Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth1

Abstract

Cattle in breeds formed by recent crossing of Bos taurus (Bt) and Bos indicus (Bi) subspecies should contain chromosomes that are a composite of Bt and Bt segments. Using data from a 50K SNP chip, we were able to identify whether a chromosome segment of 11 SNP in a composite animal descended from a Bt or a Bi ancestor. When the method was tested in purebred Bt or Brahman cattle, about 94% of segments were assigned correctly. About 10% of the genome in Australian Brahman cattle appears to be of Bt origin, as might be expected from their history. We then examined the effect of the origin of each chromosome segment on BW in a population of 515 Bt × Bi composite cattle and found 67 chromosome segments with a significant (P < 0.01) effect. We confirmed these effects by examining these 67 segments in a population of Brahman cattle and in a population of mixed breeds including composite breeds such as Santa Gertrudis and Brahman cattle. About 66% of the 67 segments had an effect in the same direction in the confirmation analyses as in the discovery population. However, the effect on BW and other traits of chromosome segment origin is small, indicating that we had low power to detect these effects with the number of animals available. Consequently, when chromosome segment origin was used in genomic selection to predict BW, the accuracy was low (0.08). Chromosome segments that had a positive effect on BW tend to be at greater frequency in composite breeds than chromosome segments with a negative effect on BW.

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

“…This is less than the 10% that was estimated based on 50 K SNP data by Bolormaa et al [10]. Similarly, the present analysis estimated that 70% of the genome of the F1 crosses was of B. indicus origin.…”

“…The genotypes were phased using Beagle so that two haplotypes were defined for each animal for each segment. The probability ('b’) that a chromosome segment in a given animal carrying the i th haplotype was of B. indicus origin was estimated using the following formula: $b=\frac{p_{B{i}_i}}{p_{B{i}_{{}_i}}+p_{B{t}_i}}$[10], where $p_{B{t}_i}$ is frequency of the i th haplotype in B. taurus and $p_{B{i}_i}$ is frequency of the i th haplotype in B. indicus animals. Preliminary results showed that, in some cases, the origin of a segment was inconclusive but that many of the surrounding segments were of the same subspecies origin.…”

“…The complication is that the SNP alleles present in the composite breeds can originate either from B. indicus or B. taurus . Therefore, to deal with this situation, all SNP alleles of the composite breeds were assigned either a B. indicus or B. taurus origin based on the identified origin (taurine or indicine) of the haplotype surrounding the SNP [10]. The opportunity is that the composite breeds will segregate for mutations that have been fixed for alternate alleles in B. taurus and B. indicus and therefore will lead to the identification of new QTL.…”

Post-partum anoestrus in tropical beef cattle: A systems approach combining gene expression and genome-wide association results

“…The genetics of Australian Brahman cattle are mostly Zebu, approximately 90% (Bolormaa et al, 2011). Tropical Composite is a term used to describe stable crosses between…”

Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest

“…We used genotype data from the Cooperative Research Centre for Beef Genetic Technologies (http://www.beefcrc.com/) originally described by [23]. From this resource, we used the genotype on 729,068 SNPs across 1,800 individual cattle samples comprised of 200 individuals from each of the following 9 breeds: Angus, Brahman, Belmont Red, Charolais, Drought Master, Hereford, Santa Gertrudis, Shorthorn and Tropical Composite.…”