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item Kuo, Alice

Submitted to: Genbank
Publication Type: Abstract Only
Publication Acceptance Date: 12/28/2005
Publication Date: 12/29/2005
Citation: Kuo, A., Fulton, J., Ashwell, C. 2005. Microsatellite markers from chromosome 27 by using the chicken genome sequence. GenBank Accession Number BV680374-BV680405.

Interpretive Summary:

Technical Abstract: Microsatellite (MS) markers have developed into the marker of choice in a number of genetic areas including genome mapping, and medical, evolutionary, and ecological genetics. Based on the previous phenotypic study from Hy-Line International, 12 existing MSs markers (defined by the genetic consensus map ( in 7 different chromosomes were selected to search for new MSs markers. New MSs markers were searched within a 10 centi-morgan (cM) interval. Physical distance (bp) between 8 existing MSs markers was determined using the chicken genome information (Ensembl). The possible MSs within 10cM physical distance were estimated by using the UCSC internal program (which we called estimated MSs), and confirmed through the Ensembl browser visually. Our selection parameter for MSs was a repeat frequency equal to or greater than 6. The MSs which fit in our category were indicated as selected MSs. The MSs remaining after excluding the mono repeats were called choice MSs. Primers were designed to amplify the choice MSs. Eight different commercial egg laying types of chickens, and parental chicken’s DNA samples were tested in two different PCR reactions. All PCR products were examined by using clearose electrophoresis gel analysis. Based on the parental PCR reaction results, 117 choice MSs were dy-labeled and genotyped with 10 parental lines’ DNA samples. Allele sizes were compared between the sires and dams. We found that macrochromosomes averaged 377540 bp, intermediate chromosomes contained 239687 bp, and microchromosomes had a mean of 64500 bp. There are more estimated and selected MSs in macrochromosomes than in microchromosomes. An average of 57.66% of the estimated MSs qualified to be selected MSs. This indicates the proportion of the MSs estimated from the UCSC internal program that fit in our first selection category. In the estimated MSs, each type of the MSs was similar in overall proportion, in every region. However, we found a greater percentage of di- repeats in the choice MSs. Using the chicken genome sequence to increase marker density can significantly decrease the time to develop new informative microsatellites and allow for ease in targeting specific chromosomal regions. This focused approach will be extremely useful in fine-mapping genome regions where QTLs have been detected.