Large White Population Research Articles

Genomic Variants Associated with Haematological Parameters and T Lymphocyte Subpopulations in a Large White and Min Pig Intercross Population.

The breeding of disease-resistant pigs has consistently been a topic of significant interest and concern within the pig farming industry. The study of pig blood indicators has the potential to confer economic benefits upon the pig farming industry, whilst simultaneously providing valuable insights that can inform the study of human diseases. In this study, an F2 resource population of 489 individuals was generated through the intercrossing of Large White boars and Min pig sows. A total of 17 haematological parameters and T lymphocyte subpopulations were measured, including white blood cell count (WBC), lymphocyte count (LYM), lymphocyte count percentage (LYM%), monocyte count (MID), monocyte count percentage (MID%), neutrophilic granulocyte count (GRN), percentage of neutrophils (GRN%), mean platelet volume (MPV), platelet distribution width (PDW), platelet count (PLT), CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8-CD3+, CD4-CD8+CD3+, CD4-CD8-CD3+, and CD3+. The Illumina PorcineSNP60 Genotyping BeadChip was obtained for all of the F2 animals. Subsequently, a genome-wide association study (GWAS) was conducted using the TASSEL 5.0 software to identify associated variants and candidate genes for the 17 traits. Significant association signals were identified for PCT and PLT on SSC7, with 1 and 11 significant SNP loci, respectively. A single nucleotide polymorphism (SNP) on SSC12 was identified as a significant predictor of the white blood cell (WBC) trait. Significant association signals were detected for the T lymphocyte subpopulations, namely CD4+/CD8+, CD4+CD8+CD3+, CD4+CD8-CD3+, and CD4-CD8+CD3+, with the majority of these signals observed on SSC7. The genes CLIC5, TRIM15, and SLC17A4 were identified as potential candidates for influencing CD4+/CD8+ and CD4-CD8+CD3+. A missense variant, c.2707 G>A, in the SLC17A4 gene has been demonstrated to be significantly associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Three missense variants (c.425 A>C, c.500 C>T, and c.733 A>G) have been identified in the TRIM15 gene as being linked to the CD4+/CD8+ trait. Nevertheless, only c.425 A>C has been demonstrated to be significantly associated with CD4-CD8+CD3+. In the CLIC5 gene, one missense variant (c.957 T>C) has been identified as being associated with the CD4+/CD8+ and CD4-CD8+CD3+ traits. Additionally, significant association signals were observed for CD4+CD8+CD3+ and CD4+CD8-CD3+ on SSC2 and 5, respectively. Subsequently, a gene ontology (GO) enrichment analysis was conducted on all genes within the quantitative trait loci (QTL) intervals of platelet count, CD4+/CD8+, and CD4-CD8+CD3+. The MHC class II protein complex binding pathway was identified as the most significant pathway among the three immune traits. These results provide guidance for further research in the field of breeding disease-resistant pigs.

Association of race/ethnicity and severe housing problems with COVID-19 deaths in the United States: Analysis of the first three waves.

The objective of this study is to assess the associations of race/ethnicity and severe housing problems with COVID-19 death rates in the US throughout the first three waves of the COVID-19 pandemic in the US. We conducted a cross-sectional study using a negative binomial regression model to estimate factors associated with COVID-19 deaths in 3063 US counties between March 2020 and July 2021 by wave and pooled across all three waves. In Wave 1, counties with larger percentages of Black, Hispanic, American Indian and Alaska Native (AIAN), and Asian American and Pacific Islander (AAPI) residents experienced a greater risk of deaths per 100,000 residents of +22.82 (95% CI 15.09, 30.56), +7.50 (95% CI 1.74, 13.26), +13.52 (95% CI 8.07, 18.98), and +5.02 (95% CI 0.92, 9.12), respectively, relative to counties with larger White populations. By Wave 3, however, the mortality gap declined considerably in counties with large Black, AIAN and AAPI populations: +10.38 (95% CI 4.44, 16.32), +7.14 (95% CI 1.14, 13.15), and +3.72 (95% CI 0.81, 6.63), respectively. In contrast, the gap increased for counties with a large Hispanic population: +13 (95% CI 8.81, 17.20). Housing problems were an important predictor of COVID-19 deaths. However, while housing problems were associated with increased COVID-19 mortality in Wave 1, by Wave 3, they contributed to magnified mortality in counties with large racial/ethnic minority groups. Our study revealed that focusing on a wave-by-wave analysis is critical to better understand how the associations of race/ethnicity and housing conditions with deaths evolved throughout the first three COVID-19 waves in the US. COVID-19 mortality initially took hold in areas characterized by large racial/ethnic minority populations and poor housing conditions. Over time, as the virus spread to predominantly White counties, these disparities decreased substantially but remained sizable.

Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles.

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low- (LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.NEW & NOTEWORTHY The duodenum is a key organ for the hunger/satiety loop and nutrient sensing. We investigated how the duodenum transcriptome and DNA methylation profiles are affected by feed intakes in pigs. We observed thousands of changes in gene expression levels between overnight-fasted and fed pigs in high-feed efficiency pig lines, but almost none in the related low-feed efficiency pig line.

Urban-rural differences in cancer mortality: Operationalizing rurality.

To assess urban-rural differences in cancer mortality across definitions of rurality as (1) established binary cut-points, (2) data-driven binary cut-points, and (3) continuous. We used Surveillance, Epidemiology, and End Results (SEER) data between 2000 and 2016 to identify incident adult screening-related cancers. Analyses were based on one testing and four validation cohorts (all n = 26,587). Urban-rural status was defined by Rural-Urban Continuum Codes, National Center for Health Statistics codes, and the Index of Relative Rurality. Each was modeled using established binary cut-points, data-driven cut-points, and as continuous. The primary outcome was 5-year cancer-specific mortality. Compared to established cut-points, data-driven cut-points classified more patients as rural, resulted in larger White populations in rural areas, and yielded 7%-14% lower estimates of urban-rural differences in cancer mortality. Further, hazard of cancer mortality increased 4%-67% with continuous rurality measures, revealing important between-unit differences. Different cut-points introduce variation in urban-rural differences in mortality across definitions, whereas using urban-rural measures as continuous allows rurality to be conceptualized as a continuum, rather than a simple aggregation. Findings provide alternative cut-points for multiple measures of rurality and support the consideration of utilizing continuous measures of rurality in order to guide future research and policymakers.

Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs.

Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

BackgroundGenomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values (GEBV) to accelerate the speed of genetic improvement in domestic animals. But after multi-generation selection, the rate of inbreeding and the occurrence of homozygous harmful alleles might increase, which would reduce performance and genetic diversity. To mitigate the above problems, we can utilize genomic mating (GM) based upon optimal mate allocation to construct the best genotypic combinations in the next generation. In this study, we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population. These factors included: the algorithm used to derive inbreeding coefficients; the trait heritability (0.1, 0.3 or 0.5); the kind of GM scheme (focused average GEBV or inbreeding); the approach for computing the genomic relationship matrix (by SNP or runs of homozygosity (ROH)). The outcomes were compared to three traditional mating schemes (random, positive assortative or negative assortative matings). In addition, the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.ResultsGenomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain. The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs. The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%–2.6% higher rates of genetic gain ΔG, and 13%–83.3% lower ΔF than positive assortative mating regardless of heritability. The rates of inbreeding were always the fastest with positive assortative mating. Results from a purebred Large White pig population, confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.ConclusionCompared with traditional mating schemes, genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population. Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

Two single nucleotide variants in the miR-23a promoter affect granulosa cell apoptosis.

microRNAs (miRNAs) are well known to be important in mammalian female fertility. However, the genetic regulation of miRNAs associated with female fertility remains largely unknown. Here, we report that two single-nucleotide variants (SNVs) in the miR-23a promoter strongly influence miR-23a transcription and function in granulosa cell (GC) apoptosis. Two novel SNVs, g.-283G>C and g.-271C>T, were detected in the porcine miR-23a promoter by pooled-DNA sequencing. Furthermore, SNVs in the promoter region influenced miR-23a transcription in porcine GCs by altering its promoter activity. Functionally, SNVs in the promoter strongly influenced miR-23a regulation of early apoptosis in porcine GCs cultured in vitro. In addition, a preliminary association analysis showed that the combined genotypes of the two SNVs, rather than a single SNV, were tentatively associated with sow fertility traits in a Large White population. Overall, our findings suggest that the SNVs g.-283G>C and g.-271C>T in the miR-23a promoter are causal variants affecting GC apoptosis and miR-23a may be a potential small-molecule nonhormonal drug for regulating female fertility.

