Skip to main content

Research Repository

Advanced Search

Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers

McCallum, John; Thomson, Susan; Pither-Joyce, Meeghan; Kenel, Fernand; Clarke, Andrew; Havey, Michael J.

Authors

John McCallum

Susan Thomson

Meeghan Pither-Joyce

Fernand Kenel

ANDREW CLARKE ANDREW.CLARKE1@NOTTINGHAM.AC.UK
Assistant Professor in Archaeogenetics

Michael J. Havey



Abstract

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

Citation

McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., & Havey, M. J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818. https://doi.org/10.21273/jashs.133.6.810

Journal Article Type Article
Acceptance Date Oct 2, 2008
Online Publication Date Nov 27, 2008
Publication Date Nov 27, 2008
Deposit Date Oct 21, 2020
Publicly Available Date Mar 28, 2024
Journal Journal of the American Society for Horticultural Science
Print ISSN 0003-1062
Electronic ISSN 2327-9788
Publisher American Society for Horticultural Science
Peer Reviewed Peer Reviewed
Volume 133
Issue 6
Pages 810-818
DOI https://doi.org/10.21273/jashs.133.6.810
Keywords Genetics; Horticulture
Public URL https://nottingham-repository.worktribe.com/output/4981112
Publisher URL https://journals.ashs.org/jashs/view/journals/jashs/133/6/article-p810.xml