bluuebunny/crossref_metadata_2025_split huggingface dataset:
149 Integration of Selection Signatures Analyses and Weighted Single-step GWAS to Prioritize Candidate Genes for Body Conformation Traits in Pigs
Authors: Vahedi Seyed Milad , Ardestani Siavash Salek , Do Duy Ngoc , Karimi Karim , Miar Younes 
Published: October 2021

Abstract
Body conformation traits such as body height (BH) and body length (BL) have been included in the swine industry’s selection criteria. The objective of this study was to identify the quantitative trait loci (QTLs) and candidate genes for pig conformation traits using an integration of selection signatures analyses and weighted single-step GWAS (WssGWAS). Body measurement records of 5,593 Yorkshire pigs of which 598 animals were genotyped with Illumina 50K panel were used. Estimated breeding values (EBVs) for BH and BL were computed using univariate animal models. Genotyped animals were grouped into top 5% and bottom 5% based on their EBVs, and selection signatures analyses were performed using fixation index (Fst), FLK, hapFLK, and Rsb statistics, which were then combined as a Mahalanobis distance (Md) framework. The WssGWAS was conducted to detect the single nucleotide polymorphisms (SNPs) associated with the studied traits. The top 1% SNPs (n=530) from Md distribution that overlapped with the top 1% SNPs from WssGWAS (n = 530) were used to detect the candidate genes. A total of 31 and six overlapped SNPs were found to be associated with BH and BL, respectively. Several candidate genes were identified for BH (PARVA, DCDC1, SYT1, CASTOR2, RGSL1, RGS8, RBMS3, TGFBR2, and HS6ST1) and BL (SNTB1, AK7, PAPOLA, KSR1, CHODL, and BMP2), explaining 2.58% and 0.42% of the trait’s genetic variation, respectively. Our results indicated that integrating data from the signatures of selection tests with WssGWAS could help elucidate genomic regions underlying complex traits.
150 Effect of Ergot Alkaloids and a Mycotoxin Deactivating Product on in vitro Rumen Fermentation Using the Rumen Simulation Technique (RUSITEC)
Authors: Sarich Jenna , Stanford Kim , Schwartzkopf-Genswein Karen S , McAllister Tim A , Blakley Barry , Penner Gregory B , Ribeiro Gabriel O 
Published: October 2021

Abstract
A rumen simulation technique (RUSITEC) investigated effects of ergot alkaloids (E) and a mycotoxin deactivating product (Biomin® AA; B) on nutrient digestion, rumen fermentation, total gas and methane emissions. Fermenters received a finishing diet of 90:10 concentrate:barley silage. Using a randomized complete block design, treatments were assigned (4 vessels/treatment) within two RUSITECs in a 2 × 2 factorial. Treatments included: 1) control diet, 2) control + 1 g B, 3) control + 20 ppm E, and 4) control + 20 ppm E + 1 g B. The study had a 14-d experimental period, with 7-d adaptation and 7-d sample collection. Data were analyzed in SAS using PROC mixed including fixed effects of E, B, and E×B interaction. Random effects included RUSITEC apparatus and cow rumen inoculum (n = 4). Ergot decreased dry matter disappearance (DMD) (P &lt; 0.05; 87.9 vs. 87.2%) and organic matter disappearance (OMD) (P &lt; 0.05; 88.8 vs. 88.4%). Adding B increased OMD (P &lt; 0.05; 88.3 vs. 88.9%) and neutral detergent fiber disappearance (NDFD) (P &lt; 0.01); however, an E×B interaction was observed for NDFD (P &lt; 0.01) with B promoting greater increases with E. Ergot decreased acetate proportions (P &lt; 0.01) and increased isovalerate (P &lt; 0.05). Consequently, acetate:propionate was reduced (P &lt; 0.05) with E. Inclusion of B increased total volatile fatty acids (P &lt; 0.01), and proportions of acetate (P &lt; 0.05) and propionate (P &lt; 0.05), and decreased valerate (P &lt; 0.01), isovalerate (P &lt; 0.01), and caproate (P &lt; 0.01). Treatments did not affect (P ≥ 0.17) ammonia-N, total gas, or methane production (mg/d or mg/g of OM fermented). In conclusion, E reduced OMD and acetate production, but these responses were reversed by the addition of B.
158 The Identification of Pig Calcium-sensing Receptor (pCaSR) Expression in Porcine Intestinal Enterocytes
Authors: Zhao Xiaoya , Hui Qianru , Azevedo Paula , Nyachoti Martin , O Karmin , Yang Chengbo 
Published: October 2021

