Haplotype-resolved 3D chromatin architecture of the hybrid pig.

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution.

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products.

Genomic prediction of pig growth traits based on machine learning.

This study aimed to assess and compare the performance of different machine learning models in predicting selected pig growth traits and genomic estimated breeding values (GEBV) using automated machine learning, with the goal of optimizing whole-genome evaluation methods in pig breeding. The research employed genomic information, pedigree matrices, fixed effects, and phenotype data from 9968 pigs across multiple companies to derive four optimal machine learning models: deep learning (DL), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGB). Through 10-fold cross-validation, predictions were made for GEBV and phenotypes of pigs reaching weight milestones (100 kg and 115 kg) with adjustments for backfat and days to weight. The findings indicated that machine learning models exhibited higher accuracy in predicting GEBV compared to phenotypic traits. Notably, GBM demonstrated superior GEBV prediction accuracy, with values of 0.683, 0.710, 0.866, and 0.871 for B100, B115, D100, and D115, respectively, slightly outperforming other methods. In phenotype prediction, GBM emerged as the best-performing model for pigs with B100, B115, D100, and D115 traits, achieving prediction accuracies of 0.547, followed by DL at 0.547, and then XGB with accuracies of 0.672 and 0.670. In terms of model training time, RF required the most time, while GBM and DL fell in between, and XGB demonstrated the shortest training time. In summary, machine learning models obtained through automated techniques exhibited higher GEBV prediction accuracy compared to phenotypic traits. GBM emerged as the overall top performer in terms of prediction accuracy and training time efficiency, while XGB demonstrated the ability to train accurate prediction models within a short timeframe. RF, on the other hand, had longer training times and insufficient accuracy, rendering it unsuitable for predicting pig growth traits and GEBV.

An Analysis of the COVID-19-Induced Flexible Grading Policy at a Public University.

To help students cope with the challenges of the COVID-19 pandemic, higher education institutions offered students flexible grading policies that blended traditional letter grades with alternative grading options such as the pass-fail or credit-no credit options. This study conducted an in-depth analysis of the flexible grading policy at a medium-sized university in the USA. We studied the differential selection of flexible grading options by course characteristics and students' sociodemographics and academic profiles between Spring 2020 and Spring 2021. We also examined the impacts of the policy on sequential courses. Our analysis utilized administrative and transcript data for undergraduate students at the study institution and employed a combination of descriptive statistics and regression models. The analysis revealed that the flexible grading policy was utilized differently depending on course characteristics, with core courses and subjects like mathematics, chemistry, and economics having higher rates of usage. Additionally, sociodemographic and academic profile factors led to varying degrees of utilization, with males, urban students, freshmen, and non-STEM majors using the policy more frequently. Furthermore, the analysis suggested that the policy may have disadvantaged some students as they struggled in subsequent courses after using the pass option. Several implications and directions for future research are discussed.

Genome-wide association studies identified loci associated with both feed conversion ratio and residual feed intake in Yorkshire pigs.

Feed occupies a significant proportion in the production cost of pigs, and the feed efficiency (FE) in pigs is of utmost economic importance. Hence, the objective of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes associated with FE-related traits, including feed conversion ratio (FCR) and residual feed intake (RFI). A genome-wide association study was conducted for FCR and RFI in 169 Yorkshire pigs using whole-genome sequencing data. A total of 23 and 33 suggestive significant SNPs (P < 1 × 10-6) were detected for FCR and RFI, respectively. However, none of SNPs achieved the genome-wide significance threshold (P < 5 × 10-8). Importantly, three common SNPs (SSC7:7987268, SSC13:42350250, and SSC13:42551718) were associated with both FCR and RFI. Additionally, the NEDD9 gene related to FCR and RFI traits was overlapped. This study detected novel SNPs on SSC7 and SSC13 common for FCR and RFI. These results provide new insights into the genetic mechanisms and candidate genes of FE-related traits in pigs.

Small extracellular vesicles derived from dermal fibroblasts promote fibroblast activity and skin development through carrying miR-218 and ITGBL1.

