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.

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
• 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