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

• Published in: Plants (Basel) Vol. 10; no. 11; p. 2514
• Main Authors: Friel, James, Bombarely, Aureliano, Fornell, Carmen Dorca, Luque, Francisco, Fernández-Ocaña, Ana Maria
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 19.11.2021; MDPI
• Subjects: Agricultural economics; Agricultural research; Bias; Clustering; Comparative analysis; Comparative studies; Cultivars; Data processing; Datasets; Enzymes; Fisheries; Fisheries research; Gene sequencing; Genetic analysis; Genetic diversity; Genetic relationship; Genomes; genotype by sequencing (GBS); Genotypes; Genotyping; Germplasm; Olea europaea; Olea europaea L; olive; Phylogeny; Population genetics; reference genome; single-nucleotide polymorphism (SNP); Whole genome sequencing; whole-genome sequencing (WGS); Mediterranean Area
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants10112514

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.