Muscle development and carcass yield of meat indigenous and exotic pigs vary significantly. DNA methylation, being a major epigenetic factor, could regulate myogenic process through regulation of gene expression. The objective of the present study was to compare genome-wide methylation in indigenous (Mali) and exotic (Hampshire) breeds of pigs. A total 1549 differentially methylated regions (P<0.1) in the genome with hypermethylation around the promoter-transcription start site of MYMK gene were identified in Mali pigs. No differences in the DNA methylation was observed with respect to promoter region of other myogenic genes. Ontology of genes whose bodies were differentially methylated, were related to gaseous exchange, lipid metabolism, opioid, nephrin and DARPP-32 signalling. Based on the study, it may be concluded that differences exist in the muscle tissue DNA methylation between Mali and Hampshire pigs. Further studies are required to understand the implication of the differential methylation in myogenic process in pigs.

In modern pig production systems, controlled breeding and regulation of ovarian function through manipulation of estrous cycle can be employed to improve reproduction and productivity. Estrous cycle can be regulated with the use of managerial and pharmacological agents which are based on controlling follicular maturation and ovulation or altering the luteal phase. In the past three decades, significant progress has been made in the area of controlled reproduction in pigs. Exogenous hormonal agents like progestogens, gonadotropin releasing hormone (GnRH), equine chorionic gonadotropin (eCG), human chorionic gonadotropin (hCG) and porcine luteinizing hormone (pLH) alone or in combination can be used to regulate estrus and ovulation in pigs. Many of these approaches can aid in batch flow management, maintaining optimal breedable pool of sows and gilts and downstream applications like fixed-time artificial insemination (FTAI). Multiple dose therapy of prostaglandin analogues, newer forms of GnRH analogues to synchronize ovulation for use in fixed-time AI (FTAI), use of pheromonal agents are some interesting developments in this field. Exogenous hormones and analogues have potential applications in pig reproduction but should not be applied as a complete alternative to good management practices. Further extensive research on potential influence of pharmaceutical agents, biologically-relevant pheromonal and other novel agents and application of targeted drug delivery on important reproductive processes could help in developing more efficient and viable controlled reproduction approaches in pigs.

Background: Principal component analysis (PCA) is a biometrical technique or a dimensionality reduction method where large number of measurements could be replaced by fewer measurements without significant loss of information. PCA is a multivariate methodology and helps to eliminate redundant traits and transforms original group of variables into another group known as principal components. It can be used with success when characteristics are correlated. PCA can help in accurate selection of superior animals. Methods: The present study was carried out in HD-K75 pigs maintained at ICAR-All India Coordinated Research on Pig, AAU, Khanapara, Guwahati, Assam, India. A total of 13 economic traits viz. age at sexual maturity (ASM), age at first fertile service (AFFS), age at first farrowing (AFF), farrowing interval (FI), litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), litter weight at weaning (LWW), teats number (TN), body weight at Birth (BWB), body weight at weaning (BWW), body weight at 5 month (BM5) and body weight at 8 month (BM8) were considered. Data were collected from a total of 164 sows. Data belonged to 8 years from 2015 to 2023. The principal component analysis was performed using the factor module in SPSS 24. Result: Factor analysis with varimax rotation uncovered four principal components, collectively explaining 84.18% of the total variance. The first, second, third and fourth principal component accounted for 29.71%, 29.33%, 12.683% and 12.452% of the variance. High component loading was found for LSW and LWW in first component, LSB for second component, BW5 for third component and BW8 for fourth component respectively. The communality values ranged from 0.980 (ASM and AFFS) to 0.608 (BWW). These findings indicate that PCA can serve as a valuable tool in breeding programmes, allowing for a significant reduction in the number of economic traits to be used in selection procedure.

