A Whole-Genome Scan to Map Quantitative Trait Loci for Conformation and Functional Traits in Canadian Holstein Bulls

Abstract

Genetic improvement of livestock populations can be achieved through detection and mapping of genetic markers linked to quantitative trait loci (QTL). With the completion of the bovine genome sequence assembly, single nucleotide polymorphism (SNP) assays spanning the whole bovine genome and research work on large-scale identification, validation, and analysis of genotypic variation in cattle has become possible. A total of 462 Canadian Holstein Bulls were used to test the association between SNP and QTL. Single locus linkage disequilibrium regression model was implemented to perform a whole genome scan to identify and map QTL affecting conformation and functional traits. One thousand five hundred thirty-six SNP markers from introns and exons of potential QTL regions for economically important traits across the bovine genome were selected for association analysis. A total of 45 and 151 SNP were found to be associated with 17 conformation and functional traits at a genome- and chromosome-wise significance level, respectively. Among the 196 significant SNP, 169 of them are newly detected in this study, whereas 27 of them have been reported in previous literature and 161 of these were located in genes and are worth further investigating to potentially identify the causative mutations underlying the QTL. The single locus linkage disequilibrium regression method using SNP marker genotypes has proven to be a successful methodology for detecting and mapping QTL in dairy cattle populations.

Dissection of Genetic Factors Modulating Fetal Growth in Cattle Indicates a Substantial Role of the Non-SMC Condensin I Complex, Subunit G (NCAPG) Gene

“…These results were in line with other studies providing evidence for QTL affecting stillbirth, dystocia, or calving ease on the same chromosome (Schrooten et al 2000;Kü hn et al 2003;Holmberg and Andersson-Eklund 2006;Kolbehdari et al 2008;Olsen et al 2008;Schulman et al 2008). This initiated our attempt to scrutinize BTA6 for the genetic background of variation in the fetal component regulating fetal growth.…”

Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

“…DNA chip technology is now available to genotype for large amount of SNPs, making it possible to undertake a whole genome scan with evenly spaced marker at a much higher density than microsatellite markers. This approach was used to fine mapping QTL for milk traits in dairy cattle (Kolbehdari et al, 2008;Daetwyler et al, 2008;Kim et al, 2009). In beef cattle, whole genome association studies with SNP arrays have found a number of QTL for feed intake traits (Barendse et al, 2007;Hulett et al, 2007).…”

The characterization of goat genetic diversity: Towards a genomic approach

“…The availability of dense marker panels throughout the genome marked a paradigm shift in the way livestock populations are investigated and analysed genetically, either for studying the population genetic structure (McKay et al, 2008), searching for QTL controlling complex traits (Kolbehdari et al, 2008), performing genome-wide marker-enhanced selection of young animals (VanRaden et al, 2009;Hayes et al, 2009), identifying patterns of recent and past selection (Luikart et al, 2003;MacEachern et al, 2009) or addressing other objectives.…”