Skip to main content
ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #232672
Title: Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

Author
item MCCALLUM, JOHN - NEW ZEALAND INST CROP
item THOMSON, SUSAN - NEW ZEALAND INST CROP
item PITHER-JOYCE, MEEGHAN - NEW ZEALAND INST CROP
item KENEL, FERNAND - NEW ZEALAND INST CROP
item CLARKE, ANDREW - INST OF MOLECULAR BIOSC
item Havey, Michael

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2008
Publication Date: 11/28/2008
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. 133:810-818.

Interpretive Summary: Although onion is a globally significant vegetable crop, the structure of genetic variation within and among populations is poorly understood. We surveyed genetic variation in cultivated onion germplasm by genotyping population samples from 90 landrace, inbred and open-pollinated varieties of wide geographical adaptation with 69 EST-SSR and 13 genomic SSR markers. EST-SSRs revealed limited allelic diversity but high heterozygosity. Re-sequencing of 25 marker products revealed additional SNPs in 17 (68%), suggesting that mutation scanning of 5’UTR amplicons from ESTs may be a more productive approach to EST marker development than electronic methods. A significant proportion of the EST primer sets amplified products in A. roylei (84%), A. fistulosum (83%) and shallot (99%), showing they can be readily used for comparative and interspecific studies. Di-nucleotide genomic SSRs were more highly polymorphic than EST-SSRs but were less suitable for genotyping population samples. Multivariate analysis of genetic distances among populations revealed genetic relationships consistent with known ancestry and origin, in particular resolving long-day and short-day populations and populations from the Indian subcontinent. Landrace and open-pollinated populations exhibited higher levels of gene diversity than landrace accessions, suggesting that widely cultivated open-pollinated varieties are a key reservoir of genetic variation in bulb onion. These results will be of interest to geneticists and breeders interested in understanding reservoirs of genetic variation in onion.

Technical Abstract: Although onion is a globally significant vegetable crop, the structure of genetic variation within and among populations is poorly understood. We broadly surveyed allelic variation in cultivated onion germplasm by genotyping population samples from 90 landrace, inbred and open-pollinated varieties of wide geographical adaptation with 69 EST-SSR and 13 genomic SSR markers. EST-SSRs revealed limited allelic diversity but high heterozygosity. Re-sequencing of 25 marker products revealed additional SNPs in 17 (68%), suggesting that mutation scanning of 5’UTR amplicons from ESTs may be a more productive approach to EST marker development than electronic methods. A significant proportion of the EST primer sets amplified products in A. roylei (84%), A. fistulosum (83%) and shallot (99%), showing they can be readily used for comparative and interspecific studies. Di-nucleotide genomic SSRs were more highly polymorphic than EST-SSRs but were less suitable for genotyping population samples. Multivariate analysis of genetic distances among populations revealed genetic relationships consistent with known ancestry and origin, in particular resolving long-day and short-day populations and populations from the Indian subcontinent. Landrace and open-pollinated populations exhibited higher levels of gene diversity than landrace accessions, suggesting that widely cultivated open-pollinated varieties are a key reservoir of genetic variation in bulb onion.