CNVR Detection for Somatic Cell Score Associated to Mastitis in Pooled Mexican Holstein Cattle

Mastitis is the most important trait in dairy cattle and many efforts have been done to improve resistance in dairy populations, but the low heritability makes this process slow. The availability of dense SNP arrays brought the possibility of identifying genomic regions associated to economically important traits in farm animals. Copy Number Variation (CNV) involves more genomic sequences and has potentially more effects than SNP alone. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell score (SCS) through CNV exploration in the Mexican Holstein population.

 200 Mexican Holstein cows and 54 US and CAN Holstein Sires, corresponding to 50 highest and lowest tail trios (sire, dam and daughter) were genotyped using the Illumina BovineSNP777HD array. Log R Ratios (LRR) and BAF were used to perform the CNV analysis using Golden Helix SNP & Variation Suite (SVS) 7.7 and Penncnv software. Association analyses were carried out using the EBV for SCS.

 After QC, 220 samples remained corresponding to 37 and 36 trios for the higher and lower tails, respectively. 248 CNV regions were found in common after consensus between those identified in the both software. 39 CNVRs and 38 CNVRs are resulted to be significantly associated with SCS, using Golden and CNVRuler, respectively.

 We acknowledge the Council of Dairy Cattle Breeding and Holstein de Mexico A.C. for sharing genomic data. This work received funding from CONACYT, México (project “IDENTIFICACIÓN DE VARIACIONES ESTRUCTURALES Y REGIONES GENÓMICAS ASOCIADAS A RESISTENCIA A MASTITIS EN BOVINOS PRODUCTORES DE LECHE”, 176039).