Association of CD4 SNPs with fat percentage of Holstein cattle

Abstract

ABSTRACT. Cluster of differentiation 4 gene (CD4) is well known for its role in immunity, but its effects on production traits remain to be elucidated. The present study was designed to explore single nucleotide polymorphisms (SNPs) in the exons, flanking introns, and promoter of CD4, as well as to analyze their effects on milk production traits (percentage of protein, fat, and lactose; mastitis indicator traits somatic cell count; and somatic cell score). A total of 10 SNPs, including eight in the exon and two in the intron regions, were identified using pooled DNA sequencing. These SNPs were screened in a population of 258 Chinese Holstein using the SNaPshot technique. We analyzed the effects of SNPs, parity, herd, year, and season of calving on the production and mastitis indicator traits. Our analysis revealed two haplotypes and strong linkage disequilibrium (D' > 0.97) among all SNPs. All 10 SNPs were significantly associated with fat percentage (P < 0.01). Cows homozygous for the wild-type genotypes had higher fat percentages than those with the other genotypes. The dominant and additive effects were also significant for fat percentage (P < 0.05). These results suggest that CD4 plays a role in production traits as well as in immune function. The identified SNPs could be used as genetic markers for selection of dairy cows with improved fat percentage. We propose further studies of these SNPs in a larger population as well as further investigations of the function of this gene.

Novel SNPs and haplotypes identified in theCD4gene and their influence on deregressed MACE EBV indexes of milk-related traits in Simmental breed

“…This study documents the occurrence of several polymorphisms in the genomic sequence of the entire CD4 gene in a sample of Simmental genomic sires. Many of these polymorphisms, as already reported by other authors (Usman et al, 2016;Zeb et al, 2020), were in perfect linkage disequilibrium in the surveyed 34 genomes. In the present work we investigated the possible effect of genomic variants in CD4 on the deregressed MACE EBV indexes for SCS, an indicator of udder health status and for milk quality and quantity.…”

“…The analysis of the genetic variants of the CD4 gene highlights that SNP 11 (rs110955838) is in very close linkage disequilibrium with most of the variants present in the coding and regulatory areas of the gene. This is also evident from the results obtained by other authors in the analysis of the association between some SNPs of CD4 and production traits in dairy cattle (Usman et al, 2016;Zeb et al, 2020). He et al (2011) reported a significant association between the SNP g.13598 C > T of the CD4 gene in intron 6, which corresponds to the SNP 29 (rs110421401) and which is in perfect linkage disequilibrium with the SNP 11, with the production traits of milk and protein yield in Chinese Holsteins, in agreement with our results on Simmental sires.…”

“…In their study, the authors also highlighted a significant effect on the somatic cell score trait, which is not highlighted in our data. Other studies reported association of SNPs in CD4 gene with fat percentage but not with SCS (Usman et al, 2016), as well as Zeb et al (2020) that describe a significant association with the frequency of clinical mastitis but not with SCS. The same authors identify possible reasons for these discrepancies in the differences in the breeds of cattle, the environment conditions, and population structure.…”

“…Sixteen SNPs (1, 9 ÷ 18, 21, 22, 25, 28 and 29), one half of the total number, were 100% in linkage disequilibrium (LD = 1). Out of these, one was chosen for the association analysis based on its location in the coding region of the gene and because it had already been used by other authors (Usman et al, 2016;Zeb et al, 2020) in association tests in dairy cattle: SNP 11 (rs110955838) in exon 2. Ten more SNPs with LD < 0.9: SNP 2 (rs109536830), SNP 3 (rs211555032), SNP 5 (rs110147215), SNP 7 (rs110894017), SNP 8 (rs110774456), SNP 19 (novel), SNP 20 (novel), SNP 27 (rs136156940), SNP 30 (novel), and SNP 31 (rs136340758) were processed for the estimation of their associations with phenotypes (deregressed MACE EBV indexes of milk, fat and protein yields, and SCS) as function of their genotype.…”

“…He et al (2011) highlighted a significant association between SNPs within CD4 gene with mastitis indicators and milk production traits. Usman et al (2016) showed a significant association between some SNPs of the CD4 gene (between exon 2 and intron 6) and the percentage of fat in milk. Recently, Zeb et al (2020) showed that four SNPs between exon 2 and exon 4 of the CD4 gene were significantly associated with clinical mastitis incidence and with annual milk yield.…”