45176

Identification of single nucleotide polymorphisms associated with somatic cell count in dairy buffaloes

Lairana Aline Sardinha  ; Nedenia Bonvino Stafuzza ; Pablo D. Castaño ; Diercles F. Cardoso ; Ana C. Freitas ; Luiz Eduardo Cruz dos Santos Correia ; Humberto Tonhati ; Guilherme C. Venturini
Download
Favorite this paper

Mastitis is a major problem in dairy industry throughout the world because it results in decreases in milk production and alterations in the fat, protein, and total solids content of milk. In order to reduce problems with mastitis, buffalo breeding programs are using genomic tools to identify single nucleotide polymorphisms (SNPs) that affect the somatic cell count (SCC). Therefore, the aim of this study was to identify SNPs associated with SCC in dairy buffaloes. The dataset used was provided by 384 female water buffaloes (Bubalus bubalis), born in 2007 and 2008, from two dairy farms in Rio Grande do Norte and S?o Paulo states, Brazil. The trait studied was SCC with overall average of 7.29 ? 1.17. DNA was extracted from the hair follicles using the phenol-chloroform-isoamyl alcohol method. Genotyping was performed using the Illumina BovineHD BeadChip (containing 777,962 SNPs), with the Infinium(R) HD assay kit and Illumina HiScanTM system, following the manufacturer's recommendations. The consistency of the data was performed using SAS program and the verification of significant effects (P<0.05) were performed by PROC MIXED function of SAS program. After data consistency, a total of 33 contemporary groups (CG) were formed according to herd, year and calving season: dry season (April to September) or rainy season (October-March). For association analysis, it was considered one by one marker using the MACRO command and the MIXED procedure of SAS program. The significance (P<0.05) of each SNP was performed by Student's t test. General model considered the fixed effects of SNP marker (as linear variable defined as 0 (AA), 1 (AB), and 2 (BB)); CG; milking number (2 levels); beyond the covariate age of buffalo (linear and quadratic). From a total of 15,745 SNPs, were identified 166 (P<0.01) and 811 (P<0.05) SNPs associated with SCC. The highest number of statistically significant SNPs at the 1% level was identified on BBU2 (14) and BBU12 (16), while the lowest number was found on BBU23 and BBU5, each one with only one significant SNP. The genomic association study in buffalo allowed the identification of a large number of SNPs associated with SCC, therefore, could be concluded which this SNPs markers affects the buffalo milk quality.