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Title: ASSIGNMENT OF 42 MICROSATELLITE MARKERS FROM CHROMOSOME 28 ON CHICKEN GENOME (GENBANK BV 680436-BV680477)

Author
item Kuo, Alice
item FULTON, JANET - HY-LINE INTERNATIONAL
item ASHWELL, CHRISTOPHER - N C STATE UNIVERSITY

Submitted to: Genbank
Publication Type: Abstract Only
Publication Acceptance Date: 12/29/2005
Publication Date: 12/29/2005
Citation: Kuo, A., Fulton, J.E., Ashwell, C. 2005. Assignment of 42 Microsatellite markers from chromosome 28 on chicken genome. GenBank Accession Number BV680436-BV680477.

Interpretive Summary:

Technical Abstract: Chicken has over 20 microchromosomes. Study reported avian sarcoma/leucosis virus receptor subtype A and C are encoded in chicken chromosome 28, position of subtype receptor C on chromosome 28 relative to markers from the consensus map of the chicken genome has been confirmed. 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, marker ADL0284 on chromosome 28 has been choice to searched new MSs markers 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. We found that microchromosomes had a mean of 64500 bp. An average of 42.86% of the estimated MSs qualified to be selected MSs in chromosome 28. 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.