Imputation of microsatellite from dense SNP in the Valdostana Red Pied cattle - A Master thesis in Animal Production

Microsatellite markers (MS) have been used efficiently for parentage verification in various livestock species and their impact on the industry to certify exact pedigree information has been massive for long time. In cattle, the International Society of Animal Genetics (ISAG) recommended a panel of 12 bovine MS markers for the individual parentage verification testing and a large MS database contains the historical data of populations. Recently, there is an increasing interest from the stakeholders in agriculture and the research community to use Single Nucleotide Polymorphism (SNP) for parental verification due to their higher genotyping accuracies, speed of genotyping, lower overall cost per genotype, and simplicity of automation. Thus, ISAG opened the parentage testing in cattle to SNP chips methodology. A tool to link the MS database to SNP markers tool have been developed in USA for main populations such as the Holstein and Brown Swiss cattle. The objective of the thesis is to develop a SNP-MS haplotype reference panel set in the Valdostana Red Pied cattle (the most common autochthonous dual purpose breed in the region Valle d’Aosta in Italy). The information on MS alleles recognized from ISAG are available from the National Association of Valdostana Breeders (A.N.A.Bo.Ra.Va.) and the genotypes obtained from the llumina BovineHD BeadChip (777,962 SNPs) array for 143 bulls are already accessible at UNIMI. Specific imputation software (e.g.: Beagle) and pipelines will be used for the haplotype estimation. This strategy may be employed in any species that has dense SNP genotypes and MS alleles information on a subset of the population large enough to define phase associations among MS alleles and SNP haplotypes. Moreover, this methodology will validate the parentage among individuals when different genotyping platforms have been used through the generations and will assess the sensitivity of such a conversion system using HD SNP data.