50 Using GPS and Genomic Technology to Provide a More Accurate Estimate of Bull Power in Western Intermountain Beef Systems

The objective of this study was to utilize GPS technology and genomic parentage testing to provide a more accurate measurement of bull power in the intermountain west beef production system. Breeding seasons are typically conducted on large, remote pastures, leading to current estimates of bull:cow ratios (1:20 or 1:25) possibly being inaccurate. With advances in genetic testing, parentage of calves can be obtained allowing producers to review which calves were sired from specific bulls, or how many cows each bull serviced (bull power). Our study fit 5 bulls from the same herd with GPS collars and collected hair samples for future DNA extraction prior to the 2018 breeding season. Bull movement was tracked over a 90-day breeding season on a large grazing allotment on the southern Utah and northern Arizona border. The GPS collars collected measurements of total distance traveled per day and distance traveled away from water, along with geocoordinates. Upon completion of the breeding season, collars were removed and data retrieved. At calving, biological material was collected and parentage testing of 104 calves was conducted and parentage determined. Results of parentage testing revealed that actually 6 bulls sired calves during the 2018 breeding season. The ranch’s bulls sired 72 (69%) calves (30, 16, 14, 10 and 2 calves, respectively). Thirty-two (31%) calves were sired by bulls from herds that grazed nearby. Interesting to note is the producer was unaware of any non-herd bulls co-mingling with this herd. While results from the current study are very preliminary, they do validate the importance of verifying bull power and sire identification to critically evaluate sire performance and increase the accuracy of selection in breeding replacements. The information presented herein may prove useful as a future selection tool to identify bulls that are high performing during breeding season in the intermountain west.

Evaluation of a Custom SNP Panel for Identifying and Rectifying of Misjudged Paternity in Deficiency Cases

Parentage testing is routinely performed by genotyping short tandem repeat (STR) through capillary electrophoresis in the present. However, ambiguous or even misjudged paternity based on STRs happens from time to time in cases where only one putative parent is available. We analyzed STR data of 7,818,969 unrelated pairs and 75 close-relative pairs and found that although the probability of a random false match between non-relatives was 4.22 × 10–6, the incidence of false or ambiguous paternity results between children and first-degree relatives of their true parent was as high as 18.67%. These results highlight the risk of false inclusion of a relative or even non-relatives in parentage testing with STRs. We then validated all ambiguous STR results by targeted sequencing with a custom panel containing 4,830 individual identification single nucleotide polymorphisms (IISNP), found that the ratio of mismatch loci to total SNPs was 1.78–6.95% in close relatives compared with 10.93–13.49% in unrelated pairs. Last, we reported three real cases with undetermined paternity by STRs and rectified them by dissecting with our IISNP panel. These results suggested that high-density IISNP panel can be used to identify and rectify misjudged cases effectively.

PSVII-22 Using GPS and genomic technologies to provide a more accurate estimate of bull power in western intermountain beef systems

The objective of this study was to utilize GPS technology and genomic parentage testing to provide a more accurate measurement of bull power in Intermountain West beef production systems. Breeding seasons in the Intermountain West are typically conducted on expansive pastures, leading to current bull:cow ratios (1:20 or 1:25) possibly being inaccurate. Traditionally, producers maintain enough bulls to satisfy established bull cow ratios, but there was not further investigation into which calves were sired from specific bulls or how many cows each bull was actually servicing. Thus, the current study fitted five bulls with GPS collars and collected hair samples for future DNA extraction prior to the 2018 breeding season. Bull movement was tracked over a 90-day breeding season on a large grazing allotment in southern Utah and northern Arizona. The GPS collars allowed for tracking total distance traveled per day, and distance traveled away from water. Upon completion of the breeding season, collars were removed and data downloaded. A total of 104 potential offspring of the collared bulls were branded, and had ear notches collected for DNA extraction and parentage analyses. Results of parentage testing revealed that actually six bulls sired calves during the 2018 breeding season. The cooperating ranch’s bulls sired 30, 16, 14, 10 and 2 calves respectively. However, a neighboring operation’s bull sired 32 calves in the cooperator’s herd during that same season. While results from the current study are very preliminary, they do validate the importance of verifying bull power and sire identification in order to critically evaluate sire performance and increase the accuracy of selection in breeding replacements. The information presented herein may prove useful as a future selection tool to identify bulls that are high performers during the breeding season in the Intermountain West.

Use of Microsatellites in Genetic Diversity Assessment, Parentage Testing and Individual Identification of the Kangal Shepherd Dog

The Kangal Shepherd Dog is considered the most common dog breed of Turkish origin. This study investigated variations in ten autosomal microsatellite markers (PEZ01, PEZ03, PEZ05, PEZ06, PEZ08, PEZ12, PEZ20, FHC2010, FHC2054 and FHC2079) for the purposes of genetic diversity assessment of the Kangal breed. In addition, the use of markers was assessed in parentage testing and individual identification within the Kangal breed. The microsatellite markers were typed in 51 Kangal dogs. The total number of alleles in the study population was 69. The mean number of alleles per locus was 6.9, and varied from four (FHC2079) to 12 (PEZ12). The polymorphic information content (PIC) ranged from 0.52 (FHC2079) to 0.87 (PEZ12), with the mean value for all loci of 0.717. Power of exclusion (PE) in 10 microsatellites investigated varied between 0.143 (FHC2054) and 0.472 (PEZ08) per locus. In order to determine the efficiency of using microsatellites for individual identification in the Kangal breed, power of discrimination (PD) and matching probability (MP) were calculated for each microsatellite marker. The panel achieved high combined MP (6.77 × 10-10) and high combined PD value of 99.99999%. The obtained results may contribute to further recognition of the Kangal breed, and confirm that the investigated microsatellites enable a reliable parentage testing and individual identification of the breed.

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle