@article{poole_mayberry_newsome_poole_galliou_khanal_poore_serao_2020, title={Evaluation of Resistance to Fescue Toxicosis in Purebred Angus Cattle Utilizing Animal Performance and Cytokine Response}, volume={12}, ISSN={["2072-6651"]}, DOI={10.3390/toxins12120796}, abstractNote={Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue; however, varying symptomatic responses potentially imply genetic tolerance to the syndrome. It was hypothesized that a subpopulation of animals within a herd would develop tolerance to ergot alkaloid toxicity. Therefore, the goals of this study were to develop selection criteria to identify tolerant and susceptible animals within a herd based on animal performance, and then examine responsive phenotypic and cytokine profiles to fescue toxicosis. Angus cows grazed endophyte-infected tall fescue at two locations for 13 weeks starting in mid-April 2016. Forage measurements were collected to evaluate ergot alkaloid exposure during the study. A post hoc analysis of animal performance was utilized to designate cattle into either tolerant or susceptible groups, and weekly physiological measurements and blood samples were collected to evaluate responses to chronic exposure to endophyte-infected tall fescue. Findings from this study support the proposed fescue toxicosis selection method formulated herein, could accurately distinguish between tolerant and susceptible animals based on the performance parameters in cattle chronically exposed to ergot alkaloids, and provides evidence to warrant additional analysis to examine the impact of ergot alkaloids on immune responsiveness in cattle experiencing fescue toxicosis.}, number={12}, journal={TOXINS}, author={Poole, Daniel H. and Mayberry, Kyle J. and Newsome, McKayla and Poole, Rebecca K. and Galliou, Justine M. and Khanal, Piush and Poore, Matthew H. and Serao, Nick V. L.}, year={2020}, month={Dec} }
 @article{galliou_khanal_mayberry_poore_poole_serao_2020, title={Evaluation of a commercial genetic test for fescue toxicosis in pregnant Angus beef cattle}, volume={4}, ISSN={["2573-2102"]}, DOI={10.1093/tas/txaa181}, abstractNote={Abstract
               Most tall fescue [Lolium arundinaceum (Schreb.) Darbysh] in the Southeastern United States contains an endophyte that causes fescue toxicosis (FT) in grazing animals, a serious disease that causes approximately $1 billion in economic losses to the animal industries in the United States. Recently, a genetic test called T-Snip (AgBotanica, LCC, Columbia, MO), was developed with the objective of identifying animals with genetic variation for FT tolerance. The aim of this study was to validate the use of this genetic test in mature, pregnant cows. Over 13 wk, weekly phenotypic data, including body weight, rectal temperatures, hair coat scores, hair shedding scores, and body condition scores, were collected on 148 pregnant purebred Angus cows at 2 locations in NC where infected fescue was the primary source of feed. Birth weights (cBW) and 205-d adjusted weaning weights (adjWW) from these cow’s calves were recorded. All cows were genotyped for T-Snip. At the end of the trial, each phenotypic trait was calculated as the slope of the linear regression of performance on weeks. The effect of T-Snip rating genotypes (4 levels) on slope traits was tested using a linear model also including the fixed-effects of location, parity, and the initial measurement for each trait (covariate). For cBW and adjWW, the model also included the sex of the calf and the month of birth as categorical effects. Associations of T-Snip genotypes were observed for body weight gain (aBWd) of pregnant cows (P = 0.15; interaction with location), change in body condition score (aBCSd; P = 0.13), and adjWW (P = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location (P = 0.017 and 0.047, respectively), which was the location with higher endophyte infection rate. For all associations, the direction of the T-Snip genotypes was the same and as expected: the greater the genotype score, the better performance. No associations were found for the other traits (P > 0.10). These results indicate that the T-Snip test may be predictive of cow performance (aBWd, aBCSd, and adjWW) in an endophyte-infected tall fescue environment.}, number={4}, journal={TRANSLATIONAL ANIMAL SCIENCE}, author={Galliou, Justine M. and Khanal, Piush and Mayberry, Kyle and Poore, Matt H. and Poole, Daniel H. and Serao, Nick V. L.}, year={2020}, month={Oct} }
 @article{khanal_maltecca_schwab_fix_bergamaschi_tiezzi_2020, title={Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine}, volume={52}, ISBN={1297-9686}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85088852317&partnerID=MN8TOARS}, DOI={10.1186/s12711-020-00561-7}, abstractNote={Abstract
Background
The objectives of this study were to evaluate genomic and microbial predictions of phenotypes for meat quality and carcass traits in swine, and to evaluate the contribution of host-microbiome interactions to the prediction. Data were collected from Duroc-sired three-way crossbred individuals (n = 1123) that were genotyped with a 60 k SNP chip. Phenotypic information and fecal 16S rRNA microbial sequences at three stages of growth (Wean, Mid-test, and Off-test) were available for all these individuals. We used fourfold cross-validation with animals grouped based on sire relatedness. Five models with three sets of predictors (full, informatively reduced, and randomly reduced) were evaluated. ‘Full’ included information from all genetic markers and all operational taxonomic units (OTU), while ‘informatively reduced’ and ‘randomly reduced’ represented a reduced number of markers and OTU based on significance preselection and random sampling, respectively. The baseline model included the fixed effects of dam line, sex and contemporary group and the random effect of pen. The other four models were constructed by including only genomic information, only microbiome information, both genomic and microbiome information, and microbiome and genomic information and their interaction.

