Monday, March 2, 2009

5th floor conference room

1:30 PM

 

Ravikiran Donthu, University of Illinois at Urbana-Champaign

 

Haplotype definition and linkage disequilibrium in a 16.3 Mbp QTL critical region on cattle chromosome 3

 

Abstract.

One of the great challenges in genetics is to identify the genes responsible for quantitative traits. In livestock,
 most quantitative trait loci (QTL) are localized to intervals of more than 10 cM, which makes identification of 
the genes and polymorphisms underlying the trait a complex and expensive endeavor. One of the major factors influencing 
the pace of discovery of genes affecting quantitative traits is the availability of dense marker maps. The recent 
elucidation of millions of single nucleotide polymorphisms (SNPs) in the bovine genome has radically changed 
the potential for resolving QTLs into their discrete genetic components. However, the current technology used 
for genome-wide association studies in cattle deploys ~55,000 SNPs, which improves QTL identification and resolution, 
but does not provide much advantage for gene discovery. Dense maps on the order of 300,000 to 1 million SNPs are 
required for fine mapping of QTL intervals and for reducing candidate genes/polymorphisms to manageable numbers.  

                The goal of our study was to fine-map the QTL interval flanked by markers BL41 and TGLA263 on cattle 
chromosome 3 (BTA3) (Heyen et al., 1999), and to identify candidate genes for the milk yield, fat yield, and protein 
percentage QTL in this interval. To fine map this QTL we developed a high density map containing 1,520 informative SNPs 
(1 SNP per 10.5 Kbp) in the 16.3 Mbp QTL critical region on BTA3, and identified signatures of selection within this region. 
These SNPs were used to define haplotypes in Dairy Bull DNA Repository (DBDR) families 1, 2 and 5 that are known to be segregating 
the milk production trait-associated QTL on BTA3. Data obtained with this high density SNP map are representative of results 
that can be expected using 300,000 SNPs in a genome-wide association study.