Effect of Runs of Homozygosity on Milk Yield Performance Breeding Value Estimation in Mexican Dairy Cattle

Runs of Homozygosity (ROH) are contiguous lengths of homozygous genotypes present in an animal, and these are a product from mating related individuals or from implementing an intensive selection program. In cattle, ROH have been evaluated and used as an indicator of inbreeding. The purpose of this study was to determine the presence of ROH through the genome of Mexican Holstein cattle and study their effect on milk yield performance. Genotype quality control (QC) excluded animals and markers with call rates <90%, and markers deviated from Hardy Weinberg equilibrium (p<0.0001). After  QC analysis, 727 animals genotyped with the GeneSeek Genomic Profiler GGP-HD Chip and 75,483 markers were used. ROH analysis included lengths of at least 50Kb and 50 Single Nucleotide Polymorphisms (SNP) by region with a minimum frequency of 20 animals. For the analysis, the SVS Golden Helix Software was used. Thirty-three ROH over the whole genome were detected in the population with a length range of 0.1 to 137Mb. When a regression analysis for milk yield estimated breeding values was performed with ROH as covariate, two regions were statistically significant (p<0.01), and those were located on chromosomes 6 and 26 with lengths of 122Mb and 51Mb respectively. The significant ROH have been referenced in the UMD_3.1 database, and the one located on chromosome 6 includes the position of the ABCG2 gene which is related with milk yield and milk quality and the one located on chromosome 26 is related with milk yield and fat and protein percentage.

This work is part of project INIFAP-SIGI: 11402733072 “Aplicación de herramientas genómicas en el mejoramiento genético de la fertilidad del ganado Holstein productor de leche”.