Effect of host genetics and gut microbiome on fat deposition traits in pigs.

Fat deposition affects meat quality, flavor, and production in pigs. Fat deposition is influenced by both genetics and environment. Symbiotic microbe with the host is an important environmental factor to influence fat deposition. In this study, the fat deposition traits were measured in 239 individuals obtained from Tongcheng pigs × Large White pigs resource population. The interactions between genetics and gut microbiome in fat deposition traits were investigated through whole-genome sequencing and cecum microbial 16S ribosomal RNA sequencing. The results showed that the percentage of leaf fat (PL) and intramuscular fat content (IMF) were significantly influenced by host genetics–gut microbiome interaction. The effects of interactions between host genetics and gut microbiome on PL and IMF were 0.13 and 0.29, respectively. The heritability of PL and IMF was estimated as 0.71 and 0.89, respectively. The microbiability of PL and IMF was 0.20 and 0.26, respectively. Microbiome-wide association analysis (MWAS) revealed Anaeroplasma, Paraprevotella, Pasteurella, and Streptococcus were significantly associated with PL, and Sharpea and Helicobacter exhibited significant association with IMF (p < 0.05). Furthermore, Paraprevotella was also identified as a critical microbe affecting PL based on the divergent Wilcoxon rank-sum test. Overall, this study reveals the effect of host genetics and gut microbiome on pig fat deposition traits and provides a new perspective on the genetic improvement of pig fat deposition traits.

A genome-wide association study of important reproduction traits in large white pigs

Augmenting the reproductive efficiency of sows remains the predominant challenge in the swine industry. This work was aimed at scrutinizing vital genetic markers for reproductive traits in this animal. This entailed probing of the records of vital attributes of Large White pigs (n = 695) inclusive of the total number of born (TNB), number of born alive (NBA), number of weaned pigs (NWP), number of healthy births (NHS), total litter weight of piglets born alive (BALWT), weaning litter weight (WNWT), and corrected litter weight at 21 days (W21). A genome-wide association study (GWAS) for the four litter traits and three traits of litter weight in the Denmark Large White population then ensued. We discovered seven significantly related SNPs and eleven potential candidate genes (e.g., TUSC3, THRB for TNB; STT3B for NBA). The subsequent functional enrichment analysis of these genes showed that the significant gene were associated with steroid hormone receptor activity. Our findings indicated that the genes TUSC3, THRB and STT3B probably contribute to litter traits in this population. This work reveals genetic mechanisms of reproduction traits and also supports ensuing genetic improvement employing marker-assisted selection in Large White pigs.

Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population.

With the broad application of genomic information, SNP-based measures of estimating inbreeding have been widely used in animal breeding, especially based on runs of homozygosity. Inbreeding depression is better estimated by SNP-based inbreeding coefficients than pedigree-based inbreeding in general. However, there are few comprehensive comparisons of multiple methods in pigs so far, to some extent limiting their application. In this study, to explore an appropriate strategy for estimating inbreeding depression on both growth traits and reproductive traits in a Large White pig population, we compared multiple methods for the inbreeding coefficient estimation based on both pedigree and genomic information. This pig population for analyzing the influence of inbreeding was from a pig breeding farm in the Inner Mongolia of China. There were 26,204 pigs with records of age at 100 kg (AGE) and back-fat thickness at 100 kg (BF), and 6,656 sows with reproductive records of the total number of piglets at birth (TNB), and the number of alive piglets at birth (NBA), and litter weight at birth. Inbreeding depression affected growth and reproductive traits. The results indicated that pedigree-based and SNP-based inbreeding coefficients had significant effects on AGE, TNB, and NBA, except for BF. However, only SNP-based inbreeding coefficients revealed a strong association with inbreeding depression on litter weight at birth. Runs of homozygosity-based methods showed a slight advantage over other methods in the correlation analysis of inbreeding coefficients and estimation of inbreeding depression. Furthermore, our results demonstrated that the model-based approach (RZooRoH) could avoid miscalculations of inbreeding and inbreeding depression caused by inappropriate parameters, which had a good performance on both AGE and reproductive traits. These findings might improve the extensive application of runs of homozygosity analysis in pig breeding and breed conservation.