Results
Inclusion of microbiome information increased predictive ability of phenotype for most traits, in particular when microbiome information collected at a later growth stage was used. Inclusion of microbiome information resulted in higher accuracies and lower mean squared errors for fat-related traits (fat depth, belly weight, intramuscular fat and subjective marbling), objective color measures (Minolta a*, Minolta b* and Minolta L*) and carcass daily gain. Informative selection of markers increased predictive ability but decreasing the number of informatively reduced OTU did not improve model performance. The proportion of variation explained by the host-genome-by-microbiome interaction was highest for fat depth (~ 20% at Mid-test and Off-test) and shearing force (~ 20% consistently at Wean, Mid-test and Off-test), although the inclusion of the interaction term did not increase the accuracy of predictions significantly.

Conclusions
This study provides novel insight on the use of microbiome information for the phenotypic prediction of meat quality and carcass traits in swine. Inclusion of microbiome information in the model improved predictive ability of phenotypes for fat deposition and color traits whereas including a genome-by-microbiome term did not improve prediction accuracy significantly.
}, number={1}, journal={GENETICS SELECTION EVOLUTION}, author={Khanal, Piush and Maltecca, Christian and Schwab, Clint and Fix, Justin and Bergamaschi, Matteo and Tiezzi, Francesco}, year={2020} }
 @article{mayberry_poole_newsome_khanal_poore_serao_poole_2019, title={Evaluation of cytokine response as an indicator of genetic resistance to fescue toxicosis in purebred Angus cattle.}, volume={97}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skz053.102}, abstractNote={Abstract
               Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue. However, varying responses among cattle potentially implies genetic tolerance to the syndrome. Therefore, the objective was to evaluate the cytokine response of cows deemed either tolerant or susceptible to endophyte-infected fescue. Angus cows, 2–4 yrs old, grazed endophyte-infected tall fescue at two locations for 13 weeks starting mid-April 2016. A post-hoc analysis of animal performance was utilized to designate cattle into either tolerant (n = 20) or susceptible (n = 20) groups, based on physiological responses (changes in ADG) to chronic exposure to endophyte-infected fescue. Blood samples collected on weeks 1, 7, and 13 were used to evaluate serum prolactin (PRL) concentration. Cytokine concentrations were evaluated via Quantibody Bovine Cytokine Arrays. Data were analyzed using PROC MIXED of SAS with repeated measures. There were no differences by location or week. Tolerant cows tended to have decreased overall PRL concentrations compared to susceptible cows (98.3 and 138.4 ng/mL, respectively; P = 0.08). G protein-coupled receptor associated sorting protein (GASP)-1, a down-regulator of G protein-coupled receptors including D2-dopamine receptor a regulator of PRL secretion, was greater in tolerant cows when compared to susceptible cows (4.7 and 4.2 ng/mL; P = 0.03). Vascular endothelial growth factor (VEGF)-A was greater in tolerant cows when compared to susceptible cows (0.5 and 0.2 ng/mL; P = 0.02). Finally, interleukin (IL)-4, an anti-inflammatory cytokine, tended to be greater in tolerant cows when compared to susceptible cows (2.2 and 0.8 ng/mL, respectively; P = 0.07). Based on these data, greater concentrations of GASP-1, VEGF-A, and IL-4 in tolerant compared to susceptible cattle may mitigate the detrimental effects of fescue toxicosis, including suppressed PRL and vasoconstriction, leading to improved animal performance in a fescue environment. Additionally, these cytokines may serve as potential biomarkers for determining an animal’s tolerance or susceptibility to negative effects associated with endophyte-infected tall fescue}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Mayberry, Kyle and Poole, Rebecca K. and Newsome, McKayla A. and Khanal, Piush and Poore, Matthew H. and Serao, Nick V. L. and Poole, Daniel H.}, year={2019}, month={Jul}, pages={45–46} }
 @article{khanal_sanglard_mayberry_sommer_poore_poole_serao_2019, title={Genes and functions associated with tolerance to fescue toxicosis in Angus cows}, volume={97}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skz122.295}, abstractNote={Abstract
