whole-genome sequencing (WGS); reference genome Olea europaea L.; olive; genotype by sequencing (GBS); single-nucleotide polymorphism (SNP); whole-genome sequencing (WGS); reference genome
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MDPI and ACS Style

Friel, J.; Bombarely, A.; Fornell, C.D.; Luque, F.; Fernández-Ocaña, A.M. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L. Plants 2021, 10, 2514. https://doi.org/10.3390/plants10112514

AMA Style

Friel J, Bombarely A, Fornell CD, Luque F, Fernández-Ocaña AM. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L. Plants. 2021; 10(11):2514. https://doi.org/10.3390/plants10112514

Chicago/Turabian Style

Friel, James, Aureliano Bombarely, Carmen Dorca Fornell, Francisco Luque, and Ana Maria Fernández-Ocaña. 2021. "Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L." Plants 10, no. 11: 2514. https://doi.org/10.3390/plants10112514

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