A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population.

BACKGROUND: Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs. RESULTS: Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function. CONCLUSIONS: We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.

Transcriptomic analysis of uterine receptivity in Guinea pigs.

The mouse is a widely used animal model for studying human reproduction. However, the mice are eccentric implantation, and ovarian progesterone and estrogen are essential for implantation, which is different from human beings. Guinea pigs are unique from mice since, like humans, they are the interstitial implantation, and ovarian progesterone alone seems to be sufficient to allow for implantation. In this study, we firstly analyzed the gene expression profiles in the receptive uterus on day 5 of pregnancy compared to the pre-receptive uterus on day 3 of pregnancy in guinea pigs using the RNA-seq method. In total, 304 up-regulated and 475 down-regulated genes were identified. Gene Ontology and pathway enrichment analyses highlighted the importance of the inflammatory response in the receptive uterus. Through gene network analysis, we identified 24 hub genes, most of which were involved in regulating endometrial receptivity. In addition, we performed a cross-species comparison of differentially expressed genes associated with uterine receptivity. A total of 14 genes were shared among guinea pigs, humans, and mice. Furthermore, Fisher's exact test revealed that gene expression patterns of uterine receptivity were more similar between guinea pigs and humans than between mice and humans. Our study may contribute to increasing the knowledge of uterine receptivity in guinea pigs.

A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations.

BACKGROUND: Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. RESULTS: In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. CONCLUSIONS: We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs.

BACKGROUND: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations. RESULTS: Our study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA, GPER1, PNPLA2 and BSCL2. CONCLUSIONS: The present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs.

Does universal health insurance coverage reduce unmet healthcare needs in China? Evidence from the National Health Service Survey.

BACKGROUND: China has nearly achieved universal health insurance coverage, but considerable unmet healthcare needs still exist. Although this topic has attracted great attention, there have been few studies examining the relationship between universal health insurance coverage and unmet healthcare needs. This study aimed to clarify the impact of universal health insurance coverage and other associated factors on Chinese residents' unmet healthcare needs. METHODS: Data was derived from the fourth, fifth, and sixth National Health Service Survey of Jiangsu Province, which were conducted in 2008, 2013, and 2018, respectively. Descriptive statistics were used to analyze the prevalence of unmet healthcare needs. Binary multivariate logistic regression was used to estimate the association between unmet healthcare needs and universal health insurance coverage, along with other socioeconomic factors. RESULTS: 8.99%, 1.37%, 53.37%, and 13.16% of the respondents in Jiangsu Province reported non-use of outpatient services, inpatient services, physical examinations, and early discharge from hospital, respectively. The trend in the prevalence of unmet healthcare needs showed a decline from 2008 to 2018. Health insurance had a significant reducing effect on non-use of outpatient services, inpatient services, or early discharge from hospital. People having health insurance in 2013 and 2018 were significantly less likely to report unmet healthcare needs compared to those in 2008. The effect of health insurance and its universal coverage on reducing unmet healthcare needs was greater in rural than in urban areas. Other socioeconomic factors, such as age, marital status, educational level, income level, or health status, also significantly affected unmet healthcare needs. CONCLUSIONS: Universal health insurance coverage has significantly reduced Chinese residents' unmet healthcare needs. Policy efforts should pay more attention to the benefits of health insurances in rural areas and optimize urban-rural health resources to promote effective utilization of healthcare.

Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models.