Abstract
Enterocytes play important roles in nutrient absorption, while the intestinal porcine enterocyte cell line (IPEC-J2) is a non-transformed and permanent commercial cell line. The calcium-sensing receptor (CaSR) has been identified as calcium ions and L-amino acids sensor in the gut and studies have demonstrated that the CaSR is involved in nutrient digestion and absorption, as well as gut barrier function. Although the expression of CaSR on the basal membrane of the villus has been found in other animal species, its expression in porcine enterocytes (pCaSR) has not been investigated to date. To investigate the expression of pCaSR in isolated porcine enterocytes and IPEC-J2, cell sorting of ileal enterocytes by fluorescence-activated cell sorting (FACS) based on sucrase-isomaltose as enterocytes marker were performed to obtain pure porcine enterocytes. The digital droplet PCR (ddPCR), immunofluorescence staining, and Western blotting were applied for the detection of pCaSR expression at the gene and protein levels, respectively. Our results showed that about 3.3% of upper epithelial cells were characterized and sorted as pure porcine enterocytes, while the other cells were negative to the enterocytes marker. In addition, neither the isolated porcine enterocytes nor the IPEC-J2 expressed the pCaSR. In summary, pure porcine enterocytes could be obtained by using FACS with the sucrase-isomaltase as enterocytes marker but pCaSR is not expressed in either isolated porcine enterocytes or IPEC-J2, which provides new insights for future work exploring the role of pCaSR in the intestine.
154 Virulence Potential of Antimicrobial Resistant Extraintestinal Pathogenic Escherichia coli from Poultry in a Caenorhabditis Elegans Model
Authors: Yang Chongwu , Diarra Moussa , Rehman Muhammad Attiq , Li Linyan , Yu Hai , Yin Xianhua , Aslam Mueen , Carrillo Catherine , Yang Chengbo , Gong Joshua 
Published: October 2021

Abstract
This study investigated virulence potential of poultry antimicrobial resistant extraintestinal pathogenic E. coli (ExPEC). A total of 46 E. coli isolates from poultry meat, feces, or humans were sequenced and identified as ExPEC. Based on their characteristics, eight of these ExPEC isolates were evaluated for their potentials using a Caenorhabditis elegans infection model. The life-span of C. elegans in response to these eight isolates was examined in three life-span experiments: 1) E. coli OP 50 (negative control), K88+ enterotoxigenic E. coli strain JG280 (positive control), and an ExPEC isolate from human urinal tract infection; 2) three ExPEC isolates from chicken and turkey retail meats; 3) four ExPEC isolates from chicken feces with different antimicrobial resistance (AMR) profiles or a various number of virulence genes (VGs). All 46 isolates belonged to 24 serotypes among which 6 were of serotype O25:H4 Sequence Type 131 (ST131). Interestingly, all ST 131 isolates from chicken or turkey retail meats clustered with a human UTI isolate belonging to the similar serotype and ST type. The types and numbers of AGRs and VGs varied among the eight selected isolates for C. elegans model. The human ExPEC induced a similar effect as the JG280 on reducing (P &lt; 0.05) survival of C. elegans. Interestingly, chicken and turkey meat ExPEC isolates, caused similar negative impacts on the survival of worms as the human ExPEC. Additionally, fecal ExPEC isolates reduced (P &lt; 0.05) the survival of C. elegans compared to OP50. However, the survival of C. elegans was not reduced with an increasing number of VGs and did not seem to be affected by AMR profiles. This study indicated the virulence potential of ExPEC isolates from retail poultry meat or feces. The relationship between specific AMR profiles and/or numbers of VGs with pathogenicity in these E. coli isolates deserves further investigations.
156 Genome-wide DNA Methylation Profile of Mammary Gland Tissues from Holstein Cattle Producing Various Milk Protein Yields
Authors: Wang Mengqi , Dudemaine Pier-Luc , Bissonnette Nathalie , Zhao Xin , Ibeagha-Awemu Eveline M 
Published: October 2021

