Detection and characterisation of amplified fragment length polymorphisms for protein yield and clinical mastitis in Canadian Holsteins

The main goal of QTL studies in livestock is to map and characterize trait loci controlling phenotypic characters like production, reproduction, and disease resistance traits of economic importance. The present study focuses on the usefulness of amplified fragment length polymorphism (AFLP) in combination with selective DNA pooling for detection of DNA markers for protein yield and clinical mastitis (CM) in Canadian Holsteins. The most promising AFLP markers for each trait are converted into sequence specific co-dominant PCR markers, mapped on the bovine genome, and their QTL linked effects on production and functional traits are estimated.;CM resistant and susceptible groups were prepared from 200 cows having extreme residual effects for clinical mastitis cases after accounting for fixed effects. DNA pools assayed by 89 EcoRI/ TaqI primer pairs and 27 promising fragments were found. The most promising fragment was characterised as CGIL4, which carries an A ⇔ G mutation. The frequency of CM susceptible allele G compared to allele A was (66% vs. 34%) in cows and was (74% vs. 26%) in bulls. The GG cows were significantly associated with higher CM, overall and first lactation somatic cell score rating, and milk yield EBV in first lactation, and with lower fat percent compared to AG cows. However, these results were not confirmed in the bull population.;A 3000-rad bovine-hamster radiation hybrid panel was used to map CGIL3 and CGIL4. The orthology of CGIL3 with human TCF7L2 gene and comparative maps of human and bovine mapped CGIL3 and bovine TCF7L2 to BTA26. Marker CGIL4 was mapped to BTA22 based on homology with published bovine lactoferrin gene sequence.;For protein yield, DNA pools were created from 200 individuals having extreme EBV. These pools were assayed by 86 EcoRI/ TaqI primer sets. A set of 21 promising AFLP fragments was found and the most promising AFLP fragment was characterised as carrying a C ⇔ T single nucleotide polymorphism. A simple PCR test for this SNP was designed and named CGIL3. The frequency of favourable allele T was higher in both Canadian Holstein cows and bulls as compared to allele C, and Canadian Holsteins were dominated by TT genotypes. Logistic regression showed that TT cows were superior to CT cows for protein, milk, and fat yield EBV in the first three lactations and overall yields. In general, the superiority of TT over CT genotype was close to 0.25 SD of EBVs. The pleiotropic effect of QTL linked to CGIL3 on production traits could not be confirmed in Holstein bulls.