BACKGROUND: More teats are necessary for sows to nurse larger litters to provide immunity and nutrient for piglets prior to weaning. Previous studies have reported the strong effect of an insertion mutation in the Vertebrae Development Associated (VRTN) gene on Sus scrofa chromosome 7 (SSC7) that increased the number of thoracic vertebrae and teat number in pigs. We used genome-wide association studies (GWAS) to map genetic markers and genes associated with teat number in two Duroc pig populations with different genetic backgrounds. A single marker method and several multi-locus methods were utilized. A meta-analysis that combined the effects and P-values of 34,681 single nucleotide polymorphisms (SNPs) that were common in the results of single marker GWAS of American and Canadian Duroc pigs was conducted. We also performed association tests between the VRTN insertion and teat number in the same populations. RESULTS: A total of 97 SNPs were found to be associated with teat number. Among these, six, eight and seven SNPs were consistently detected with two, three and four multi-locus methods, respectively. Seven SNPs were concordantly identified between single marker and multi-locus methods. Moreover, 26 SNPs were newly found by multi-locus methods to be associated with teat number. Notably, we detected one consistent quantitative trait locus (QTL) on SSC7 for teat number using single-locus and meta-analysis of GWAS and the top SNP (rs692640845) explained 8.68% phenotypic variance of teat number in the Canadian Duroc pigs. The associations between the VRTN insertion and teat number in two Duroc pig populations were substantially weaker. Further analysis revealed that the effect of VRTN on teat number may be mediated by its LD with the true causal mutation. CONCLUSIONS: Our study suggested that VRTN insertion may not be a strong or the only candidate causal mutation for the QTL on SSC7 for teat number in the analyzed Duroc pig populations. The combination of single-locus and multi-locus GWAS detected additional SNPs that were absent using only one model. The identified SNPs will be useful for the genetic improvement of teat number in pigs by assigning higher weights to associated SNPs in genomic selection.

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.

Integrated Single-Trait and Multi-Trait GWASs Reveal the Genetic Architecture of Internal Organ Weight in Pigs.

Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.

Genome-Wide Association Study for Somatic Skeletal Traits in Duroc × (Landrace × Yorkshire) Pigs.

The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.

Genome-wide association study for loin muscle area of commercial crossbred pigs.

OBJECTIVE: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY). METHODS: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows). RESULTS: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [GHR] and 3-oxoacid Co A-transferase 1 [OXCT1]) that are associated with fat deposition and muscle growth and found further additional genes (MYOCD, ARHGAP44, ELAC2, MAP2K4, FBXO4, FBLL1, RARS1, SLIT3, and RANK3) that are presumed to have an effect on LMA. CONCLUSION: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.

BACKGROUND: Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs. RESULTS: We produced WGS data (18,695,907 SNPs and 2,106,902 INDELs exceed quality control) from 1,469 sequenced Duroc × (Landrace × Yorkshire) pigs and developed a reference panel for meat quality including meat color score, marbling score, L* (lightness), a* (redness), and b* (yellowness) of genomic prediction. The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population. Using different marker density panels derived from WGS data, accuracy differed substantially among meat quality traits, varied from 0.08 to 0.47. Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39% to 75%. We optimized the marker density and found medium- and high-density marker panels are beneficial for the estimation of heritability for meat quality. Moreover, we conducted genotype imputation from 50K chip to WGS level in the same population and found average concordance rate to exceed 95% and r2 = 0.81. CONCLUSIONS: Overall, estimation of heritability for meat quality traits can benefit from the use of WGS data. This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions.

BACKGROUND: The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain. RESULTS: In the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase. CONCLUSIONS: The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs.

The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.

Universal Health Insurance Coverage and the Economic Burden of Disease in Eastern China: A Pooled Cross-Sectional Analysis From the National Health Service Survey in Jiangsu Province.

China has achieved universal social health insurance coverage, but it is unclear whether this has alleviated the economic burden of disease for individuals. This was investigated in the present study by analyzing National Health Service Survey (2008-2018) data from Jiangsu province. Ordinary least squares and binary multivariate logistic regression of pooled cross-sectional data were carried out to evaluate the effect of universal health insurance coverage and other socioeconomic factors on the economic burden of disease. Total health expenses (THE) first increased and then decreased during the survey period while out-of-pocket health expenses (OOP) decreased except for urban residents, for whom OOP increased after 2013. Household catastrophic health expenditure (HCHE) was stable between 2008 and 2013 but increased after 2013. Social health insurance had a significant positive effect on the annual THE and OOP and a negative effect on HCHE, however, universal health insurance coverage could alleviated THE and the economic burden of disease on individuals (OOP) while it was insufficient to protect against the economic risk of diseases (HCHE), with greater benefits for urban as compared to rural residents. Other socioeconomic factors including age, marital status, education, income, and health status also influenced the economic burden of disease.

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis.

Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1, and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1, and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggest that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Backfat thickness (BFT) is a complex and economically important trait in the pig industry because it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, two Duroc populations were genotyped using SNP chips, and genome-wide association analysis was used to identify SNPs and candidate genes related to BFT. A number of genetic markers and candidate genes including MC4R, RYR1, HMGA1, NUDT3, SIRT2, NKAIN2, AMH, SORCS1, and SORCS3 were identified to be significantly related to BFT. Our data suggest that many of the candidate genes can be directly used for genetic improvement through molecular markers.

