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United States Department of Agriculture

Agricultural Research Service


Location: Vegetable Crops Research

Title: Transcriptome sequencing to produce SNP-based genetic maps of onion

item Duangjit, Janejira
item Bohanec, Borut
item Town, Christopher
item Chan, Agnes
item Havey, Michael

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2012
Publication Date: 3/18/2013
Citation: Duangjit, J., Bohanec, B., Town, C., Chan, A., Havey, M.J. 2013. Transcriptome sequencing to produce SNP-based genetic maps of onion [abstract]. Plant and Animal Genome. Paper No. P048.

Interpretive Summary:

Technical Abstract: We used the 454 platform to sequence from normalized cDNA libraries from each of two parental inbred lines of onion: 5225 is a red, doubled-haploid onion and OH1 is a yellow inbred that shows high frequency of gynogenic haploid production. From approximately 1.6 million reads from each inbred, 27,065 and 33,254 cDNA contigs were assembled from OH1 and 5225, respectively. In total, 3,364 single nucleotide polymorphisms (SNPs) on 1,716 cDNA contigs were identified between these two inbred onions. One SNP on each of 1,256 contigs was randomly selected for genotyping using the KASPar (LGC Genomics) platform. OH1 and 5225 were crossed and 186 gynogenic haploids were extracted from hybrid plants and used for SNP mapping. A total of 474 SNPs segregated in the OH1 x 5225 haploid family and a genetic map of 9 linkage groups (LOD=4) was constructed. Newly identified SNPs were also mapped using a previously developed F2 family from BYG15-23 x AC43, and common markers were used to join the maps and assign linkage groups to chromosomes. Concurrently, haploid plants were asexually propagated and evaluated in replicated plantings across three environments. Bulb-quality traits were measured and quantitative analyses are in progress. Because no heterozygosity exists in the haploids, there are no inter-allelic interactions; however inter-locus interactions or epigenetic, mutation, or environmental effects on bulb-quality attributes are possible.

Last Modified: 10/16/2017
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