Information on global transcriptomic changes in the porcine ampulla after ovulation is crucial for understanding of oviductal physiology at the molecular level. The objective of the present study was to investigate the differentially expressed genes (DEGs) and signalling pathways regulating the functionality of ampulla in pigs post-ovulation. The RNA-sequencing of the post-ovulatory ampulla (POA) and early luteal ampulla (ELA) tissues was conducted using Illumina NextSeq2000. The R package NOISeq was used to obtain significantly differentially expressed genes (DEGs) with the probability of differential expression (1-FDR) value ≥ 0.95 and log2 fold change (log2FC) ≥ 1, which revealed 817 DEGs (657 up- and 160 down-regulated) in the POA vs. ELA group comparison. These DEGs were functionally annotated with various gene ontology terms like sterol biosynthetic process, growth, cell migration, and Reactome pathways like signal transduction, metabolism, and cell cycle, indicating key role of these molecular events in POA. The WNT, TNFR2 non-canonical NF-kB, and hedgehog signalling pathways along with the activation of the immune system process, were enriched in the POA vs. ELA group, which indicates their role in cell–cell interactions and cell fate determination in remodelling the oviductal microenvironment during transition from estrogen to progesterone domination. The highly connected upregulated hub genes ESR1, RAD51, YARS1, TYMS and CDK2 can be regarded as key regulatory factors in synchronizing the changes in POA at the molecular level in the oviduct. The present study revealed several DEGs, signalling pathways and novel modulatory factors associated with the ampullary physiology during early embryonic development in the POA, which may influence fertility and litter size in pigs.

Investigations on heat stress induced transcriptomic changes is critical to characterization of candidate genes for thermal adaptability in livestock. Continues spells of high ambient temperature due to climate change has amplified reproductive dysfunctions, necessitating immediate attention. The present study aimed to explore the transcriptomic signature of heat stressed granulosa cells (GCs) and signalling pathways regulating their adaptability to thermal challenge. The GCs were collected from small follicles (3-6 mm) of pig ovary. The GCs primary culture was subjected to in vitro heat stress challenge at 42 OC for 6 h. RNA sequencing was conducted for heat stress (treated) and non-heat stress (control) groups using Illumina NextSeq2000 sequencing platform. The significant DEGs were selected using NOISeq R package with cut-offs, probability value >= 0.95 and log2 fold change >= 1. Bioinformatics analysis was conducted for exploring gene ontology enrichment, functional pathways, hub genes in protein-protein interaction network and functional clusters regulating cellular homeostasis and survivability during heat stress challenge. The analysis pipeline yielded a total of 12156 protein coding transcripts, which were expressed during heat stress challenge in GCs, out of which 4904 were differentially (prob. >= 0.95) expressed; 2936 were upregulated and 1968 were downregulated. The large number of DEGs and gene ontologies in the study specifies the concerted mechanisms involving multiple signalling pathways like MAPK, HIPPO, WNT, PI3-AKT, NFKB, NOTCH and many more operating in the cell to maintain cellular homeostasis. Thermal stress induced differentially expressed hub genes HSP90, HSPA8, HSPA5, TGFB1 and PPARG are key elements in stress, regulating multiple pathways and expression of transcription factors. The TNF signalling pathway, phosphatidyl inositol signalling system and DERL3 gene network linked ubiquitin-dependent endoplasmic reticulum associated protein degradation pathway, which regulates cell viability, proliferation, apoptosis and estrogen synthesis, can be regarded as novel regulators involved in stress adaptation in pigs.

The angiogenic cytokine vascular endothelial growth factor A (VEGFA) also exerts non-angiogenic effects on endocrine functionality of porcine luteal cells critical for progesterone (P4) production. The expression dynamics of VEGFA-FLT/KDR system were investigated using RT-qPCR during luteal stages and VEGFA gene knock out (KO) porcine luteal cells were generated using CRISPR/Cas9 technology. The downstream effects of VEGFA ablation were studied using RT-qPCR, Annexin V, MTT, ELISA for P4 estimation and scratch wound assay. Bioinformatics analysis of RNA-Seq data of porcine mid-luteal stage was conducted for exploring protein–protein interaction network, KEGG pathways, transcription factors and kinase mapping for VEGFA-FLT/KDR interactomes. The VEGFA-FLT/KDR system expressed throughout the luteal stages with highest expression during mid- luteal stage. Cellular morphology, structure and oil-red-o staining for lipid droplets did not differ significantly between VEGFA KO and wild type cells, however, VEGFA KO significantly decreased (p < 0.05) viability and proliferation efficiency of edited cells on subsequent passages. Expression of apoptotic gene, CASP3 and hypoxia related gene, HIF1A were significantly (p < 0.05) upregulated in KO cells. The relative mRNA expression of VEGFA and steroidogenic genes STAR, CYP11A1 and HSD3B1 decreased significantly (p < 0.05) upon KO, which was further validated by the significant (p < 0.05) decrease in P4 output from KO cells. Bioinformatics analysis mapped VEGFA-FLT/KDR system to signalling pathways associated with steroidogenic cell functionality and survival, which complemented the findings of the study. The ablation of VEGFA gene resulted in decreased steroidogenic capability of luteal cells, which suggests that VEGFA exerts additional non-angiogenic regulatory effects in luteal cell functionality.

