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United States Department of Agriculture

Agricultural Research Service

Title: Assessment of Genetic Diversity in Bulb Onion (Allium Cepa L.) Using Simple Sequence Repeat Markers

item Mccallum, John - CROP & FOOD RES, NZ
item Havey, Michael

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: December 2, 2005
Publication Date: January 21, 2006
Citation: Mccallum, J., Havey, M.J. 2006. Assessment of genetic diversity in bulb onion (ALLIUM CEPA L.) using simple sequence repeat markers [Abstract]. Plant and Animal Genome Abstracts. Available:

Technical Abstract: Onions are the second most-valuable vegetable in the world, following only tomato. Despite their economic significance, knowledge of onion genetic diversity and resources is limited, owing to a paucity of public marker and germplasm resources and their out-breeding, biennial habit. The unusually large (16 pg), diploid genome has prevented effective use of RFLP and dominant PCR-based marker systems such as AFLP and RAPD for fingerprinting studies. We previously mined onion EST resources to develop simple sequence repeat (SSR) markers to aid development of the onion linkage map. These have proven highly informative, portable across pedigrees and are providing a low-density set of anchor loci across the onion and interspecific Allium linkage maps. We used these optimized markers to conduct the first large-scale DNA-based survey of genetic variation in onion. The panel for this survey comprised samples of 25 individuals from 96 short- and long-day onion populations including key open-pollinated varieties widely exploited by breeders and a wide selection of landrace accessions from the USDA-ARS collection. We are surveying allelic content of population samples by sizing fluorescent-labelled PCR products on standard capillary sequencers. Results to date show good concordance of molecular data with known pedigrees.

Last Modified: 4/22/2015
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