Genotyping by sequencing for SNP marker development in onion

Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 [F.sub.2] plants, parents of the [F.sub.2] plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the [F.sub.2] and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean [H.sub.e] = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers. Key words: genetic map, doubled haploid lines, genotyping by sequencing, germplasm, single nucleotide polymorphism, population genetics. L'oignon (Allium cepa) ne se prete pas facilement au developpement de marqueurs moleculaires en raison de la grande taille de son genome nucleaire (16 gigabases pour 1C). Les polymorphismes mononucleotidiques (SNP) sont utiles pour la caracterisation genetique et la selection assistee chez l'oignon en raison de leur codominance et de leur abondance au sein du materiel ameliore. Les auteurs ont realise un genotypage par sequencage (GBS) pour identifier des SNP chez l'oignon au moyen de 46 plantes [F.sub.2], des parents des [F.sub.2] (Ailsa Craig 43 et Brigham Yellow Globe 15-23), de deux lignees haplo'ides doublees (DH; DH2107 et DH2110), ainsi que de 94 accessions du USDA National Plant Germplasm System (NPGS). Les SNP ont ete appeles en utilisant le pipeline bioinformatique TASSEL 3.0 UNEAK ('Universal Network Enabled Analysis'). Les sequences des plantes [F.sub.2] et DH ont ete employees pour construire un pseudo-genome de reference a l'aide duquel les genotypes ont ete appeles pour toutes les accessions. Des filtres de qualite ont ete identifies un ensemble de 284 SNP de haute qualite, lesquels ont ete positionnes sur une carte genetique existante pour la famille F2. Les accessions presentaient un niveau modere de diversite genetique (indice [H.sub.e] moyen = 0,341) et des evidences de consanguinite (indice F moyen = 0,592). Le GBS se montre prometteur pour l'identification de SNP chez l'oignon, bien que l'absence d'un genome de reference necessite de nombreux scripts maison pour l'analyse bioinformatique afin d'identifier des SNP de haute qualite. [Traduit par la Redaction] Mots-cles: carte genetique, lignees haplo'ides doublees, genotypage par sequencage, germoplasme, polymorphisme mononucleotidique, genetique des populations.
Introduction Bulb onion (Allium cepa L.) is a widely produced and highly valuable vegetable crop (FAO 2018). Onion cultivars have been selected for bulbing and flowering across diverse day-length and [...]