Helicobacter species (spp.) is a gram-negative spiral-shaped motile bacterium that causes gastritis in pigs and also colonizes in the human stomach. The present study assessed the prevalence of Helicobacter spp. in pig gastric mucosa and the stool of pig farmers in Assam, India. A total of 403 stomach samples from pig slaughter points, 74 necropsy samples of pigs from pig farms, and 97 stool samples from pig farmers were collected. Among the pig stomach samples, 43 (20.09%) of those with gastritis showed the presence of Gram-negative, spiral-shaped organisms, while only 3.04% of stomach samples without lesions had these organisms. Scanning Electron Microscopy (SEM) of urease-positive stomach samples revealed tightly coiled Helicobacter bacteria in the mucus lining. Histopathological examination showed chronic gastritis with hemorrhagic necrosis, leucocytic infiltration, and lymphoid aggregates. PCR confirmed the presence of Helicobacter suis in 19.63% of pig stomach samples and 2.08% of pig farmer stool samples. Additionally, 3.12% of the stool samples from pig farmers were positive for Helicobacter pylori. Phylogenetic analysis revealed distinct clusters of Helicobacter suis with other Helicobacter spp. These findings highlight the prevalence of Helicobacter in both pig gastric mucosa and pig farmer stool. The findings highlight the need for improved sanitation and hygiene practices among pig farmers to minimize the risk of Helicobacter infection in humans.

Pig posture is closely linked with livestock health and welfare. There has been significant interest among researchers in using deep learning techniques for pig posture detection. However, this task is challenging due to variations in image angles and times, as well as the presence of multiple pigs in a single image. In this study, we explore an object detection and segmentation algorithm based on instance segmentation scoring to detect different pig postures (sternal lying, lateral lying, walking, and sitting) and segment pig areas in group images, thereby enabling the identification of individual pig postures within a group. The algorithm combines a residual network with 50 layers and a feature pyramid network to extract feature maps from input images. These feature maps are then used to generate regions of interest (RoI) using a region candidate network. For each RoI, the algorithm performs regression to determine the location, classification, and segmentation of each pig posture. To address challenges such as missing targets and error detections among overlapping pigs in group housing, non-maximum suppression (NMS) is used with a threshold of 0.7. Through extensive hyperparameter analysis, a learning rate of 0.01, a batch size of 512, and 4 images per batch offer superior performance, with accuracy surpassing 96%. Similarly, the mean average precision (mAP) exceeds 83% for object detection and instance segmentation under these settings. Additionally, we compare the method with the faster R-CNN object detection model. Further, execution times on different processing units considering various hyperparameters and iterations have been analyzed.

Objective Optimizing reproductive efficiency in terms of estrus induction and production performance using simplified hormonal intervention using GnRH, gonadotropins and progesterone at farmers’ field conditions to bred animals with superior quality semen and also to reduce the maintenance cost. Method T he present study was planned for optimizing reproductive efficiency using four different easily available hormonal agents with simplified protocols at farmers’ field. A total of 126 females were used in the study. Hormonal protocols I, II, III and IV using GnRH + (PMSG+ hCG), (PMSG+ hCG), PMSG alone and prepared progesterone gel respectively were used for estrus induction in gilts and sows. Results The estrus induction/rate was (77.77%, 81.36%, 78.57% and 50% respectively. The corresponding figures for interval (hrs) of heat exhibition from hormonal administration (121.33±4.93, 121.54±3.60, 78.52±4.52 and 192±24), conception rate (%) (72.22%, 81.25%, 68.18% and 33.33%) farrowing rate (55.55%, 68.29%, 68.18% and 33.33 %), total litter size at birth (7.2±0.64, 7.90±0.47, 8.90±0.47 and 7.00±0) and hormonal cost (Rs.) per animal (570, 335, 280 and 250 Rs.) were respectively. The easier to use protocol was III followed by II, I and IV. Conclusion It was found that protocol II and III are effective and easier so can be used for optimizing reproductive efficiency in pigs at farmers’ field.