Introgression of Trifolium ambiguum Into Allotetraploid White Clover (Trifolium repens) Using the Ancestral Parent Trifolium occidentale as a Bridging Species

White clover (Trifolium repens) is an allotetraploid pasture legume widely used in moist temperate climates, but its vulnerability to drought, grazing pressure and pests has restricted its wider use. A related species, Caucasian clover (Trifolium ambiguum), is a potential source of resistances to drought, cold, grazing pressure and pests that could potentially be transferred to white clover by interspecific hybridization. Although direct hybridization has been achieved with difficulty, the hybrids have not been easy to backcross for introgression breeding and no interspecific chromosome recombination has been demonstrated. The present work shows that interspecific recombination can be achieved by using Trifolium occidentale, one of the ancestral parents of T. repens, as a bridging species and that large white clover breeding populations carrying recombinant chromosomes can be generated. A 4x hybrid between T. ambiguum and T. occidentale was crossed with T. repens and then backcrossed for two generations. Five backcross hybrid plants with phenotypes appearing to combine traits from the parent species were selected for FISH-GISH analyses. Recombinant chromosome segments from T. ambiguum were found in all five plants, suggesting that recombination frequencies were significant and sufficient for introgression breeding. Despite early chromosome imbalances, the backcross populations were fertile and produced large numbers of seeds. These hybrids represent a major new resource for the breeding of novel resilient forms of white clover.

Assessment of Structural Barriers and Racial Group Disparities of COVID-19 Mortality With Spatial Analysis

Although social determinants of health (SDOH) are important factors in health inequities, they have not been explicitly associated with COVID-19 mortality rates across racial and ethnic groups and rural, suburban, and urban contexts. To explore the spatial and racial disparities in county-level COVID-19 mortality rates during the first year of the pandemic. This cross-sectional study analyzed data for all US counties in 50 states and the District of Columbia for the first full year of the COVID-19 pandemic (January 22, 2020, to February 28, 2021). Counties with a high concentration of a single racial and ethnic population and a high level of COVID-19 mortality rate were identified as concentrated longitudinal-impact counties. The SDOH that may be associated with mortality rate across these counties and in urban, suburban, and rural contexts were examined. The 3 largest racial and ethnic groups in the US were selected: Black or African American, Hispanic or Latinx, and non-Hispanic White populations. County-level characteristics and community health factors (eg, income inequality, uninsured rate, primary care physicians, preventable hospital stays, severe housing problems rate, and access to broadband internet) associated with COVID-19 mortality. Data on county-level COVID-19 mortality rates (deaths per 100 000 population) reported by the US Centers for Disease Control and Prevention were analyzed. Four indexes were used to measure multiple dimensions of SDOH: socioeconomic advantage index, limited mobility index, urban core opportunity index, and mixed immigrant cohesion and accessibility index. Spatial regression models were used to examine the associations between SDOH and county-level COVID-19 mortality rate. Of the 3142 counties included in the study, 531 were identified as concentrated longitudinal-impact counties. Of these counties, 347 (11.0%) had a large Black or African American population compared with other counties, 198 (6.3%) had a large Hispanic or Latinx population compared with other counties, and 33 (1.1%) had a large non-Hispanic White population compared with other counties. A total of 489 254 COVID-19-related deaths were reported. Most concentrated longitudinal-impact counties with a large Black or African American population compared with other counties were spread across urban, suburban, and rural areas and experienced numerous disadvantages, including higher income inequality (297 of 347 [85.6%]) and more preventable hospital stays (281 of 347 [81.0%]). Most concentrated longitudinal-impact counties with a large Hispanic or Latinx population compared with other counties were located in urban areas (114 of 198 [57.6%]), and 130 (65.7%) of these counties had a high percentage of people who lacked health insurance. Most concentrated longitudinal-impact counties with a large non-Hispanic White population compared with other counties were in rural areas (23 of 33 [69.7%]), included a large group of older adults (26 of 33 [78.8%]), and had limited access to quality health care (24 of 33 [72.7%]). In urban areas, the mixed immigrant cohesion and accessibility index was inversely associated with COVID-19 mortality (coefficient [SE], -23.38 [6.06]; P < .001), indicating that mortality rates in urban areas were associated with immigrant communities with traditional family structures, multiple accessibility stressors, and housing overcrowding. Higher COVID-19 mortality rates were also associated with preventable hospital stays in rural areas (coefficient [SE], 0.008 [0.002]; P < .001) and higher socioeconomic status vulnerability in suburban areas (coefficient [SE], -21.60 [3.55]; P < .001). Across all community types, places with limited internet access had higher mortality rates, especially in urban areas (coefficient [SE], 5.83 [0.81]; P < .001). This cross-sectional study found an association between different SDOH measures and COVID-19 mortality that varied across racial and ethnic groups and community types. Future research is needed that explores the different dimensions and regional patterns of SDOH to address health inequity and guide policies and programs.

Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs

BackgroundThe genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability are described as variance QTL (vQTL). This study focuses on litter size (total number born, TNB) and its variability in a Large White pig population. The variability of TNB was evaluated either using a simple method, i.e. analysis of the log-transformed variance of residuals (LnVar), or the more complex double hierarchical generalized linear model (DHGLM). We also performed a single-SNP (single nucleotide polymorphism) genome-wide association study (GWAS). To our knowledge, this is only the second study that reports vQTL for litter size in pigs and the first one that shows GWAS results when using two methods to evaluate variability of TNB: LnVar and DHGLM.ResultsBased on LnVar, three candidate vQTL regions were detected, on Sus scrofa chromosomes (SSC) 1, 7, and 18, which comprised 18 SNPs. Based on the DHGLM, three candidate vQTL regions were detected, i.e. two on SSC7 and one on SSC11, which comprised 32 SNPs. Only one candidate vQTL region overlapped between the two methods, on SSC7, which also contained the most significant SNP. Within this vQTL region, two candidate genes were identified, ADGRF1, which is involved in neurodevelopment of the brain, and ADGRF5, which is involved in the function of the respiratory system and in vascularization. The correlation between estimated breeding values based on the two methods was 0.86. Three-fold cross-validation indicated that DHGLM yielded EBV that were much more accurate and had better prediction of missing observations than LnVar.ConclusionsThe results indicated that the LnVar and DHGLM methods resulted in genetically different traits. Based on their validation, we recommend the use of DHGLM over the simpler method of log-transformed variance of residuals. These conclusions can be useful for future studies on the evaluation of the variability of any trait in any species.

Genetic diversity of the Central European wild boar (Sus scrofa scrofa) population and domestic pig (Sus scrofa domesticus) breeds based on a microsatellite DNA locus.

The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p <0.05) decrease in the level of genetic variability in bred breeds was shown. The expected heterozygosity and Shannon index were as follows: in the wild boar, Ho = 0.763 ± 0.026, I = 1.717 ± 0.091; in the Duroc breed, Ho = 0.569 ± 0.068, I = 1.191 ± 0.157; in the Landrace, Ho = 0.618 ± 0.062, I = 1.201 ± 0.147; in the Large White, Ho = 0.680 ± 0.029, I = 1.362 ± 0.074; and in the Yorkshire, Ho = 0.642 ± 0.065, I = 1.287 ± 0.156. The results of checking genotypic Hardy–Weinberg equilibrium based on the G-test of maximum likelihood demonstrated that the overwhelming majority of loci in the wild boar population were in the state of said equilibrium. By contrast, in pig breed populations, some loci demonstrated a significant deviation from the indicated equilibrium. In addition, the Yorkshire, Large White, and Landrace populations had loci, for which the hypothesis of neutrality was reliably rejected based on the results of the Ewens–Watterson test. The revealed private alleles, characteristic of the wild boar and breeds, can later be used to identify them. The ordination of the centroids of different herds in the space of the first two principal coordinates based on the matrix of pairwise estimates of Nei’s genetic distances showed that the most distant populations are the Duroc and Boar breeds, and the most genetically close are the Yorkshire and Landrace breeds. The closest to the wild boar population was the Large White breed. The assessment of the effective size, carried out using the method based on the linkage disequilibrium and the molecular coancestry method, showed that in all studied groups, including the wild boar population, the effective size was less than 100 individuals. The low effective size of the wild boar population (Ne = 21.8, Neb = 4.0) is probably caused by the death and shooting of animals due to Pestis africana suum.

