Genome-wide association study for stature in New Zealand dairy cattle : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science at Massey University, Palmerston North, New Zealand
The objective of this thesis was to perform a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) associated with stature in New Zealand dairy cattle. The phenotype data set used for this study contained the animal key, sire code of the bull, birth date, breed code, proportion of Holstein-Friesian genes, proportion of Jersey genes, percentage of North American Holstein genes, estimated breeding values (EBV) for live weight and stature and their reliabilities of 3140 bulls. The genotype data set contained the genotype of 692,598 SNPs for every bull and another file contained the name and position of the SNPs.
The GWAS was performed on Holstein-Friesian, Jersey and Holstein-Friesian × Jersey crossbred bulls using PLINK software version 1.07. Stature EBV was used as the phenotype. The phenotypes were adjusted for percentage of Holstein-Friesian, Jersey, North American Holstein genes and year of birth using multiple regression. Manhattan plots and multi Manhattan plots of P-values adjusted to genomic control against the chromosomes were plotted to identify top SNPs with the most significant P-values above the significant threshold line.
Based on the top 50 SNPs according to the P-value, this study identified nine chromosomes or BTA in the HF population with SNPs significantly associated with stature, BTA2, 3, 4, 5, 6, 11, 12, 14 and 24. SNPs with significant effect on stature were detected in six chromosomes, BTA9, 10, 12, 18, 19 and 25 in the JE population while the SNPs determined to be significantly associated with stature were located on eleven chromosomes, BTA1, 3, 4, 5, 7, 9, 10, 14, 18, 22 and 24 in the XB population. Several SNPs located above the suggestive threshold in the Manhattan plots were also inspected and kept in view for future studies.
The results from this study suggest that the highlighted SNPs with significant associations to stature can serve as candidate SNPs for further investigation to determine the regions of QTLs and ultimately the exact genes that affect stature with other correlated traits in dairy cattle.