Candidate gene association analysis for milk yield, composition, urea nitrogen and somatic cell scores in Brown Swiss cows

Abstract

The aim of this study was to investigate 96 single-nucleotide polymorphisms (SNPs) from 54 candidate genes, and test the associations of the polymorphic SNPs with milk yield, composition, milk urea nitrogen (MUN) content and somatic cell score (SCS) in individual milk samples from Italian Brown Swiss cows. Milk and blood samples were collected from 1271 cows sampled once from 85 herds. Milk production, quality traits (i.e. protein, casein, fat and lactose percentages), MUN and SCS were measured for each milk sample. Genotyping was performed using a custom Illumina VeraCode GoldenGate approach. A Bayesian linear animal model that considered the effects of herd, days in milk, parity, SNP genotype and additive polygenic effect was used for the association analysis. Our results showed that 14 of the 51 polymorphic SNPs had relevant additive effects on at least one of the aforementioned traits. Polymorphisms in the glucocorticoid receptor DNA-binding factor 1 ( GRLF1), prolactin receptor ( PRLR) and chemokine ligand 2 ( CCL2) were associated with milk yield; an SNP in the stearoyl-CoA desaturase ( SCD-1) was related to fat content; SNPs in the caspase recruitment domain 15 protein ( CARD15) and lipin 1 ( LPIN1) affected the protein and casein contents; SNPs in growth hormone 1 ( GH1), lactotransferrin ( LTF) and SCD-1 were relevant for casein number; variants in beta casein ( CSN2), GH1, GRLF1 and LTF affected lactose content; SNPs in beta-2 adrenergic receptor (ADRB2), serpin peptidase inhibitor (PI) and SCD-1 were associated with MUN; and SNPs in acetyl-CoA carboxylase alpha (ACACA) and signal transducer and activator of transcription 5A ( STAT5A) were relevant in explaining the variation of SCS. Although further research is needed to validate these SNPs in other populations and breeds, the association between these markers and milk yield, composition, MUN and SCS could be exploited in gene-assisted selection programs for genetic improvement purposes.

Genetic variation and effects of candidate-gene polymorphisms on coagulation properties, curd firmness modeling and acidity in milk from Brown Swiss cows

“…However, since CSN2 rs109299401 (which distinguishes the I allele from the A 2 allele) and CSN2 rs43703012 (which distinguishes the A 3 allele from the A 2 allele) were found to be monomorphic in the present population, the C allele herein acts as a marker of the CSN2*A 2 variant, whereas the A allele (frequency of 0.23) corresponds to the A 1 , B and (rarely) C variants (Caroli et al, 2009). As noted by Cecchinato et al (2014), the CSN2 rs43703013 C allele discriminates the B and C alleles from the A 1 allele. Here, the B allele (frequency, 0.16) was overrepresented compared with the A 1 allele (0.07) in the CSN2 rs43703011 allele C genes.…”

“…Briefly, a total of 1271 Brown Swiss cows from 85 herds located in Trento Province (Italy) were sampled once. Details on the milk sampling procedure, cows, herds and pedigree were previously reported (Cecchinato et al, 2014).…”

“…Blood sampling, DNA extraction, SNP selection and genotyping Blood sampling, DNA extraction and SNP selection and genotyping were performed as previously described (Cecchinato et al, 2014). Briefly, DNA was extracted using a DNeasy ® 96 Blood & Tissue Kit (Qiagen, Hilden, Germany) from 100 µl of individual whole blood, quantified using the QBit system (Invitrogen, Carlsbad, CA, USA) and assessed for integrity by 1% agarose gel electrophoresis.…”

“…The 96 selected SNPs, which are located in 54 genes and span 22 chromosomes, were genotyped with the GoldenGate system (Illumina, San Diego, CA, USA). We retained 51 polymorphic SNPs (in 37 candidate genes) for the association analysis (Cecchinato et al, 2014).…”

“…In a previous study (Cecchinato et al, 2014), we analyzed 96 SNPs in 54 candidate genes within a population of Brown Swiss cows. We retained 51 polymorphic SNPs (in 37 candidate genes) for an association analysis with milk yield, composition, milk urea nitrogen content and somatic cell score.…”