Ovarian follicular development is a critical determinant of reproductive performance in litter bearing species like pigs, wherein economic gains depend on litter size. The study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating follicular growth and maturation in Ghoongroo pigs. Transcriptome profiling of porcine small follicles (SF) and large follicles (LF) was conducted using NovaSeq600 sequencing platform and DEGs were identified using DESeq2 with threshold of Padj. < 0.05 and log2 fold change cut off 0.58 (LF vs. SF). Functional annotations and bioinformatics analysis of DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular dynamics. Transcriptome analysis revealed 709 and 479 genes unique to SF and LF stages, respectively, and 11,993 co-expressed genes in both the groups. In total, 507 DEGs (284 upregulated and 223 downregulated) were identified, which encoded for diverse proteins including transcription factors (TFs). These DEGs were functionally linked to response to stimulus, lipid metabolic process, developmental process, extracellular matrix organisation along with the immune system process, indicating wide-ranging mechanisms associated with follicular transition. The enriched KEGG pathways in LF stage consisted of ovarian steroidogenesis, cholesterol and retinol metabolism, cell adhesion molecules, cytokine receptor interaction and immune signalling pathways, depicting intra-follicular control of varied ovarian function. The hub gene analysis revealed APOE, SCARB1, MMP9, CYP17A1, TYROBP as key regulators of follicular development. This study identified candidate genes and TFs providing steroidogenic advantage to LFs which makes them fit for selection into the ovulatory pool of follicles.

Luteal steroidogenesis is critical to implantation and pregnancy maintenance in mammals. The role of androgen receptors (AR) in the progesterone (P4) producing luteal cells of porcine corpus luteum (CL) remains unexplored. The aim of the present study was to establish AR gene knock out (KO) porcine luteal cell culture system model by CRISPR/Cas9 genome editing technology and to study the downstream effects of AR gene deficiency on steroidogenic potential and viability of luteal cells. For this purpose, genomic cleavage detection assay, microscopy, RT-qPCR, ELISA, annexin, MTT, and viability assay complemented by bioinformatics analysis were employed. There was significant downregulation (p < 0.05) in the relative mRNA expression of steroidogenic marker genes STAR, CYP11A1, HSD3B1 in AR KO luteal cells as compared to the control group, which was further validated by the significant (p < 0.05) decrease in the P4 production. Significant decrease (p < 0.05) in relative viability on third passage were also observed. The relative mRNA expression of hypoxia related gene HIF1A was significantly (p < 0.05) downregulated in AR KO luteal cells. Protein-protein interaction analysis mapped AR to signaling pathways associated with luteal cell functionality. These findings suggests that AR gene functionality is critical to luteal cell steroidogenesis in porcine.

Hair or bristle is one of the key by-products of humane slaughter of pigs. In the present study, Fourier-transform infrared (FTIR) spectroscopy was used for examining protein secondary structure of hair fiber from different breeds of pigs (Ghungroo, Ninag Megha, Hampshire, and Duroc). Prominent amide I (1635–1648 cm−1) and amide II (1517–1528 cm −1) bands could be observed in the spectra. Differences in presence/absence of certain FTIR bands between breeds suggests influence of genetic background in the structure of hair fiber. Deconvolution resolved secondary structure of protein in amide I region of spectra into corresponding α-helix (38.0 ± 2.9%), β-sheets (32.2 ± 2.0%), β-turns (19.4 ± 3.1%) and unorganized structural components (10.3 ± 2.5%). Heating of fibers from 80°C to 120°C resulted in changes in amide regions and α-helix to β-sheet ratio of amide I band. Further, correlations were calculated between area under the curve of various FTIR bands and tensile properties of the fiber. Area of FTIR band at 1635 cm −1 was positively correlated with tenacity, initial modulus, extensibility, and work of rupture (r = 0.30 to 0.39). In nutshell, the study reveals subtle differences in secondary structure of hair with respect to breed or temperature treatment and suggests relation between FTIR spectral characteristics and tensile properties.

