The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease

Lipkin, E.; Strillacci, M.G.; Eitam, Harel; Yishay, M.; Schiavini, F.; Soller, M.; Bagnato, A.; Shabtay, Ariel

doi:10.1371/journal.pone.0153423

Cited by 22 publications

(36 citation statements)

References 68 publications

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“…An objective QTL selection logic is therefore paramount. In contrast to a study by Lipkin et al (2016) that considered P-values only, our QTL selection logic accounted for both Pvalues and the long-range LD (r 2 ) usually observed in dairy cattle. In our study, we report 11 MS QTL, of which 4 QTL are in limited pleiotropy with CM and SCS, suggesting that faster milking cows can be selected for, at least with QTL reported here, with only minimal risk of increases in SCS or CM.…”

Section: Discussionmentioning

confidence: 83%

Genome-wide association study for milking speed in French Holstein cows

Marete¹,

Sahana²,

Fritz³

et al. 2018

Journal of Dairy Science

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Using a combination of data from the BovineSNP50 BeadChip SNP array (Illumina, San Diego, CA) and a EuroGenomics (Amsterdam, the Netherlands) custom single nucleotide polymorphism (SNP) chip with SNP pre-selected from whole genome sequence data, we carried out an association study of milking speed in 32,491 French Holstein dairy cows. Milking speed was measured by a score given by the farmer. Phenotypes were yield deviations as obtained from the French evaluation system. They were analyzed with a linear mixed model for association studies. We identified SNP on 22 chromosomes significantly associated with milking speed. As clinical mastitis and somatic cell score have an unfavorable genetic correlation with milking speed, we tested whether the most significant SNP on these 22 chromosomes associated with milking speed were also associated with clinical mastitis or somatic cell score. Nine hundred seventy-one genome-wide significant SNP were associated with milking speed. Of these, 86 were associated with clinical mastitis and 198 with somatic cell score. The most significant association signals for milking speed were observed on chromosomes 7, 8, 10, 14, and 18. The most significant signal was located on chromosome 14 (ZFAT gene). Eleven novel milking speed quantitative trait loci (QTL) were observed on chromosomes 7, 10, 11, 14, 18, 25, and 26. Twelve candidate SNP for milking speed mapped directly within genes. Of these, 10 were QTL lead SNP, which mapped within the genes HMHA1, POLR2E, GNB5, KLHL29, ZFAT, KCNB2, CEACAM18, CCL24, and LHPP. Limited pleiotropy was observed between milking speed QTL and clinical mastitis.

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Section: Discussionmentioning

confidence: 83%

Genome-wide association study for milking speed in French Holstein cows

Marete¹,

Sahana²,

Fritz³

et al. 2018

Journal of Dairy Science

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“…Neibergs et al [ 35 ] estimated heritability of BRD incidence to be 17% and 29% when using case-control or graduated scoring analyses, respectively, as opposed to binomial (yes or no) morbidity classification. Recent findings of QTL associated with BVD persistent infection [ 18 ] and BRD susceptibility or response [ 19 , 20 , 21 ] also provide evidence for continued genetic investigation regarding host-pathogen interactions. Increases in U.S. feedlot mortality from the early 1990s into the 2000s [ 36 , 37 ] attributed to BRD is perplexing given improved vaccination recommendations and implementation of beef quality assurance programs.…”

Section: Resultsmentioning

confidence: 99%

“…Investigations regarding cattle breed and family influences on BRD incidence [ 8 , 9 , 16 , 17 ] have shown selection potential for improved health, but are very limited, particularly for specific BRD pathogens. Recent findings have identified genomic regions affecting BRD incidence or responses [ 18 , 19 , 20 , 21 ], and improved understanding of complex host-pathogen relationships require detailed phenotypes and quantifiable causative components to advance potential cattle management strategies. The objective of this study was to investigate potential interactions of sire lines with BRD vaccine treatments on weight gain and feed intake following a standardized BVDV1b challenge under common U.S. cattle management and production conditions.…”

Section: Introductionmentioning

confidence: 99%

Feed Intake and Weight Changes in Bos indicus-Bos taurus Crossbred Steers Following Bovine Viral Diarrhea Virus Type 1b Challenge Under Production Conditions

et al. 2017

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Bovine viral diarrhea virus (BVDV) has major impacts on beef cattle production worldwide, but the understanding of host animal genetic influence on illness is limited. This study evaluated rectal temperature, weight change and feed intake in Bos indicus crossbred steers (n = 366) that were challenged with BVDV Type 1b, and where family lines were stratified across three vaccine treatments of modified live (MLV), killed, (KV) or no vaccine (NON). Pyrexia classification based on 40.0 °C threshold following challenge and vaccine treatment were investigated for potential interactions with sire for weight change and feed intake following challenge. Pyrexia classification affected daily feed intake (ADFI, p = 0.05), and interacted with day (p < 0.001) for ADFI. Although low incidence of clinical signs was observed, there were marked reductions in average daily gain (ADG) and cumulative feed intake during the first 14 day post-challenge; ADG (CV of 104%) and feed efficiency were highly variable in the 14-day period immediately post-challenge as compared to the subsequent 14-day periods. A sire × vaccine strategy interaction affected ADFI (p < 0.001), and a sire by time period interaction affected ADG (p = 0.03) and total feed intake (p = 0.03). This study demonstrates that different coping responses may exist across genetic lines to the same pathogen, and that subclinical BVDV infection has a measurable impact on cattle production measures.

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“…Nevertheless, visual inspection of the chromosomal Manhattan plots by families showed distinct clusters of markers with high −LogP values intermixed with markers with low −LogP values ( Figure 1 ). Therefore, following Lipkin et al [ 41 ], we identified QTL by using a moving average of −LogP (mAvg) to smooth the Manhattan plots. We used a window size of ~0.1 Mb (27 markers) with a step size of 1 marker and a critical threshold mAvg of −LogP = 2.0 ( p = 0.01) to declare significance, and Log drop 1 [ 42 ] to define QTLR boundaries.…”

Section: Methodsmentioning

confidence: 99%

Mapping QTL Associated with Resistance to Avian Oncogenic Marek’s Disease Virus (MDV) Reveals Major Candidate Genes and Variants

Smith

Lipkin

Soller

et al. 2020

Genes

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Marek’s disease (MD) represents a significant global economic and animal welfare issue. Marek’s disease virus (MDV) is a highly contagious oncogenic and highly immune-suppressive α-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The Major Histocompatability Complex (MHC) is known to play a role in disease resistance, along with a handful of other non-MHC genes. In this study, one of the largest to date, we used a multi-facetted approach to identify QTL regions (QTLR) influencing resistance to MDV, including an F6 population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in eight pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, miRNAs, lncRNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using eight pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped and candidate genes identified. Various QTLR elements were shown to have a strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy, whether by means of selective breeding, improved vaccine design, or gene-editing technologies.

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The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease

Cited by 22 publications

References 68 publications

Genome-wide association study for milking speed in French Holstein cows

Genome-wide association study for milking speed in French Holstein cows

Feed Intake and Weight Changes in Bos indicus-Bos taurus Crossbred Steers Following Bovine Viral Diarrhea Virus Type 1b Challenge Under Production Conditions

Mapping QTL Associated with Resistance to Avian Oncogenic Marek’s Disease Virus (MDV) Reveals Major Candidate Genes and Variants

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