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

Olive, <i>Olea europaea</i> 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 pe...

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Autores principales:	James Friel, Aureliano Bombarely, Carmen Dorca Fornell, Francisco Luque, Ana Maria Fernández-Ocaña
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Olea europaea</i> L. olive genotype by sequencing (GBS) single-nucleotide polymorphism (SNP) whole-genome sequencing (WGS) reference genome Botany QK1-989
Acceso en línea:	https://doaj.org/article/32e0247e42f74350af4e599cf506eabb
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spelling	oai:doaj.org-article:32e0247e42f74350af4e599cf506eabb2021-11-25T18:47:15ZComparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.10.3390/plants101125142223-7747https://doaj.org/article/32e0247e42f74350af4e599cf506eabb2021-11-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2514https://doaj.org/toc/2223-7747Olive, <i>Olea europaea</i> 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.James FrielAureliano BombarelyCarmen Dorca FornellFrancisco LuqueAna Maria Fernández-OcañaMDPI AGarticle<i>Olea europaea</i> L.olivegenotype by sequencing (GBS)single-nucleotide polymorphism (SNP)whole-genome sequencing (WGS)reference genomeBotanyQK1-989ENPlants, Vol 10, Iss 2514, p 2514 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Olea europaea</i> L. olive genotype by sequencing (GBS) single-nucleotide polymorphism (SNP) whole-genome sequencing (WGS) reference genome Botany QK1-989
spellingShingle	<i>Olea europaea</i> L. olive genotype by sequencing (GBS) single-nucleotide polymorphism (SNP) whole-genome sequencing (WGS) reference genome Botany QK1-989 James Friel Aureliano Bombarely Carmen Dorca Fornell Francisco Luque Ana Maria Fernández-Ocaña Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
description	Olive, <i>Olea europaea</i> 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.
format	article
author	James Friel Aureliano Bombarely Carmen Dorca Fornell Francisco Luque Ana Maria Fernández-Ocaña
author_facet	James Friel Aureliano Bombarely Carmen Dorca Fornell Francisco Luque Ana Maria Fernández-Ocaña
author_sort	James Friel
title	Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
title_short	Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
title_full	Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
title_fullStr	Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
title_full_unstemmed	Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.
title_sort	comparative analysis of genotyping by sequencing and whole-genome sequencing methods in diversity studies of <i>olea europaea</i> l.
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/32e0247e42f74350af4e599cf506eabb
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Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of <i>Olea europaea</i> L.

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