Thermal stress in pigs, especially during hot summer seasons, can severely impact profitability of pig farming. Some of the key measures to alleviate stress on animal will include adopting optimal management options including housing, modified managemental practices, genetic selection of animals with increase stress tolerance, improved biosecurity for prevention, early diagnosis and treatment of animal diseases and development of alternate feed resources.

To better understand the molecular basis of corpus luteum (CL) development and function RNA-Seq was utilized to identify differentially expressed genes (DEGs) in porcine CL during different physiological stages of the estrous cycle viz. early (EL), mid (ML), late (LL) and regressed (R) luteal. Stage wise comparisons obtained 717 (EL vs. ML), 568 (EL vs. LL), 527 (EL vs. R), 786 (ML vs. LL), 474 (ML vs. R) and 534 (LL vs. R) DEGs with log2(FC) ≥1 and p < 0.05. The process of angiogenesis, steroidogenesis, signal transduction, translation, cell proliferation and tissue remodelling were significantly (p < 0.05) enriched in EL, ML and LL stages, where as apoptosis was most active in regressed stage. Pathway analysis revealed that most annotated genes were associated with lipid metabolism, translation, immune and endocrine system pathways depicting intra-luteal control of diverse CL function. The network analysis identified genes AR, FOS, CDKN1A, which were likely the novel hub genes regulating CL physiology.

Porcine circovirus2 (PCV2) infection in pigs is one of the major causes of economic loss to the farmers in terms of low production, slow growth and increase post-weaning mortality rate. The effect of PCV2 infection on haemogram, serum biochemical profile and oxidant/anti-oxidant status is not well established in pigs. In the present study, haemogram, serum biochemical profile and oxidant/anti-oxidant status were assessed in pigs confirmed positive for PCV2 infections as evidenced by commercially available enzyme-linked immunosorbent assay kit (n = 151) and polymerase chain reaction (PCR) (n = 42) among a total of 306 number of pigs included in the study. Non-infected healthy pigs (n = 6) served as healthy control. The total erythrocyte count (TEC), haemoglobin (Hb), packed cell volume (PCV), total leukocyte count (TLC), differential leukocyte count (DLC) and thrombocyte count were measured. The levels of total protein, albumin, globulin, total bilirubin, direct bilirubin, blood urea nitrogen (BUN), creatinine and glucose and enzymes viz. alanine transaminase (ALT), aspartate transaminase (AST), gamma-glutamyl transferase (GGT) and alkaline phosphatase (ALP) were measured. Oxidative stress indicators such as plasma malondialdehyde (MDA) and total anti-oxidant activity (TAOA) were measured using commercially available kits. The mean values of TLC, lymphocytes and thrombocyte count were significantly (P < 0.05) low in PCV2-infected pigs. The levels of globulin, AST, GGT, BUN and creatinine were significantly increased (P < 0.05) whereas levels of albumin and glucose significantly (P < 0.05) decreased in PCV2-infected pigs. The significant increase (P < 0.05) in MDA level and significant decrease (P < 0.05) in TAOA level were noticed in PCV2-infected animals as compared with healthy control. The present study supports immunosuppression, possible multiple organ damage and oxidative stress associated with naturally occurring PCV2 infection in pigs. Timely vaccination and managemental practices can reduce PCV2 infection in farms. In spite of many research studies, there is still paucity of detailed systemic study on haemato-biochemical alteration and oxidative stress associated with PCV2 infection.

Blood collection for assessment of stress markers such as cortisol, involves restraining and induction of stress on animals. The present study examined the relationship between circulating cortisol levels with its levels in other biological sources (saliva, urine, faeces) to assess utility of non-invasive methods of sample collection for stress assessment in crossbred pigs (Hampshire × Ghungroo). Urine samples were collected after 1 and 2 h of blood and saliva collection, whereas faecal samples were collected after 24 and 48 h of initial sample collection. Mean cortisol levels in plasma and saliva was positively correlated. The correlation between plasma cortisol and second hour mean urinary cortisol values was higher compared to first hour samples. The faecal reactive metabolite levels were weakly correlated to plasma, saliva and urinary cortisol levels. It is concluded that the salivary cortisol values reflect its plasma levels at the time of collection most closely amongst the biological samples studied.