Copy number variation of amylase alpha 2B gene is associated with feed efficiency traits in Large White pigs

Copy number variation (CNV) of the AMY gene in humans has been enthusiastically studied for its association with starch digestibility and obesity. The alpha-amylase (AMY) is a major starch digestive enzyme in mammals. This study aimed to determine the association between CNV of the porcine pancreatic amylase (AMY2B) gene and feed efficiency. Improvement of feed efficiency in growing pigs is of great economic interest. We assayed the copy number of AMY2B by using real-time quantitative PCR (qPCR) in a Large White pig population. We identified three genotypes for AMY2B CNVs, namely I/I (homozygotes of haplotype I; a chromosome with one copy of AMY2B), I/II (heterozygotes of haplotype I and II; a chromosome with two copies) and II/II (homozygotes of haplotype II). We tested the genotypes of the parental generation consisting of six males, 21 females and 265 offspring piglets to validate the AMY2B CNV genotyping. With very few mistyping exceptions, copy numbers of AMY2B were transmitted to piglets in segregation ratios following Mendelian inheritance. Finally, we performed an association analysis between the CNV of the AMY2B gene and feed efficiency traits in 207 uncastrated male pigs. The generalised linear model analysis showed the significant effects of AMY2B CNV genotype on average daily feed intake, total feed intake and feed conversion ratio during growth from 30 kg to 100 kg body weight. However, it was not associated with average daily gain, backfat thickness and loin eye muscle area. Individuals with the genotype I/I had about 76.6 ± 27.1 g lower average daily feed intake, 5.35 ± 1.90 kg lower total feed intake and 0.089 8 ± 0.026 5 lower feed conversion ratio than individuals with I/II and II/II genotypes. Thus, AMY2B CNV has the potential to be an effective genetic marker that could reduce feed costs for pig farming.

Socioeconomics of coronary artery calcium: Is it scored or ignored?

ImportanceChicago is one of the most racially segregated cities in the US, with the largest mortality gap between neighborhoods. Computed tomographic coronary artery calcium scoring (CACS) is an excellent risk stratification tool, but costs about $200 out-of-pocket, making it inaccessible to some. ObjectiveTo determine whether this ACC/AHA guideline-recommended screening tool is accessible to all populations and neighborhoods, we evaluated the price and availability of CACS in Chicago area hospitals. DesignWe used the Illinois Department of Public Health list of area hospitals to inquire about CACS availability and price. We compared these results to US Census Bureau data for each hospital's service area's demographic, ethnic and socioeconomic population characteristics. ResultsOut of the 40 hospitals in Chicagoland, 30 offered CACS. The 10 hospitals without CACS were smaller hospitals in zip codes with a higher population density (p ​< ​0.01), higher poverty rates (22% vs. 13%, p ​< ​0.01), lower percentage of white population (p ​< ​0.02), lower frequency of higher education (35% vs. 51%, p ​< ​0.05), and a trend toward more black residents (p ​< ​0.10). Life expectancy was greater in areas with CACS available (78 vs. 75 years, p ​< ​0.05).Even in areas with CACS, there was wide price variation, with higher prices in poorer areas (r ​= ​0.57, p ​< ​0.01). The highest vs. lowest quintile of income had higher education, larger white population (80% vs. 14%, p ​< ​0.0001), and longer life expectancy (81 vs. 72 years, p ​< ​0.0002), but tended to have a lower price of CACS ($86 vs. $487, p ​< ​0.08). Conclusions and relevanceCACS is a powerful, evidenced-based clinical tool, but the availability and price vary widely in Chicagoland, and directly correlate with the socioeconomic and health care disparities that are known to exist. Removing these barriers to coronary artery disease screening may be one method to improve the poor cardiovascular outcomes in these areas.

Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds.

SummaryThe number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.

Political frames of public health crises: Discussing the opioid epidemic in the US Congress

When and how do politicians talk about public health crises? Using evidence from the opioid crisis in the United States, this paper assembles and analyzes novel data on Congressional statements to explore the conditions under which politicians (1) issue public statements about opioids and (2) frame the opioid crisis as a predominantly public health or law enforcement problem. We examined 3.8 million Congressional floor speeches and 111,000 public statements to identify (1) floor speeches about drug crises in the 97th to 114th Congresses (1981–2017) and (2) public statements about the opioid crisis in the 116th Congress (2019–2020). Moderate ideology, women, greater overdose deaths, and larger white populations are associated with significantly higher frequencies of opioid statements. Using a dictionary-based text analysis approach, we find that ideologically liberal and African American legislators are more likely to use public health framing, while ideologically conservative members are more likely to use law enforcement framing and refer to national borders or foreign countries in opioid statements. Democrats/liberals more often referenced medication treatment for opioids. These findings imply two broader conclusions about the nature of political discourse in public health crises. First, that political extremists are least likely to talk about opioids suggests that increasing partisan polarization may result in less discussion, emphasis, and expertise in public health issues. Second, the tenor of discourse about opioids and other public health crises is likely to change with partisan electoral waves, potentially hindering long term planning of public health capacity.

