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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

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

Authors
item Duangjit, J -
item Bohanec, B -
item Chan, A -
item Town, C -
item HAVEY, MICHAEL

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 6, 2013
Publication Date: May 21, 2013
Repository URL: http://handle.nal.usda.gov/10113/56776
Citation: Duangjit, J., Bohanec, B., Chan, A.P., Town, C.T., Havey, M.J. 2013. Transcriptome sequencing to produce SNP-based genetic maps of onion. Theoretical and Applied Genetics. 126(8)2093:2101.

Interpretive Summary: We sequenced from the expressed regions of the onion genome from two inbred lines of onion (OH1 and 5225). From approximately 1.6 million sequencing reads from each inbred, 27,065 and 33,254 reads assembled into contigs from OH1 and 5225, respectively. In total, 3,364 single nucleotide polymorphisms (SNPs) on 1,716 cDNA contigs were identified between these two onions. One SNP on each of 1,256 contigs was randomly selected for genotyping. OH1 and 5225 were crossed and 182 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 10 linkage groups was constructed. Newly identified SNPs were also mapped using a previously developed family from BYG15-23 x AC43, and common markers were used to join the maps and assign linkage groups to chromosomes. These new SNPs will be of interest to onion breeders in the public and private sectors and should useful for genetic mapping, gene tagging, marker-aided selection, quality-control of seed lots, and fingerprinting of cultivars.

Technical Abstract: We used the 454 platform to sequence from normalized cDNA libraries from each of two inbred lines of onion (OH1 and 5225). 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 onions. One SNP on each of 1,256 contigs was randomly selected for genotyping. 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 10 linkage groups (LOD=4) was constructed. Newly identified SNPs were also mapped using a previously developed segregating family from BYG15-23 x AC43, and common markers were used to join the maps and assign linkage groups to chromosomes. Because these new SNPs are in expressed regions of the onion genome and commonly occur among elite germplasms, they will be useful for genetic mapping, gene tagging, marker-aided selection, and fingerprinting.

Last Modified: 9/29/2014
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