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United States Department of Agriculture

Agricultural Research Service

Title: Fine mapping of QTL for twinning and ovulation rate using low density SNP map in conjunction with microsatellite marker information in the USMARC twinning population

Authors
item Allan, Mark
item Thallman, Richard
item Cushman, Robert
item Echternkamp, Sherrill
item Kuehn, Larry
item Snelling, Warren

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 3, 2006
Publication Date: January 2, 2007
Citation: Allan, M.F., Thallman, R.M., Cushman, R.A., Echternkamp, S.E., Kuehn, L.A., Snelling, W.M. 2007. Fine mapping of QTL for twinning and ovulation rate using low density SNP map in conjunction with microsatellite marker information in the USMARC twinning population [abstract]. Plant & Animal Genome XV Conference. Poster No. 521. p. 231.

Technical Abstract: The USMARC twinning population originated from 307 females and 53 males representing 12 different breeds of cattle and has been under selection for 25 years. The objective of this study was to initiate fine mapping of QTL for twinning and ovulation rate previously found on BTA5. This population has 9,272 twinning and 29,484 ovulation rate records for multiple generations of animals, but a significant number of these do not have tissue samples available for DNA genotyping. To overcome this, 27 SNP were genotyped across a 17 cM region in 48 animals representing 33 founding alleles that comprise 70% of the population at the QTL peak. Marker data on 20 microsatellites on BTA5 with 297 to 3,395 animals per marker were used in conjunction with pedigree information to estimate genotypic probabilities, using GenoProb, for 14,714 animals. Genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a two trait mixed model analysis using MTDFREML. Each SNP was analyzed individually followed by backward selection fitting all individually significant SNP simultaneously and then removing the least significant SNP until only significant SNP were left. Three significant SNP associations were detected (P<0.01) for twinning rate. For ovulation rate, seven significant associations were found (P<0.01). Two of these SNP were significant for both twinning and ovulation rate. Initial low density SNP mapping suggests two regions may be contributing to the QTL for twinning and ovulation rate on BTA5.

Last Modified: 12/19/2014
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