               The objective of this study was to identify differentially expressed genes (DEG) and functions associated with tolerance to fescue toxicosis (FT). Forty pregnant purebred Angus cows were selected based on their growth at two locations in North Carolina (Butner Beef Cattle Field Laboratory, BBFCL; Upper Piedmont Research Station, UPRS) and classified as either high tolerant (HT) or low tolerant (LT) to FT with 20 cows in each group balanced by location. Blood samples were collected on weeks 1, 5, 9, and 13 for RNA sequencing. Counts were analyzed using a negative binomial model including the effects of genetic group, location, time, all possible interactions of these effects, flow cell, covariate of RNA integrity number, and normalized library size as offset. Genotype-by-location-by-time interaction was evident with a high number (4,453) of DEG (q-value<0.1) between genetic groups on week 5 at UPRS compared to all other possible interactions. So further analyses were focused on week 5 at UPRS. The most significant upregulated genes in LT and HT animals were ENPP6 and MESP2, respectively, with log2 fold changes of 1.90 [95% confidence interval = 0.89, 2.92] q-value=0.005) and 0.91 [0.35, 1.47] (q-value=0.01), respectively. Other top 5 upregulated genes for HT animals were CTBS, CLDN19, SPDYC, HEYL, and SDC2, and for LT animals were OLIG1, IL13, ANXA13, ENSBTAG00000024188and CXCL13. Enrichment analysis (P < 0.05) showed that DEG between genetic groups have general functions, such as metabolic, biosynthetic, and catabolic processes, as well as DNA and RNA-related functions, such as translation, transcription, and repair. These findings helped characterizing the genetic basis of tolerance to FT in cattle. In addition, we identified genes that may serve as potential biomarkers for tolerance to FT}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Khanal, Piush and Sanglard, Leticia Pereira and Mayberry, Kyle and Sommer, Jeffrey and Poore, Matthew H. and Poole, Daniel H. and Serao, Nick V. L.}, year={2019}, month={Jul}, pages={167–167} }
 @article{khanal_maltecca_schwab_gray_tiezzi_2019, title={Genetic parameters of meat quality, carcass composition, and growth traits in commercial swine}, volume={97}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072057293&partnerID=MN8TOARS}, DOI={10.1093/jas/skz247}, abstractNote={AbstractSwine industry breeding goals are mostly directed towards meat quality and carcass traits due to their high economic value. Yet, studies on meat quality and carcass traits including both phenotypic and genotypic information remain limited, particularly in commercial crossbred swine. The objectives of this study were to estimate the heritabilities for different carcass composition traits and meat quality traits and to estimate the genetic and phenotypic correlations between meat quality, carcass composition, and growth traits in 2 large commercial swine populations: The Maschhoffs LLC (TML) and Smithfield Premium Genetics (SPG), using genotypes and phenotypes data. The TML data set consists of 1,254 crossbred pigs genotyped with 60K SNP chip and phenotyped for meat quality, carcass composition, and growth traits. The SPG population included over 35,000 crossbred pigs phenotyped for meat quality, carcass composition, and growth traits. For TML data sets, the model included fixed effects of dam line, contemporary group (CG), gender, as well as random additive genetic effect and pen nested within CG. For the SPG data set, fixed effects included parity, gender, and CG, as well as random additive genetic effect and harvest group. Analyses were conducted using BLUPF90 suite of programs. Univariate and bivariate analyses were implemented to estimate heritabilities and correlations among traits. Primal yield traits were uniquely created in this study. Heritabilities [high posterior density interval] of meat quality traits ranged from 0.08 [0.03, 0.16] for pH and 0.08 [0.03, 0.1] for Minolta b* to 0.27 [0.22, 0.32] for marbling score, except intramuscular fat with the highest estimate of 0.52 [0.40, 0.62]. Heritabilities of primal yield traits were higher than that of primal weight traits and ranged from 0.17 [0.13, 0.25] for butt yield to 0.45 [0.36, 0.55] for ham yield. The genetic correlations of meat quality and carcass composition traits with growth traits ranged from moderate to high in both directions. High genetic correlations were observed for male and female for all traits except pH. The genetic parameter estimates of this study indicate that a multitrait approach should be considered for selection programs aimed at meat quality and carcass composition in commercial swine populations.}, number={9}, journal={JOURNAL OF ANIMAL SCIENCE}, publisher={Oxford University Press US}, author={Khanal, Piush and Maltecca, Christian and Schwab, Clint and Gray, Kent and Tiezzi, Francesco}, year={2019}, month={Sep}, pages={3669–3683} }
 @article{mayberry_khanal_poore_serao_poole_2018, title={Evaluation of Angus Calf Performance Based on Dams Tolerance or Susceptibility to Fescue Toxicosis.}, volume={96}, ISSN={["1525-3163"]}, DOI={10.1093/jas/sky027.103}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Mayberry, K. and Khanal, P. and Poore, M. H. and Serao, N. V. L. and Poole, D. H.}, year={2018}, month={Mar}, pages={55–55} }