Identification of TLR polymorphisms of the main cattle breeds in russia

NOVÁK, Karel, DUNIN, M.I. a KALASHNIKOV, A.E. Identification of TLR polymorphisms of the main cattle breeds in russia. Journal of Animal Science, 2016, roč. 94(Supplement 4), s. Supplement 4, 90-91. ISSN .
Kateg. publikaceOstatní..
Interní odkaz16221.pdf

The study of the genetic structure and variability of the Toll-like receptors (TLR) in cattle is aimed to detect polymorphisms, which are responsible for resistance of cattle breeds in Russia for important infections. On the other hand, it is important to know how structural changes of TLR in natural killers (NK) and other immune cells affects the detection of pathogens. The survey comprised Russian breeds Kholmogory — both pure Pechersky type and a hybrid with Holstein, Yaroslavl — both the pure type and a hybrid with Holstein, Simmental-milk type, Yakut, Yakut x Simmental crossbreed, Simmental-meat type, Kholmogory breed of Yakutian origin, Kholmogory x Yakut breed, Black pied and a bovine hybrid with wood bison in a total number of N = 275. The target region comprised coding sequences of TLR1–TLR10 and was amplified in a series of 80 overlapping PCR reactions. The sequencing on PacBio platform provided reads from 400 to 1200 nt long with 3–12x coverage for individual animals. The groups of antibacterial (TLR1, 2, 4, 5, 6) and antiviral (TLR3, 7, 8, 9, 10) members of the TLR family were processed in separate pools. After primary data processing with the RS Touch and Dashboard software (Pacific Biosciences), an independently developed pipeline for processing long reads, which are characteristic for PacBio technology, was applied. The bioinformatic processing comprised primary data quality check with FastQC (PicardTools) and filtering quality (, assembly with Ugene and removal of duplicate with Picard tools, followed by variant calling using SAMtools, Free Bayers and filtration with VCFFilter. The annotation of the found polymorphisms was performed using VeIP. The detected polymorphism was assigned to individual animals with subsequent genotyping

OdděleníGenetika a šlechtění hospodářských zvířat