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ERIC Number: ED526157
Record Type: Non-Journal
Publication Date: 2009
Pages: 125
Abstractor: As Provided
Reference Count: 0
ISBN: ISBN-978-1-1095-8082-2
Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3
Donthu, Ravikiran
ProQuest LLC, Ph.D. Dissertation, University of Illinois at Urbana-Champaign
The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a 16.3 Mbp region was selected for the development of a high density map of single nucleotide polymorphisms (SNPs). A SNP discovery pipeline was developed to identify 13,000 SNPs, of which 1,039 were validated in 18 cattle breeds, for fine mapping QTLs in any region of cattle genome. This pipeline was utilized along with other sources of information to select 2,500 SNPs within the QTL critical region. We identified 1,520 SNPs heterozygous in at least one of the genotyped individuals from three Dairy Bull DNA Repository (DBDR) half sib families that were known to segregate QTLs on BTA3. These SNPs have average density of 1 SNP every 10.8 Kbp (median = 0.8 Kbp). Using genotypes obtained from the offspring of three half sib families, paternal and maternal haplotypes of the offspring were reconstructed in addition to the six sire haplotypes. A 9.7 Mbp haplotype block likely to be identical by descent was identified in sires, S1 and S2. This shared haplotype block was found to be associated with high milk yield in families, F1 and F2, confirming previous studies. Maternal haplotypes of offspring were then used to define linkage disequilibrium (LD) within the QTL critical region. There were 15 LD blocks found to be shared among all three sires, covering 0.5 Mbp within the 9.7 Mbp region. These regions may contain QTL alleles carried by all three sires. F[subscript st] analysis and integrated haplotype scores (iHS) identified signatures of selection in a 3 Mbp subregion of the QTL critical region. For genes located in the QTL critical region, functions were predicted on the basis of human gene annotation. To identify orthologous genomic regions containing candidate genes, a bioinformatics tool, SyntenyTracker was developed. Within the QTL critical region, eight genes with well established functions related to metabolism, membrane transport or mammary gland function were identified. These results show that the combination of a high density marker map, haplotype analysis, characterization of LD, and identification of genomic regions and nucleotides under selection is a powerful approach for QTL fine mapping. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page:]
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Publication Type: Dissertations/Theses - Doctoral Dissertations
Education Level: N/A
Audience: N/A
Language: English
Sponsor: N/A
Authoring Institution: N/A