Skin thickness is closely related to the appearance of human skin, such as sagging and wrinkling, which primarily depends on the level of collagen I synthesized by dermal fibroblasts (DFs). Small extracellular vesicles (SEVs), especially those derived from human DFs (HDFs), are crucial orchestrators in shaping physiological and pathological development of skin. However, the limited supply of human skin prevents the production of a large amount of HDFs-SEVs, and pig skin is used as a model of human skin. In this study, SEVs derived from DFs of Chenghua pigs (CH-SEVs), considered to have superior skin thickness, and Large White pigs (LW-SEVs) were collected to compare their effects on DFs and skin tissue. Our results showed that, compared with LW-SEVs, CH-SEVs more effectively promoted fibroblast proliferation, migration, collagen synthesis and contraction; in addition, in mouse model injected with both SEVs, compared with LW-SEVs, CH-SEVs increased the skin thickness and collagen I content more effectively. Some differentially expressed miRNAs and proteins were found between CH-SEVs and LW-SEVs by small RNA-seq and LC-MS/MS analysis. Interestingly, we identified that CH-SEVs were enriched in miRNA-218 and ITGBL1 protein, which played important roles in promoting fibroblast activity via activation of the downstream TGFß1-SMAD2/3 pathway in vitro. Furthermore, overexpression of miRNA-218 and ITGBL1 protein increased the thickness and collagen I content of mouse skin in vivo. These results indicate that CH-SEVs can effectively stimulate fibroblast activity and promote skin development and thus have the potential to protect against and repair skin damage.

Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire, Liangshan, and Qingyu pigs.

Here we used two kinds of chips data from 5 pig breeds, Chinese Duroc (DD), Landrace (LL), Yorkshire (YY), Liangshan (LS), and Qingyu pigs (QY) in China to identify genes which show evidence of selection during domestication. Four breed pairs, LS-YY, QY-YY, DD-YY, and LL-YY pair, were performed to detect selection signatures using the Fst method. Then we identified a list of genes that played key roles in domestication and artificial selection. For example, the PTPRM gene was shared in LS-YY, QY-YY, and DD-YY pairs and it regulates a variety of cellular processes including cell growth, differentiation as signaling molecules. The HACD3 gene was shared in QY-YY and DD-YY pairs, and the HACD3 protein is involved in the production of very long-chain fatty acids of different chain lengths. Besides, the MYH11 gene that related to muscle contraction was found in LS-YY and LL-YY pair. These results suggested that genes related to immunity, disease resistance, and metabolism were subjected to strong selection pressure in Chinese domestic pigs in the progress of domestication and evolution; however, genes related to appearance, production performance, and reproduction were undergone strong artificial selection in commercial pig breeds.

Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs.

The Chinese Qingyu pig is a typical domestic fatty pig breed and an invaluable indigenous genetic resource in China. Compared with the Landrace pig, the Qingyu pig has unique meat characteristics, including muscle development, intramuscular fat, and other meat quality traits. At present, few studies have explored epigenetic differences due to DNA methylation between the Qingyu pig and the Landrace pig. In this study, 30 Qingyu pigs and 31 Landrace pigs were subjected to reduced representation bisulfite sequencing (RRBS). Genome-wide differential DNA methylation analysis was conducted. Six genomic regions, including regions on Sus scrofa chromosome (SSC) 1: 266.09-274.23 Mb, SSC5: 0.88-10.68 Mb, SSC8: 41.23-48.51 Mb, SSC12: 45.43-54.38 Mb, SSC13: 202.15-207.95 Mb, and SSC14: 126.43-139.85 Mb, were regarded as key regions that may be associated with phenotypic differences between the Qingyu pig and the Landrace pig. Furthermore, according to further analysis, five differentially methylated genes (ADCY1, FUBP3, GRIN2B, KIT, and PIK3R6) were identified as key candidate genes that might be associated with meat characteristics. Our findings provide new insights into the differences in DNA methylation between the Qingyu pig and the Landrace pig. These results enrich the epigenetic research of the Chinese Qingyu pig.

Transcriptome analysis reveals key genes and pathways associated with piglet fetal mummification.

