Genomic Regions Associated to the Mexican Performance Index for Holstein Cattle

Dairy selection has focused on increasing milk yield in the final decades of the last century affecting negatively some traits. As a result, performance indices have been proposed in many populations and powerful techniques as Genome Wide Association Studies (GWAS) have been used to detect genes or quantitative traits loci (QTL) to improve genetic selection. The aim of this study was to identify significant SNP associated with the Mexican Performance Index (INVAC), and to investigate if the significant SNP have been previously reported in the UMD_3.1 database. The phenotypes were breeding values for INVAC which includes milk yield, mil components and conformation final score. After the quality control analysis, a total of 21,152 SNP and 1,895 animals were included. GWAS were performed with a mixed model and regression analysis, accounting for the genomic kinship matrix, using the GenABEL package. SNP with a p<0.0001 were assumed significant and searched in the QTL database. Chromosomes and position of the significant SNP found are: 3:28061335, 4:59710881, 5:41565285, 7:38458456, 10:95629821, 12:60863971, 13:29718368, 14:(1801116, 2217163, 2239085, 2386688, 2826632, 2909929, 4176618, 4364952, 5462752), 15:77142114, 16:16475491, 20:70333233, 20:71067704, 20:71094690, 22:7022169, 31:143626961. Contiguous significant SNP were only located on chromosome 14 and two regions were differentiated, one from 1801116-2909929 and the other from 4176618-5462752. The first one has been associated to milk yield, fat and protein yields and percentages, somatic cell score, body condition and conception rate and the second one, has been related with milk yield, fat and protein percentages in dairy cattle.