The Genetic Architecture of Meat Quality Traits in a Crossbred Commercial Pig Population.

Meat quality is of importance in consumer acceptance and purchasing tendency of pork. However, the genetic architecture of pork meat quality traits remains elusive. Herein, we conducted genome-wide association studies to detect single nucleotide polymorphisms (SNPs) and genes affecting meat pH and meat color (L*, lightness; a*, redness; b*, yellowness) in 1518 three-way crossbred pigs. All individuals were genotyped using the GeneSeek Porcine 50K BeadChip. In sum, 30 SNPs and 20 genes are found to be associated with eight meat quality traits. Notably, we detect one significant quantitative trait locus (QTL) on SSC15 with a 143 kb interval for meat pH (pH_12h), together with the most promising candidate TNS1. Interestingly, two newly identified SNPs located in the TTLL4 gene demonstrate the highest phenotypic variance of pH_12h in this QTL, at 2.67%. The identified SNPs are useful for the genetic improvement of meat quality traits in pigs by assigning higher weights to associated SNPs in genomic selection.

Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population.

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56-3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs.

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.

Using nontargeted LC-MS metabolomics to identify the Association of Biomarkers in pig feces with feed efficiency.

BACKGROUND: Improving feed efficiency is economically and environmentally beneficial in the pig industry. A deeper understanding of feed efficiency is essential on many levels for its highly complex nature. The aim of this project is to explore the relationship between fecal metabolites and feed efficiency-related traits, thereby identifying metabolites that may assist in the screening of the feed efficiency of pigs. RESULTS: We performed fecal metabolomics analysis on 50 individuals selected from 225 Duroc x (Landrace x Yorkshire) (DLY) commercial pigs, 25 with an extremely high feed efficiency and 25 with an extremely low feed efficiency. A total of 6749 and 5644 m/z features were detected in positive and negative ionization modes by liquid chromatography-mass spectrometry (LC/MS). Regrettably, the PCA could not classify the the samples accurately. To improve the classification, OPLS-DA was introduced. However, the predictive ability of the OPLS-DA model did not perform well. Then, through weighted coexpression network analysis (WGCNA), we found that one module in each positive and negative mode was related to residual feed intake (RFI), and six and three metabolites were further identified. The nine metabolites were found to be involved in multiple metabolic pathways, including lipid metabolism (primary bile acid synthesis, linoleic acid metabolism), vitamin D, glucose metabolism, and others. Then, Lasso regression analysis was used to evaluate the importance of nine metabolites obtained by the annotation process. CONCLUSIONS: Altogether, this study provides new insights for the subsequent evaluation of commercial pig feed efficiency through small molecule metabolites, but also provide a reference for the development of new feed additives.

Genome-wide association studies reveals polygenic genetic architecture of litter traits in Duroc pigs.

With continuous improvement of sow litter size, breeders are gradually paying more attention to the quality of litter traits that directly impact the production efficiency of pig companies, such as the rate of piglets born alive (RBA) and the rate of healthy births (RHB). The objectives of this study are to dissect the genetic basis of litter traits in pig and to identify valuable genes and genetic markers, especially pleiotropic, for pig breeding. Herein, 1140 Duroc pigs and 2046 reproduction records, 5 litter traits, including the number of healthy births (NHB), number of deformed fetuses (NDF), number of stillborn (NSB), RBA, and RHB, were used in this study. Subsequently, a genome-wide association study (GWAS) was performed for the five litter traits in the first two parities from two Duroc populations. A total of 76 significantly related SNPs and 10 potential candidate genes (CAV1, DAB2, FGF12, FHOD3, DYNC2H1, GRHL1, TCTN3, PYROXD2, MMP8, MMP13, and PGR) were detected, including 13 pleiotropic SNPs that affected more than one litter trait. Finally, the functional enrichment analysis of functional genes that were closest to these significant SNPs indicated that most of the significant pathways were associated with hormone secretion and embryo and organ development. This study advances our understanding of the genetic mechanisms of litter traits, especially the survival rate of piglets born, and provides an opportunity to increase the quality of litter using marker-assisted selection or genomic selection in pigs.