Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

Abstract

BackgroundBovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling rate are also relevant and usually neglected. The BLV provirus persists throughout a lifetime and an inter-individual variation is observed in the level of infection (LI) in vivo. High LI is strongly correlated with disease progression and BLV transmission among herd mates. In a context of high prevalence, classical control strategies are economically prohibitive. Alternatively, host genomics studies aiming to dissect loci associated with LI are potentially useful tools for genetic selection programs tending to abrogate the viral spreading. The LI was measured through the proviral load (PVL) set–point and white blood cells (WBC) counts. The goals of this work were to gain insight into the contribution of SNPs (bovine 50KSNP panel) on LI variability and to identify genomics regions underlying this trait.ResultsWe quantified anti–p24 response and total leukocytes count in peripheral blood from 1800 cows and used these to select 800 individuals with extreme phenotypes in WBCs and PVL. Two case-control genomic association studies using linear mixed models (LMMs) considering population stratification were performed. The proportion of the variance captured by all QC-passed SNPs represented 0.63 (SE ± 0.14) of the phenotypic variance for PVL and 0.56 (SE ± 0.15) for WBCs. Overall, significant associations (Bonferroni’s corrected -log10p > 5.94) were shared for both phenotypes by 24 SNPs within the Bovine MHC. Founder haplotypes were used to measure the linkage disequilibrium (LD) extent (r2 = 0.22 ± 0.27 at inter-SNP distance of 25−50 kb). The SNPs and LD blocks indicated genes potentially associated with LI in infected cows: i.e. relevant immune response related genes (DQA1, DRB3, BOLA-A, LTA, LTB, TNF, IER3, GRP111, CRISP1), several genes involved in cell cytoskeletal reorganization (CD2AP, PKHD1, FLOT1, TUBB5) and modelling of the extracellular matrix (TRAM2, TNXB). Host transcription factors (TFs) were also highlighted (TFAP2D; ABT1, GCM1, PRRC2A).ConclusionsData obtained represent a step forward to understand the biology of BLV–bovine interaction, and provide genetic information potentially applicable to selective breeding programs.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4523-2) contains supplementary material, which is available to authorized users.

Early events following bovine leukaemia virus infection in calves with different alleles of the major histocompatibility complex DRB3 gene

“…Therefore, it is possible that the polymorphisms at the peptide-binding cleft in MHC class II molecules, responsible for the affinity of the bound peptides, influence the magnitude and extent of the elicited adaptive immune response and therefore the level of the proviral load. A genome-wide scan for single-nucleotide polymorphisms influencing the level of the proviral load in 800 BLV-infected cattle showed that all 24 significant associations were mapped to bovine chromosome 23, delimiting a region within the MHC [50]. Another conceivable mechanism underlying the control of the proviral load could be the action of other polymorphic genes within the MHC, acting independently or in linkage disequilibrium with BoLA-DRB3.…”

Genetic variant of <i>SPARC</i> gene and its association with growth traits in Chinese cattle

“…The single nucleotide polymorphism (SNP) is the one nucleotide variation in the DNA sequence which will produce many polymorphisms in the genome of animals. It involves the transformation or transversion of a single nucleotide, which occurs in the sequence of the encoded protein or in the sequence of introns and intergenic regions (Dang et al, 2014). The SNP which happens in the CDS region will change and affect the protein if the mutation is the missense type.…”

Single nucleotide polymorphism rs110861313 in the intergenic region of chromosome 23 is associated with the development of leukosis in the Russian Black Pied cattle

“…Устойчивость к лейкозу связана с большим количеством генетических маркеров, многие из которых специфичны для отдельных пород КРС (Юдин и др., 2018б). В частности, недавно с помощью полногеномного анализа ассоциаций (GWAS) было идентифицировано несколько однонуклеотидных полиморфных маркеров (ОНП), связанных с чувствительностью КРС к инфекции ВЛКРС (Abdalla et al, 2016;Brym et al, 2016;Carignano et al, 2018). Но все эти исследования были выполнены на КРС голштинской породы и их гибридах.…”

“…Целью исследования была проверка ассоциации ОНП rs110861313 в межгенном участке хромосомы 23 с лейкозом у крупного рогатого скота черно-пестрой породы. Ранее по результатам полногеномного анализа этот ОНП был ассоциирован с провирусной нагрузкой ВЛКРС и количеством лейкоцитов в крови у голштинов и гибридов голштинов с джерси в Аргентине (Carignano et al, 2018).…”