China has the largest pork consumption worldwide. However, the high incidence of piglet fetal mummification (3%-5%) is an important factor that causes the slow improvement of pig reproductive capacity, and the genetic mechanism is still unclear. This study aimed to identify candidate genes associated with piglet fetal mummification. RNA-seq technology was used to compare transcriptome profiling of blood from healthy and mummified piglets at different stages of pregnancy (35, 56, 77, and 98 days). A total of 137-420 differentially expressed genes (DEGs) were detected at each stage. Seven DEGs were significantly differentially expressed at various stages. IL-9R, TLR8, ABLIM3, FSH-α, ASCC1, PRKCZ, and GCK may play important roles in the course of piglet fetal mummification. The differential genes we identified between the groups were mainly enriched in immune and inflammation regulation, while others were mainly enriched in reproduction. Considering the function of candidate genes, IL-9R and TLR8 were suggested as the most promising candidate genes involved in mummified piglet traits. We speculate that during pregnancy, it may be the combined effects of the above-mentioned inflammation, immune response, and reproduction-related signaling pathways that affect the occurrence of mummified piglets and further affect pig reproduction.

MicroRNA-126b-5p Exacerbates Development of Adipose Tissue and Diet-Induced Obesity.

Obesity has become a worldwide epidemic, caused by many factors such as genetic regulatory elements, unhealthy diet, and lack of exercise. MicroRNAs (miRNAs) are non-coding single-stranded RNA classes, which are about 22 nucleotides in length and highly conserved among species. In the last decade, a series of miRNAs were identified as therapeutic targets for obesity. In the present study, we found that miR-126b-5p was associated with adipogenesis. miR-126b-5p overexpression promoted the proliferation of 3T3-L1 preadipocytes by upregulating the expression of proliferation-related genes and downregulating the expression of apoptosis-related genes; the inhibition of miR-126b-5p gave rise to opposite results. Similarly, miR-126b-5p overexpression could promote the differentiation of 3T3-L1 preadipocytes by increasing the expression of lipid deposition genes and triglyceride (TG) and total cholesterol (TC) levels. Moreover, luciferase reporter assay demonstrated that adiponectin receptor 2 (Adipor2) and acyl-CoA dehydrogenase, long chain (ACADL) were the direct target genes of miR-126b-5p. Moreover, overexpression of miR-126b-5p could exacerbate the clinical symptoms of obesity when mice were induced by a high-fat diet, including increased adipose tissue weight, adipocyte volume, and insulin resistance. Interestingly, overexpression of miR-126b-5p in preadipocytes and mice could significantly increase total fatty acid content and change the fatty acid composition of adipose tissue. Taken together, the present study showed that miR-126b-5p promotes lipid deposition in vivo and in vitro, indicating that miR-126b-5p is a potential target for treating obesity.

miR-370-3p Regulates Adipogenesis through Targeting Mknk1.

Excessive fat accumulation can lead to obesity, diabetes, hyperlipidemia, atherosclerosis, and other diseases. MicroRNAs are a class of microRNAs that regulate gene expression and are highly conserved in function among species. microRNAs have been shown to act as regulatory factors to inhibit fat accumulation in the body. We found that miR-370-3p was expressed at lower levels in the fat mass of mice on a high-fat diet than in mice on a normal control diet. Furthermore, our data showed that the overexpression of miR-370-3p significantly suppressed the mRNA expression levels of adipogenic markers. Thus, miR-370-3p overexpression reduced lipid accumulation. Conversely, the inhibition of miR-370-3p suppressed 3T3-L1 preadipocyte proliferation and promoted preadipocyte differentiation. In addition, Mknk1, a target gene of miR-370-3p, plays an opposing role in preadipocyte proliferation and differentiation. Moreover, consistent results from in vitro as well as in vivo experiments suggest that the inhibition of fat accumulation by miR-370-3p may result from the inhibition of saturated fatty acids that promote the accumulation of polyunsaturated fatty acids. In conclusion, these results suggest that miR-370-3p plays an important role in adipogenesis and fatty acid metabolism through the regulation of Mknk1.

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.

Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.

MicroRNA-351-5p mediates skeletal myogenesis by directly targeting lactamase-ß and is regulated by lnc-mg.

