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Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

Title: Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa

Author
item Romanov, D - Russian Agrarian University
item Divashuk, M - Russian Agrarian University
item Havey, Michael
item Khrustaleva, L - Russian Agrarian University

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2015
Publication Date: 6/15/2015
Publication URL: http://handle.nal.usda.gov/10113/61715
Citation: Romanov, D., Divashuk, M., Havey, M.J., Khrustaleva, L. 2015. Tyramide-FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa. Genome. 58(3):111-119. doi: 10.1139/gen-2015-0019.

Interpretive Summary: Chromosome 5 of onion carries genes controlling major traits of interest to breeders, including dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors. A plethora of molecular markers in expressed regions of the onion genome have been mapped; however there is little information on the relationships between genetic and physical distances in onion. We used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced DNA probes that carried introns to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of the relatively short target DNA sequences. Through the integration of genetic and chromosomal maps we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion. This research will be of interest to geneticists and breeders of onion and is important towards the long-term goal of sequencing the onion genome and map-based cloning of important genes.

Technical Abstract: Chromosome 5 of onion carries major quantitative trait loci (QTL) of interest to breeders that control dry-matter content, pungency and storability of bulbs, amounts and types of epicuticular waxes, and resistances to abiotic factors. SNPs, SSRs and RFLPs in expressed regions of the onion genome have been mapped and we used these clones and sequences from the NCBI database to develop DNA probes for in situ hybridization to integrate the genetic and physical maps of onion chromosome 5. We produced DNA probes that carried introns to increase the hybridization specificity of the probes and to enlarge the target DNA sizes. Tyramide-FISH technique was used to increase the detection sensitivity of the relatively short target DNA sequences. Through the integration of genetic and chromosomal maps we were able to estimate the distribution of recombination events along onion chromosome 5. We demonstrated the efficiency of chromosomal in situ mapping of exon-intron genomic clones for the extremely large genome of onion.