A Simple Method for Evaluating the Genotype Quality of the Sire X Chromosome Using Half‑Sib Families
Recent studies have shown that the bovine X chromosome contains more than a thousand genes, some of which may be economically important. However, since males are heterogametic for the X chromosome, it has, to date, largely been ignored for genomic prediction and its information content has not been fully explored. The genotyping quality of the X chromosome is the first question that must be addressed. In this study, we suggest a simple method to impute the X chromosome of the sire using a half-sib family in order to check genotyping accuracy. The results showed that the suggested method allows for a robust imputation of the X chromosome in ungenotyped sires and is useful for the routine quality control of the genomic data.
Increased accuracy of the Poll DNA marker test for Australian beef cattle
The Poll DNA marker test is used to determine the poll genetics of an animal, given the alleles observed within the poll locus. This paper describes improvements made to the commercially available Poll DNA marker test, to capture more variability, enable predictions that are more accurate and clarify uncertainty of polled probabilities.
Current status of Australia's diagnostic poll haplotype test
Australia's diagnostic poll haplotype test requires reliable and varied phenotype submissions to estimate polled probabilities of haplotypes, and is dependent on unbiased sampling of the population. This paper provides a review of the effectiveness of the haplotype poll test and shows clear potential for significant ascertainment bias to be affecting the accuracy of the test, resulting from industry submission of mostly unknown or polled phenotypes, with little control over phenotype scoring accuracy. A new project targeting the supplementation with horned animals is underway to address the resulting phenotype proportions, with the aim of greatly increasing the accuracy of the test. Keywords: poll, horn, haplotype, beef.
Implementation of single-step genomic BREEDPLAN evaluations in Australian beef cattle
Single-step GBLUP (ssGBLUP) procedures have now been implemented into Australia's BREEDPLAN genetic evaluation system for beef cattle. This major remodelling required the development of many new features and modifications to existing procedures. The first requirement was the construction of a flexible but robust set of procedures for handling and processing of raw SNP genotypes to enable the construction of suitable genomic relationship matrices. The analytical processes were modified to replace with and for the explicit fitting of genetic groups. A new accuracy algorithm was developed and the solver was revised. Examples from Australian Angus and Brahman breeds comparing current BLUP evaluation with ssGBLUP are presented to show the resultant changes and effects of implementing the new genomic evaluations.