Skeletal muscle is an important and complex organ with a variety of functions in humans and animals. Skeletal myogenesis is a multistep and complex process, and increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) play critical roles in skeletal myogenesis. In this study the expression of miR-351-5p is dynamically regulated during skeletal myogenesis in vitro and in vivo. Cell-counting kit-8, qRT-PCR, and EdU immunofluorescence analysis showed that miR-351-5p overexpression promoted the proliferation and inhibited the differentiation of C2C12 myoblast, whereas inhibition of miR-351-5p had the opposite effect. In addition, miR-351-5p mediated the regulation of muscle fiber type transition in vivo. In vitro, loss of miR-351-5p in muscle tissues promoted muscle hypertrophy and increased slow-twitch fibers in the gastrocnemius muscles of mice. Luciferase reporter assay and functional analyses demonstrated that lactamase ß ( LACTB) is a direct target of miR-351-5p involved in the regulation of skeletal myogenesis. Expression levels of a myogenesis-associated lncRNA ( lnc-mg) correlated negatively with miR-351-5p and positively with LACTB during C2C12 myoblast proliferation and differentiation. Further analyses showed that lnc-mg acted as a molecular sponge for miR-351-5p, demonstrating its involvement in the negative regulation of LACTB by miR-351-5p during skeletal myogenesis. These findings indicate that miRNA-351-5p functions in skeletal myogenesis by targeting LACTB and is regulated by lnc-mg, supporting the role of the competing endogenous RNA network in skeletal myogenesis.-Du, J., Zhang, P., Zhao, X., He, J., Xu, Y., Zou, Q., Luo, J., Shen, L., Gu, H., Tang, Q., Li, M., Jiang, Y., Tang, G., Bai, L., Li, X., Wang, J., Zhang, S., Zhu, L. MicroRNA-351-5p mediates skeletal myogenesis by directly targeting lactamase ß and is regulated by lnc-mg.

Correction to: Intrathecal Epigallocatechin Gallate Treatment Improves Functional Recovery After Spinal Cord Injury by Upregulating the Expression of BDNF and GDNF.

Since the publication of our article [1] it has come to our attention that there was an error in Figure 4 in which the bottom left immunochemistry panel Control/Bax was a duplication of the bottom right immunohistochemistry panel EGCG/GDNF in Figure 3.

Whole-genome sequencing association analysis reveals the genetic architecture of meat quality traits in Chinese Qingyu pigs.

The Chinese Qingyu pig breed is an invaluable indigenous genetic resource. However, few studies have investigated the genetic architecture of meat quality traits in Qingyu pigs. Here, 30 purebred Qingyu pigs were subjected to whole-genome sequencing. After quality control, 18 436 759 SNPs were retained. Genome-wide association studies (GWAS) were then performed for meat pH and color at three postmortem time points (45 min, 24 h, and 48 h) using single-marker regression analysis. In total, 11 and 69 SNPs were associated with meat pH and color of the longissimus thoracis muscle (LTM), respectively, while 54 and 29 SNPs were associated with meat pH and color of the semimembranosus muscle (SM), respectively. Seven SNPs associated with pork pH were shared by all three postmortem time points. Several candidate genes for meat traits were identified, including four genes (CXXC5, RYR3, BNIP3, and MYCT1) related to skeletal muscle development, regulation of Ca2+ release in the muscle, and anaerobic respiration, which are promising candidates for selecting superior meat quality traits in Qingyu pigs. To our knowledge, this is the first study investigating the postmortem genetic architecture of pork pH and color in Qingyu pigs. Our findings further the current understanding of the genetic factors influencing meat quality.

Bidirectional regulation of genistein on the proliferation and differentiation of C2C12 myoblasts.

Genistein is a widely studied phytoestrogen. The effects of genistein on myoblasts were reported long ago, but the conclusions are controversial. In this study, we evaluated the effects of different concentrations of genistein on C2C12 myoblasts. Genistein treatment promoted myoblast proliferation in a dose-dependent manner in the concentration range of 0-2 µM/L, reaching its maximum effect at 2 µM/L. Proliferation then declined, and a concentration higher than 20 µM/L showed significant inhibition. In addition, genistein treatment promoted myoblast differentiation at a dose of 10 µM/L. However, at treatment concentrations higher than 10 µM/L, the effect on myoblast differentiation was rapidly inhibited as the concentration increased. Genistein treatment also down-regulated the expression of miR-222, resulting in increased expression of its target genes, MyoG, MyoD, and ERα and thereby promoting myoblast differentiation. Our results suggest that genistein has a dose-dependent and bidirectional regulation effect on myoblast proliferation and differentiation. We also found that genistein is a miRNA inducer, and it specifically affects the expression of miR-222 to regulate myoblast differentiation.

SNPs associated with body weight and backfat thickness in two pig breeds identified by a genome-wide association study.

