A candidate gene association study for nine economically important traits in Italian Holstein cattle

Abstract

We genotyped 58 single nucleotide polymorphisms (SNPs) in 25 candidate genes in about 800 Italian Holstein sires. Fifty-six (minor allele frequency >0.02) were used to evaluate their association with single traits: milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP), milk protein percentage (PP), milk somatic cell count (MSCC); and complex indexes: longevity, fertility and productivity-functionality type (PFT), using deregressed proofs, after adjustment for familial relatedness. Thirty-two SNPs were significantly associated (proportion of false positives <0.05) with different traits: 16 with MSCC, 15 with PY, 14 with MY, 12 with PFT, eight with longevity, eight with FY, eight with PP, five with FP and two with fertility. In particular, a SNP in the promoter region of the PRLR gene was associated with eight of nine traits. DGAT1 polymorphisms were highly associated with FP and FY. Casein gene markers were associated with several traits, confirming the role of the casein gene cluster in affecting milk yield, milk quality and health traits. Other SNPs in genes located on chromosome 6 were associated with PY, PP, PFT, MY (PPARGC1A) and MSCC (KIT). This latter association may suggest a biological link between the degree of piebaldism in Holstein and immunological functions affecting somatic cell count and mastitis resistance. Other significant SNPs were in the ACACA, CRH, CXCR1, FASN, GH1, LEP, LGB (also known as PAEP), MFGE8, SRC, TG, THRSP and TPH1 genes. These results provide information that can complement QTL mapping and genome-wide association studies in Holstein.

Association of 20 candidate gene markers with milk production and composition traits in sires of Reggiana breed, a local dairy cattle population

“…The strong effects of the DGAT1 p.K232A mutation in Reggiana sires confirm its relevant effects already shown in other dairy cattle breeds (e.g., Grisart et al, 2002;Winter et al, 2002). However, two differences were noted compared to studies in other breeds (e.g., Spelman et al, 2002;Thaller et al, 2003;Sanders et al, 2006;Fontanesi et al, 2014): 1) the absence of relevant effect on MY and 2) the positive effect of the KA genotype on PY compared to the AA genotype. In most other breeds genotype AA increases MY and PY compared to the other two genotypes, whereas in Reggiana no significant effects were noted for MY (MY was just above the P nominal threshold of 0.10; data not shown).…”

“…Of the three CRH missense mutations that were genotyped, only the p.S45D showed significant or suggestively significant associations with FY and PP, respectively (Table 3). This polymorphism was associated with PY and PP in Holstein (Fontanesi et al, 2014) with a similar effect (namely genotype DD increased PY, FY and PP trait values compared to the other genotypes in both breeds). This gene is centered in a QTL region located in the middle of BTA14 that is clearly separated from the telomeric QTL region that includes the effects of the DGAT1 gene (Russo et al, 2012).…”

“…The significant (PY) and suggestively significant (FY and MY) associations of the TG polymorphism confirm the complex QTL situation on the proximal part of BTA14. The TG gene was first associated with beef marbling (Barendse, 1999) and subsequently with milk production traits in Holstein, but with contrasting results (Khatib et al, 2007;Fontanesi et al, 2014). The TT genotype, that in beef cattle was associated with a higher marbling score (Casas et al, 2007), positively affected the three previously indicated milk production traits in Reggiana (Table 3).…”

“…Thus, to account for multiple testing we applied the Proportion of False Positives (PFP; Fernando et al, 2004) approach. PFP threshold was calculated as described by Bagnato et al (2008) and applied by Fontanesi et al (2014) in association studies with candidate genes. In the present study a P PFP ¼0.10, corresponding to a P nominal value of $0.01, was considered as the threshold level for significance.…”

Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size

“…The identification of candidate genes responsible for variation in quantitative traits has been a challenge in modern genetics (Fontanesi et al 2014). Until now, no references have been given on the role of GnIH in the control of litter size in animals.…”