Abstract
Milk protein content is attracting considerable attention due to increasing demand for high-quality products. Epigenetic marks including DNA methylation have demonstrated considerable potential to contribute to the achievement of increased gain in bovine milk traits. To investigate potential roles of DNA methylation in regulating milk protein productivity, whole genome bisulfite sequencing was used to profile the global DNA methylation of mammary gland (MG) tissues from Canadian Holstein cows producing milk with high protein (HMP) (&gt;4.0%, n = 5) or low protein (LMP) (&lt; 3.0%, n = 7) contents. Bioinformatics processing using standard tools and construction of the methylation landscape of MG was based on methylation sites with ≥10× coverage. A total of 2420 differentially methylated CpG (DMC) sites, including 1842 with higher and 578 with lower methylation levels (FDR&lt; 0.1) were identified when HMP group was compared with LMP group. DMCs were most abundant on chromosomes 2 (n=347) and 27 (N=535), respectively. The most DMCs were annotated to mRNAs, followed by lncRNAs, pseudogenes and rRNAs. Eight genes harbored five or more DMCs each, including LOC112443250 (5S ribosomal RNA) and LOC112443149 (liprin-alpha-1-like, LIP1) (harbored 20 hypermethylated and 1 hypomethylated sites, each), followed by miR-2287-1 (12 hypomethylated sites), etc. LIP1, a liprin family member interacts with LAR family members to play important roles in MG development. MiR-2287-1 and other family members are frequently identified in MG tissues and milk and are associated with many livestock diseases. Interestingly, among the DMCs that overlap with QTLs related to milk production were clusters on chromosomes 27 (N=534) and 14 (N=91) that associated with milk protein yield. In conclusion, DNA methylation showed potential involvement in the genetic variation underlying milk protein content and MG biological processes. More analysis with a higher sample size is however necessary to adequately quantify the involvement of DNA methylation in the regulation of milk protein content and mammary gland development.
157 Starch and Dry Matter Digestibility Values Are Not Associated with Improved Growth and Feed Efficiency in Weanling Pigs Fed a Therapeutic Multi-antimicrobial-supplemented Diet
Authors: Chen Jiali , Wang Min , Archbold Tania L , Wang Weijun , Fan Wenyi , Yin Xindi , Cheng Laurence , Fan Ming Z Z 
Published: October 2021

Abstract
The porcine terminal small intestinal starch digestive activity and capacity undergo further developmental changes during the acute and adaptive weaning transition. Objective of this study was to address the hypothesis that weanling porcine growth promotion associated with therapeutic antimicrobials was mediated via improving intestinal starch digestion. A total of 170 crossbred barrows (n = 34 pens; 5 barrows/pen), weaned on d 19–21 with an average initial BW of 6.9±0.1 kg, were randomly assigned to two dried whey, corn and SBM-based diets, i.e., control vs. antimicrobials, for 21 d according to a randomized complete block design. The therapeutic multi-antimicrobial diet was supplemented with aureomycin 220, tiamulin 31.2 and ZnO 2,358 at mg/kg diet. The apparent ileal, cecal and total tract digestibility values of total starch and DM were determined by using the titanium dioxide as the digestibility marker (0.30% in the diets). There were no differences (P &gt; 0.05) in the starch digestibility at the ileal (control, 98.3±0.9% vs. antimicrobials, 98.3±0.5%), cecal (control, 96.3±0.6% vs. antimicrobials, 97.1±0.6%) and total tract (control, 98.5±0.3% vs. antimicrobials, 98.7±0.3%) levels between the two diets. Furthermore, there were no differences (P &gt; 0.05) in the DM digestibility at the ileal (control, 75.7±2.2% vs. antimicrobials, 72.7±2.0%), cecal (control, 80.6±1.2% vs. antimicrobials, 81.3±1.2%) and total tract (control, 85.8±0.8% vs. antimicrobials, 84.7±0.9%) levels between the two diets. The Spearman’s correlation analyses revealed no significant associations (P &gt; 0.05) between the growth performance endpoints of ADG, ADFI and F: G and the digestibility values of total starch and DM at the levels of ileal, cecal and total tract. Our results suggest that starch is near complete digestion at the distal small intestine, thus not limiting growth and feed conversion efficiency of weanling pigs fed corn and SBM-based diets. Hence, therapeutic multi-antimicrobial effects are unlikely channeled through modulating digestive utilization efficiency of starch and DM in weanling pigs.
166 Livestock Resiliency: Concepts and Approaches
Authors: Baes Christine F , Miglior Filippo , Schenkel Flavio S , Goddard Ellen , Kistemaker Gerrit , van Staaveren Nienke , Cerri Ronaldo , Sirard Marc Andre A , Stothard Paul 
Published: October 2021

