Factors affecting incorrect paternity assignment in the Israeli Holstein population.
ABSTRACT A total of 6040 Israeli Holstein cows from 181 Kibbutz herds listed as progeny of 11 sires were genotyped for 104 microsatellites. Seventeen markers were deleted due to a frequency of erroneous genotypes >1%, leaving 160,470 valid genotypes. Conflicts between the putative sire and daughter in at least 2 markers and for at least 10% of the markers genotyped per cow were required to reject paternity. Cows that did not meet the requirements for paternity confirmation or rejection were deleted from further analysis. The frequency of rejected paternity was 11.7%. The effects of recorded sire, birth year, geographical region, herd, and inseminator on the frequency of paternity rejection were analyzed with linear and nonlinear models. Only the effects of inseminator and recorded sire were significant in all models tested that included these effects. The main causes of incorrect paternity recording appear to be inseminator recording mistakes, and possibly mistakes with respect to semen labeling at the AI institutes. Incorrect paternity recording due to multiple inseminations by different sires could explain, at most, 20% of the paternity mistakes. Instituting a system of quality control, especially at the level of the inseminator, should reduce paternity errors to no more than 8%, and increase genetic progress by at least 1%.
SourceAvailable from: Zhe Zhang[Show abstract] [Hide abstract]
ABSTRACT: Pedigree is an important information source in the studies on human genetics and animal/plant breeding. Pedigree error is a common data error in breeding practice. It can affect the reliability of results from researches such as gene mapping, genetic or phenotypic value prediction. By using genetic markers, several approaches can identify the suspected pedigrees, but most of them are complex and the allowed number of genetic markers is limited, such as Cervus. Since the wide use of high density single nucleotide polymorphisms (SNPs) in human genetic and animal/plant breeding, a new parentage identification approach (named EasyPC, Easy Pedigree Checking) based on whole genome genetic data was proposed in this study. EasyPC was compared with Cervus on efficiency, and validated with a Chinese Holstein cattle (n=2180) and a Duroc swine (n=191) population. Results showed that EasyPC was much less time demanding than Cervus, and pedigree error rates were 20% for cattle and 6% for swine. Result from the cattle population is in accordance with previous study. By analyzing the empirical distribation of Mendelian error rate calculated in a population using all available SNPs, EasyPC not only can identify the correctness of a pedigree in a simple, fast, and accurate manner, but also can correct the wrong pedigree. EasyPC provides a promising alternative solution to traditional pedigree correction approaches and eases the data analysis of whole genome related studies.