Growth and fat deposition are important economic traits due to the influence on production in pigs. In this study, a dataset of 1200 pigs with 345,570 SNPs genotyped by sequencing (GBS) was used to conduct a GWAS with single-marker regression method to identify SNPs associated with body weight and backfat thickness (BFT) and to search for candidate genes in Landrace and Yorkshire pigs. A total of 27 and 13 significant SNPs were associated with body weight and BFT, respectively. In the region of 149.85-149.89 Mb on SSC6, the SNP (SSC6: 149876737) for body weight and the SNP (SSC6: 149876507) for BFT were in the same locus region (a gap of 230 bp). Two SNPs were located in the DOCK7 gene, which is a protein-coding gene that plays an important role in pigmentation. Two SNPs located on SSC8: 54567459 and SSC11: 33043081 were found to overlap weight and BFT; however, no candidate gene was found in these regions. In addition, based on other significant SNPs, two positional candidate genes, NSRP1 and CADPS, were proposed to influence weight. In conclusion, this is the first study report using GBS data to identify the significant SNPs for weight and BFT. A total of four particularly interesting SNPs and one potential candidate genes (DOCK7) were found for these traits in domestic pigs. This study improves our knowledge to better understand the complex genetic architecture of weight and BFT, but further validation studies of these candidate loci and genes are recommended in pigs.

Genome-wide association study for backfat thickness at 100 kg and loin muscle thickness in domestic pigs based on genotyping by sequencing.

Both backfat thickness at 100 kg (B100) and loin muscle thickness (LMT) are economically important traits in pigs. In this study, a total of 1,200 pigs (600 Landrace and 600 Yorkshire pigs) were examined with genotyping by sequencing. A total of 345,570 single nucleotide polymorphisms (SNPs) were obtained from 1,200 pigs. Then, a single marker regression test was used to conduct a genome-wide association study for B100 and LMT. A total of 8 and 90 significant SNPs were detected for LMT and B100, respectively. Interestingly, two shared significant loci [located at Sus scrofa chromosome (SSC) 6: 149876694 and SSC12: 46226580] were detected in two breeds for B100. Furthermore, three potential candidate genes were found for LMT and B100. The positional candidate gene FAM3C (SSC18: 25573656, P = 2.48 × 10-9), which controls the survival, growth, and differentiation of tissues and cells, was found for LMT in Landrace pigs. At SSC9: 6.78-6.82 Mb in Landrace pigs, the positional candidate gene, INPPL1, which has a negative regulatory effect on diet-induced obesity and is involved in the regulation of insulin function, was found for B100. The candidate gene, RAB35, which regulates the adipocyte glucose transporter SLC2A4/GLUT4, was identified at approximately SSC14: 40.09-40.13 Mb in Yorkshire pigs. The results of this GWAS will greatly advance our understanding of the genetic architecture of the LMT and B100 traits. However, these identified loci and genes need to be further verified in more pig populations, and their functions also need to be validated by more biological experiments in pigs.

A genome wide association study for the number of animals born dead in domestic pigs.

BACKGROUND: The number of animals born dead, which includes the number of mummified (NM) and stillborn (NS) animals, is the most important trait to directly quantify the reproductive loss in domestic pigs. In this study, 282 Landrace sows and 250 Large White sows were genotyped by sequencing (GBS). A total of 816 and 1068 litter records for NM and NS were collected from them. A genome-wide association study (GWAS) was conducted to reveal the genetic difference between NM and NS. RESULTS: A total of 248 and 10 genome-wide significant SNPs were detected for NM and NS across numerous parities in Landrace pigs. The corresponding numbers for Large White pigs were 175 and 6, respectively. All of the detected SNPs were parity specific for both NM and NS in two breeds. Based on significant SNPs, in total 242 (146 for Landrace pig, 96 for Large White pig) and 10 significant chromosome regions (8 for Landrace pigs, 2 for Large White pigs) were found for NM and NS, respectively. Among them, 237 (142 for Landrace pig, 95 for Large White pig) and 8 significant chromosome regions (6 for Landrace pigs, 2 for Large White pigs) for NM and NS were not reported in previous studies. A list of candidate genes at the identified loci was proposed, including HMGB1, SOX5, KCNJ8, ABCC9 and YY1 for NM, ASTN1 for NS. CONCLUSION: This is the first time when GBS data was used to identify genetic regions affecting NM and NS in Landrace and Large White pigs. Many identified informative SNPs and candidate genes advance our understanding of the genetic architecture of NM and NS in pigs. However, further studies are needed to validate using larger populations with more breeds.

Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs.

In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.