Abstract
Genetic improvement of health, welfare, efficiency, and fertility traits is challenging due to expensive and fuzzy phenotypes, the polygenic nature of traits, antagonistic genetic correlations to production traits and low heritabilities. Nevertheless, many organizations have introduced large-scale genetic evaluations for such traits in routine selection indexes. Medium and high-density arrays can be applied in genomic selection strategies to improve breeding value accuracy, and also in genome-wide association studies (GWAS) to identify causative mutations responsible for economically important traits. Genomic information is particularly helpful when traits have low heritability. The objective here is to provide a framework for including health, welfare, efficiency, and fertility traits taken from large-scale genetic and genomic analyses and identifying areas of potential improvement in terms of trait definition and performance testing. General tendencies between trait groups confirmed that a number of moderate unfavourable correlations (+/-0.20 or higher) exist between economically important trait complexes and health, welfare, and fertility traits. A number of trait complexes were identified in which “closer-to-biology” phenotypes could provide clear improvements to routine genetic and genomic selection programs. Here we outline development of these phenotypes and describe their collection. While conventional variance component estimation methods have underpinned the genomic component of some traits of economic interest, performance testing for health, welfare, efficiency, and fertility traits remains an elusive goal for breeding programs. Although our results are encouraging, there is much to be done in terms of trait definition and obtaining better measures of physiological parameters for wide-scale application in breeding programs. Close collaboration between veterinarians, physiologists, and geneticists is necessary to attain meaningful advancement in such areas. We would like to acknowledge the support and funding from all national and international partners involved in the RDGP project through the Large Scale Applied Research Project program from Genome Canada
167 Impacts on Biodiversity, Environment and Society of Beef Production in the Mexican Tropics: A Life Cycle Assessment Approach
Authors: Huerta Adriana Rivera , Hernández Patricia Güereca 
Published: October 2021

Abstract
Beef production exerts strong environmental pressures and can also generate negative social effects. In this study, the impacts on biodiversity, environment and society of beef production in the Mexican tropics, were evaluated through the Life Cycle Assessment (LCA) approach. The functional unit of the study was 1 kg live weight of calf and focused on three productive systems: native silvopastoral (NSP), intensive silvopastoral (ISP) and monoculture (MC). This research was divided into four analysis steps. (1) social impacts; (2) damage to biodiversity; (3) methane emissions and 4) environmental LCA impacts. Using the Social-LCA, we evaluated 18 social indicators, grouped into five categories: human rights, working conditions, health and safety, socio-economic repercussions, and governance. The results showed similarities between the three livestock systems, which revealed a deficient social performance. For projecting the biodiversity damage of pasture land use from an LCA perspective, characterization factors (CFs) were estimated. CFs consist of dimensionless figures representing the potential for damage per unit area of pasture land (potential species loss per m2). The CFs were calculated for three levels of pasture land use intensity (minimal/NSP, light/ISP, intense/MC). Based on the characterization factors developed, the MC showed the least potential species loss. Enteric methane emissions from the production systems were determined using the IPCC Tier 2. The results revealed that the emissions values from enteric methane calculated with Tier 1 overestimated the emissions compared to Tier 2 methodology. LCA indicated a lower environmental impact of the MC on four of the seven categories analyzed, highlighting its lower contribution to climate change and reducing species loss. However, consumption of water and scarcity of fossil fuel resources increased. To achieve tropical sustainable livestock farming, further lines of research should be aimed at evaluating its economic impacts and propose management systems that guarantee better social and environmental performance.
172 Scenario-based Training Is an Effective Tactic for Teaching Applied Livestock Management Practices to Extension Personnel
Authors: Ivey Jennie L , Strickland Lew G , Rhinehart Justin D 
Published: October 2021

