Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. H...

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Bibliographic Details
Published in:Animal biotechnology 2017-07, Vol.28 (3), p.228-236
Main Authors: Novák, Karel, Pikousová, Jitka, Czerneková, Vladimíra, Mátlová, Věra
Format: Article
Language:English
Subjects:
Animals
Breeding
Cattle
Cattle - genetics
Czech Republic
Female
Fragments
Gene sequencing
genetic resources
Genotyping
Genotyping Techniques
Haplotypes
Immune system
Immunity
innate immunity
Livestock breeding
Male
Next-generation sequencing
Polymerase chain reaction
Polymorphism, Single Nucleotide - genetics
Proteins
Single-nucleotide polymorphism
TLR4 protein
Toll-Like Receptor 4 - genetics
Toll-like receptors
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Summary:The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.
ISSN:1049-5398
1532-2378
DOI:10.1080/10495398.2017.1279170