Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression.

ssp. (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease.

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments.

The Genome Analysis Toolkit (GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data. The current GATK recommendation for RNA sequencing (RNA-seq) is to perform variant calling from individual samples, with the drawback that only variable positions are reported. Versions 3.

A Meta-Analysis Including Pre-selected Sequence Variants Associated With Seven Traits in Three French Dairy Cattle Populations.

A within-breed genome-wide association study (GWAS) is useful when identifying the QTL that segregates in a breed. However, an across-breed meta-analysis can be used to increase the power of identification and precise localization of QTL that segregate in multiple breeds. Precise localization will allow including QTL information from other breeds in genomic prediction due to the persistence of the linkage phase between the causal variant and the marker.

A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds.

Using GWAS to identify candidate genes associated with cattle morphology traits at a functional level is challenging. The main difficulty of identifying candidate genes and gene interactions associated with such complex traits is the long-range linkage disequilibrium (LD) phenomenon reported widely in dairy cattle. Systems biology approaches, such as combining the Association Weight Matrix (AWM) with a Partial Correlation in an Information Theory (PCIT) algorithm, can assist in overcoming this LD.

A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds.

Background: Domestication and artificial selection have resulted in strong genetic drift, relaxation of purifying selection and accumulation of deleterious mutations. As a consequence, bovine breeds experience regular outbreaks of recessive genetic defects which might represent only the tip of the iceberg since their detection depends on the observation of affected animals with distinctive symptoms. Thus, recessive mutations resulting in embryonic mortality or in non-specific symptoms are likely to be missed.