Abstract
Developing livestock and equine trainings to empower county Extension agents is challenging, especially when spanning in-person and online delivery modules. Real life application of training concepts is difficult, particularly when participants have varied backgrounds and experience. Thus, we assessed if scenario-based training modules were an effective training method across in-person and virtual formats. The same scenario-based training was delivered at three, regional in-person trainings (n = 42), and one virtual training (n = 32). Training format consisted of four, species-specific lectures addressing various production topics. Small groups then developed recommendations for a specific scenario, followed by a debriefing session consisting of group reactions and specialist recommendations. Topic-area application to county programs, instructor effectiveness, and overall benefit of the training session were evaluated (Qualtrics, in-person n = 26, 62% completion; virtual n = 17, 53% completion). Data were assessed using analysis of variance and mean comparisons (α=0.05), with Tukey’s pairwise post hoc analysis where appropriate (STATA 16). Across all sessions, likert scale responses (1=poor and 5=excellent, n = 43) indicated lecture sessions were applicable to county areas of need across material content (mean±SD, cattle=4.71±0.57, equine=4.64±0.50), teaching effectiveness (cattle=4.77±0.42, equine=4.75±0.43), and overall quality (cattle=4.68±0.57, equine=4.67±0.51), respectively. Scenario-based training benefit was not influenced by the number of times an agent had attended in-service training on livestock species, agent appointment (youth vs. adult educator), or training location (p &gt;0.05). Attendance at previous in-service trainings (cattle P = 0.005; equine P = 0.013) and agent appointment (cattle P = 0.0006; equine P = 0.05) had a significant impact on the number of questions agents reported to have received on scenario topics in the last 12 months. More topic area questions were reported by agents with adult education responsibilities and previous training attendance. Based upon these results, scenario-based training is an effective in-person and virtual training tool for 4-H and adult Extension agents of varying experience.
173 Grazing Cover Crops: Effects of Cattle Removal Date on Forage Production and Cattle Performance
Authors: Carrell Russell C , Dillard Sandra L , Mullenix Mary K , Gamble Audrey , Muntifering Russ B 
Published: October 2021

Abstract
Use of cool-season annual cover crops through grazing has been shown to be a potential tool in extending the grazing season, while still mitigating environmental risks associated with warm-season row crop production. Although data describing the effects of grazing on soil health are not novel, effects of grazing length on animal performance and cover crop production are limited. The objective was to determine cattle performance and forage production when grazing a cool-season annual cover-crop. Twelve, 1.2-ha pastures were established in a four species forage mix and randomly allocated to be grazed through either mid-February (FEB), mid-March (MAR), or mid-April (APR) with a non-grazed control (CON). Three tester steers were randomly placed in each paddock and a 1:1 forage allowance was maintained in each paddock using put-and-take steers. Animals were weighed every 30 d for determination of average daily gain (ADG). Forage was harvested bi-weekly and analyzed for forage production, neutral detergent fiber (NDF), and acid detergent fiber (ADF). Fiber fractions were measured using an ANKOM fiber analyzer (ANKOM Tech, Macedon, NY). All data were analyzed using MIXED procedure of SAS version 9.4 (SAS Inst., Cary, NC). Differences in forage mass were detected between CON and FEB (3,694.75 vs. 2,539.68 kg/ha; P &lt; 0.003), CON and MAR (3,694.75 vs. 1,823.45 kg/ha; P &lt; 0.001), and CON and APR (3,694.75 vs. 1,976.23 kg/ha; P &lt; 0.001). Differences in total gain/acre were detected between APR and MAR (212.24 vs. 101.74 kg/ha; P &lt; 0.0001), APR and FEB (212.24 vs 52.65 kg/ha; P &lt; 0.0001), and FEB and MAR (101.74 vs. 52.65 kg/ha; P &lt; 0.003). No differences were detected for tester ADG (1.23 kg/day, P = 0.56), NDF (44.9%, P = 0.99), or ADF (27.2%, P = 0.92) among treatments. These results indicate that cattle removal date effected forage yield and total gain/hectare.