Haplotype Disequilibrium in the TLR Genes of Czech Red Pied Cattle

Abstract

Hybrid resequencing of the antibacterial innate immune genes coding for toll-like receptors, namely TLR1, TLR2, TLR4, TLR5, and TLR6, using HiSeq and PacBio technologies of pooled population samples of Czech Simmental (Czech Red) cattle allowed us to determine haplotypes formed by the polymorphisms present. Directly determined haplotypes within the range of the large proximal amplicon in TLR2 formed two clusters in the network tree graph. The distribution of the statistically reconstructed haplotypes based on individual genotyping of the present SNPs was consistent. Similarly, the statistically reconstructed haplotypes in TLR5 and TLR6 formed two clusters. The trend of bimodal distribution was also observed in TLR4, while the limited diversity of TLR1 did not allow for any conclusion. The observed bimodal distribution is consistent with earlier reports for cattle populations worldwide. The stability of this phenomenon cannot be ascribed to historical origin but rather to a long-term effect of balancing selection. The equilibrium might be based on two different essential functions performed by the TLR genes or their products. The formation of two kinds of heterodimers by the TLR2 product, namely, TLR2/TLR1 and TLR2/TLR6 with different ligand specificities, is considered to be a particular case. On the other hand, the better expression of the bimodal groups in the 5′-proximal SNPs supports the localization of the selection targets in the upstream regulatory regions or the functional interactions in the proximal part of the transcripts.

Association of Variants in Innate Immune Genes TLR4 and TLR5 with Reproductive and Milk Production Traits in Czech Simmental Cattle

“…In gene TLR5, tentative associations of the neutral SNPs with reproductive traits were observed as well. Mutually similar association patterns for the early reproductive traits observed in SNPs g.545, g.3714, and g.4628 might reflect the absolute linkage of g.545 and g.3714 consistently with two major TLR5 haplotypes [20].…”

“…The genotyped SNPs are probably not the true causal variants and could just be in linkage disequilibrium with the causal SNPs in extended haplotypes covering the regulatory regions [28]. The haplotype structure in the coding regions of TLR4 and TLR5 in the CRP population was described by Novák et al [29] and Samaké and Novák [20].…”

“…The allelic frequencies based on individual genotyping data were matched with the frequencies derived from the NGS read representation (averaged for the two technologies used). The NGS-based frequencies and genotyping-based frequencies were partially published elsewhere [16,20]. The Hardy-Weinberg (H-W) equilibrium of the genotype classes was tested with the χ 2 criterion.…”

“…When considered in detail, allele g.5087A was associated with g.9422C and g.9787C in haplotype A2, according to the traditional classification of the TLR4 haplotypes [14,20], while the complementary allele g.5087G was paralleled with the bases g.9422T and g.9787T in haplotypes A5 and B1, respectively. Consistently with this assumption, the g.5087A>Glinked mutations g.9422T>C (rs8193060), albeit synonymous, were associated with reproductive traits, including maternal calving ease, in our work.…”

“…Consistently with this assumption, the g.5087A>Glinked mutations g.9422T>C (rs8193060), albeit synonymous, were associated with reproductive traits, including maternal calving ease, in our work. Another SNP linked to g.5087A>G in these haplotypes, g.9787C>T (c.2021) [14,20], is known to affect signal transfer due to the functionally relevant amino acid change (Thr674Ile) in the transmembrane region of the molecule [14]. This mutation has been traditionally studied due to its demonstrated association with somatic cell score [11,12].…”