Longevity and lifetime reproductive trait genetic parameter estimates from Thai Landrace and Large White pig populations.

The objective of this study was to estimate genetic parameters for age at first farrowing (AFF), length of productive life (LPL), lifetime number of piglets born alive (LNBA), lifetime number of piglets weaned (LNW), lifetime wean to first service interval (LW2S), and lifetime pig efficiency (LTP365) from commercial Thai Landrace and Large White populations. Data from 12,843 Landrace (LR) and 14,757 Large White (LW) sows in a Thai commercial pork production system were utilized in this study. The genetic parameters for each trait were estimated using the average information restricted maximum likelihood algorithm where a multivariate animal model was implemented. Heritability estimates for AFF and LPL were low for LR (0.11 and 0.02, respectively) and LW (0.19 and 0.07, respectively). Heritability estimates for lifetime traits ranged from 0.01 to 0.05 for LR and 0.04 to 0.09 for LW. The genetic correlation between LPL with LNBA, LNW, LW2S and LTP365 were positive for LR (0.39 to 0.90) and LW (0.59 to 0.94). Favourable genetic correlations were observed between AFF and LPL for LR (- 0.14) and LW (- 0.14). The phenotypic correlations between LPL and lifetime traits ranged from 0.64 to 0.92 for LR and 0.61 to 0.91 for LW. Favourable phenotypic correlation between AFF and lifetime production traits was observed in the present study. The estimated heritability for the length of productive life and lifetime traits was relatively lowly heritable; length of productive life is genetically associated with lifetime traits. These findings indicate that sow lifetime productivity could be improved using selection on LPL and AFF without antagonism. Thus, improving sow lifetime productivity in the commercial pork production system, AFF and LPL should be included in a maternal line genetic evaluation programme.

Endocrine Fertility Parameters-Genomic Background and their Genetic Relationship to Boar Taint in German Landrace and Large White.

Simple SummaryBreeding against boar taint compounds androstenone and skatole can be an efficient alternative for surgical castration of young piglets during their first week of life to avoid boar taint. Physiological links of androstenone to steroid hormones in the synthesis pathway are documented and they have to be analyzed for their genetic effects on reproduction and fertility. While using boar taint and hormone data from Landrace and Large White pigs (commercial nucleus populations and herd book populations), the effects of breeding against androstenone on fertility were evaluated. Moreover, the genetic foundation of the chosen hormones’ testosterone, 17β-estradiol, luteinizing hormone, follicle-stimulating hormone, and progesterone was analyzed and then checked for possible pleiotropic effects with boar taint compounds. The results showed consistent unfavorable side effects of breeding against androstenone on testosterone and 17β-estradiol in both breeds. The other hormones showed contrary results regarding unfavorable relationships between boar taint and endocrine fertility parameters. The genetic foundation showed a high potential of breeding against boar taint but the impact on fertility potential should be supervised.The surgical castration of young male piglets without anesthesia is no longer allowed in Germany from 2021. One alternative is breeding against boar taint, but shared synthesis pathways of androstenone (AND) and several endocrine fertility parameters (EFP) indicate a risk of decreasing fertility. The objective of this study was to investigate the genetic background between AND, skatole (SKA), and six EFP in purebred Landrace (LR) and Large White (LW) populations. The animals were clustered according to their genetic relatedness because of their different origins. Estimated heritabilities (h2) of AND and SKA ranged between 0.52 and 0.34 in LR and LW. For EFP, h2 differed between the breeds except for follicle-stimulating hormone (FSH) (h2: 0.28–0.37). Both of the breeds showed unfavorable relationships between AND and testosterone, 17-β estradiol, and FSH. The genetic relationships (rg) between SKA and EFP differed between the breeds. A genome-wide association analysis revealed 48 significant associations and confirmed a region for SKA on Sus Scrofa chromosome (SSC) 14. For EFP, the results differed between the clusters. In conclusion, rg partly confirmed physiologically expected antagonisms between AND and EFP. Particular attention should be spent on fertility traits that are based on EFP when breeding against boar taint to balance the genetic progress in both of the trait complexes.