Angus Genome Project (AGP)

Current Status:

Initially we designed the genotyping for this project to be completed in two stages due to the large number of animals (N=3,840) involved. The first stage would be a course map with an average intermarker interval of 20 cM followed by a second stage where we would fine map only 8-10 of the most economically important QTL. However, due to increased throughput and a drastic decrease in genotyping costs, we decided to only have one stage of microsatellite genotyping. We are currently scoring all 3,840 animals for 421 microsatellites with an average spacing of 7.5 cM. We anticipate the genotyping portion of this project will be completed by early summer 2006 and will produce roughly 1.6 million microsatellite genotypes.

Preliminary Results:

We have conducted preliminary analyses on several of the chromosomes that have completed genotypes. These results were presented at the International Plant and Animal Genome Conference XIV earlier this year (http://www.intl-pag.org/pag/). Below are the abstracts. You can download the posters as a pdf file by clicking on each of the titles.

QTL Mapping and Candidate Gene Analysis on BTA1 in Angus

Natalya S. Morsci, Erin M. Sellner, Robert D. Schnabel, Jae-Woo Kim, Ping Yao, Matthew C. McClure, Jeremy F. Taylor

The objectives of this study were to detect QTLs and analyze the candidate genes Adiponectin (APM1) and Somatostatin (SST) on BTA1 for their effects on carcass yield and quality traits in a commercially relevant Angus population. Our mapping population consisted of a 14-generation pedigree of 1,678 registered Angus AI sires and 1,510 purebred commercial Angus steers grouped into 36 halfsib families consisting of no less than 30 progeny per sire. Twenty-four genetic markers were used to generate 98,764 genotypes and construct a sex-averaged linkage map for BTA1 spanning 174 Haldane cM. Individual halfsib steer and AI sire families were analyzed by least-squares regression under a halfsib model. A multipoint Bayesian linkage analysis of the extended Angus AI sire pedigree and of a pedigree integrating all of the halfsib steer families was performed using LOKI. Combined results from these analytical approaches provide compelling evidence for several carcass yield and quality QTL on BTA1 in Angus. APM1 and SST were completely resequenced in five Angus sires for polymorphism detection and five loci were genotyped across the population. Both genes were excluded as being causal for any of the QTL detected on BTA1.

Mapping Marbling QTL On 11 Bovine Chromosomes In Commercial Angus Cattle

Matthew C. McClure, Robert D. Schnabel, Natalya S. Morsci, Erin M. Sellner, Ping Yao, Jae-Woo Kim, Jeremy F. Taylor

We have genotyped two large Angus mapping populations for 172 microsatellite and 7 SNP markers on chromosomes 1, 2, 5, 9, 10, 11, 12, 14, 24, 25 and 29 and have tested for QTLs influencing marbling. The first population comprised 1,678 AI sires born after 1955, the second comprised 36 halfsib families containing 1,510 steers produced in the Circle A Ranch Sire Alliance. Data were analyzed using QTL Express under a halfsib design and by LOKI using the full pedigree. At least one marbling QTL was detected on each chromosome and several QTL were detected on most of the chromosomes. At a chromosomewise P<0.05 significance level, we estimate there to be as many as 36 marbling QTL on these 11 chromosomes in Angus with only 11 having been previously reported. This suggests that the majority of QTL segregate within all Bos taurus breeds of cattle but that either novel QTL exist within specific breeds or that marbling QTL have been selectively reported. These results support our approach to QTL mapping within commercially relevant populations.

Confirmation of Birth weight QTL on Bovine Chromosome 2 and a Maternal Milk QTL on BTA14 in Angus

Ping Yao, Robert D. Schnabel, Erin M. Sellner, Matthew C. McClure, Jae-Woo Kim and Jeremy F. Taylor

We previously reported the localization of QTL influencing growth and carcass EPDs to BTA2 and BTA14 using a population comprised of registered Angus sires. In this study, we extend these results to include 36 paternal halfsib families comprised of 1,510 steers produced by the Circle A Ranch Sire Alliance and measured for growth and carcass traits. Using 60 microsatellites and 2 SNPs within DGAT1 and TG, we have confirmed our earlier findings in the registered Angus sire population and have now identified several additional QTL on each of these chromosomes. We found strong evidence for four birth weight QTL on BTA2 at 10, 2, 40 and 130-cM (Haldane). Work is underway to fine-map these QTL regions in both Angus populations, to identify haplotypes predictive of QTL genotype and to identify positional candidate genes underlying the QTL. We also show that DGAT1 is a maternal milk QTL and that there is no effect of TG on marbling in Angus cattle.