The present study aimed to characterize the immune response, differential gene expression, and functional alterations observed following an in vivo challenge of Classical Swine Fever Virus (CSFV) in crossbred pigs. RNA-sequencing was performed on whole blood samples collected from three pigs before and at 7 days post-infection. A total of 3428 differentially expressed genes (DEGs) were identified, including 970 significantly upregulated and 261 downregulated genes (|log2 fold change| ≥ 1.5, adjusted p < 0.05). The most prominent DEG was LAMB4, a gene associated with cellular attachment receptors facilitating CSFV binding to porcine cells. Several cytokine-cytokine receptor interaction genes, such as CXCL12, CCL2, CCR1, and IL10RA, were upregulated, indicating a strong activation of innate immune responses. Simultaneously, multiple adaptive immune genes, including CD28, CD83, SLA-DQB1, and IL1A, IL12A, IL26 were downregulated, suggesting viral-mediated suppression of antigen presentation and T-cell signaling. Pathway analysis highlighted the involvement of platelet activation and coagulation cascades during viral evasion. Protein-protein interaction (PPI) analysis revealed a core antiviral module comprising MX1, MX2, ISG15, IFIH1, OASL, IFIT1, and UBE2L6, which are central to interferon signaling and viral restriction. Transcription factors such as ETV7, TOX3, and MSC were upregulated, pointing to immune modulation and possible T-cell exhaustion. Conversely, downregulation of HES1, PRDM6, and MYOG indicated impaired lymphocyte differentiation and tissue repair. Overall, the findings suggest a dual host response to CSFV, with strong innate activation alongside adaptive immune suppression, providing valuable insights for vaccine and therapeutic development.

The aim of the study was to evaluate the efficacy of minerals and potential multi-strain probiotic (MSP) intervention in early life of piglets on immunoglobulin A (IgA), IgG and secretory IgA (sIgA) concentrations and growth performance and mortality. A total of eight piglet litters from parity-matched sows were enrolled and allocated into one of the four interventions: normal saline (control), multimineral (MM), MSP, and MSP+MM. The MM was injected on day 0 and 7 of birth and MSP were administered once daily per os for first 7 days of life. The growth and piglet survival rates were significantly higher in the MSP group as compared to control group. The mean sIgA concentrations were significantly elevated on day 7 in control and MSP groups, and day 21 in MM+MSP group. A significant rise of mean IgA concentration was observed on days 14 and 21 in control and MSP groups and days 7, 14, and 21 in the MM+MSP group. The mean IgG concentrations were significantly increased on days 7, 14, and 21 in the control, MM, and MM+MSP groups. The comparison of the mean IgA and IgG concentrations among the groups showed a significantly higher IgA levels on days 14 and 21 in MSP and MM+MSP groups and significantly lower IgG levels on days 0, 7, and 14 in the MM, MSP, and MM+MSP groups, and day 21 in MSP and MM+MSP groups when compared with control group. The study indicated that neonatal MSP intervention improves growth and reduces the mortality of piglets until weaning through augmenting the systemic and mucosal immune parameters.

Subclinical mastitis (SCM) is a major constraint in dairy production and is driven by complex host–pathogen interactions. Although transcriptional responses associated with SCM have been widely investigated, the epigenetic mechanisms that stably regulate these programs remain less well characterized, particularly in crossbred cattle populations. This study aimed to characterize DNA methylation-based regulatory networks by integrating whole-genome methylation and transcriptome data from milk somatic cells of Vrindavani (Bos taurus × Bos indicus) cattle. Whole-genome methylation (n = 6) and corresponding transcriptome profiling (n = 6) were performed on milk somatic cells from SCM-affected and healthy control cows. Differential methylation analysis (q-value < 0.05) identified 62,940 differentially methylated cytosines (DMCs), 7,706 differentially methylated regions (DMRs), and 6,203 differentially methylated genes (DMGs), with a predominant bias toward hypomethylation in SCM. Integrative analysis using stringent thresholds for both methylation (≥ 10

IntroductionSubclinical endometritis (SCE) is a postpartum uterine disorder characterized by cytological inflammation without clinical signs, impairing fertility and productivity in dairy cattle. Diagnosis relies on endometrial cytology, which is invasive and impractical under field conditions. Doppler ultrasonography enables non-invasive assessment of uterine blood flow (UBF) and may detect inflammation-associated vascular changes. However, uterine hemodynamic characterization in indigenous Bos indicus breeds affected with SCE remains limited. This study evaluated Doppler-derived uterine perfusion dynamics in healthy and SCE-affected Tharparkar cows.Materials and methodsTwenty lactating multiparous Tharparkar cows (70 ± 3.34 days postpartum) were screened using endometrial cytology; cows with ≥5% polymorphonuclear cells were classified as SCE-positive (n = 10), and healthy cows served as controls (n = 10). Transrectal color and spectral Doppler examinations of the middle uterine artery (MUA) were performed every three days throughout one complete estrous cycle. Resistance index (RI), pulsatility index (PI), time-averaged maximum velocity (TAMV), blood flow volume (BFV), and MUA diameter were recorded. Serum progesterone (P4) was measured by ELISA. Data were analyzed using independent t-tests, repeated-measures ANOVA (GLM), and Pearson correlation.ResultsSCE cows exhibited significantly lower RI and PI across multiple cycle days (P < 0.05), indicating increased uterine perfusion. TAMV, BFV, and MUA diameter were significantly higher in SCE cows (P < 0.05). RI positively correlated with P4 concentration (r = 0.77; P < 0.0001) and corpus luteum size (r = 0.64; P < 0.0001), while BFV showed positive correlations with TAMV (r = 0.82; P < 0.0001) and MUA diameter (r = 0.78; P < 0.0001), and negative correlations with RI (r = −0.57; P < 0.0001) and P4 (r = −0.59; P < 0.0001). Production traits had no significant influence on Doppler indices (P > 0.05).ConclusionSubclinical endometritis in Tharparkar cows is associated with distinct uterine hemodynamic alterations characterized by increased blood flow and reduced Doppler resistance indices. These findings establish baseline Doppler reference patterns for an indigenous Bos indicus breed and support the potential utility of Doppler ultrasonography as a non-invasive adjunct tool for detecting uterine inflammation. Further studies integrating vascular and biochemical markers are warranted to enhance diagnostic precision.

India possesses a rich diversity of indigenous cattle that are well adapted to varied agro-climatic regions. These populations exhibit remarkable variation in stature (height at withers), ranging from short-statured types such as Vechur, Punganur, Malnad Gidda, and Khariar to tall and heavy breeds like Kankrej, Ongole and other milch breeds (Sahiwal, Gir, etc.). The short-statured breeds offer potential advantages in feed efficiency, disease resilience, and cultural value besides being economical to maintain. However, their genetic basis for stature remains underexplored. This study leverages whole-genome resequencing (WGS) data on short-statured (n = 19) and tall (Kankrej as representative; n = 19) Indian cattle to delineate the copy number variation (CNV) landscape and selection signatures underpinning stature divergence. Post-quality control, CNVs were detected from duplicate-marked bam files using CNVnator with read-depth methodology, filtered (q0 < 0.5, p < 0.01, size 1 kb-5 Mb), and concatenated into CNV regions (CNVRs). Selection signatures were identified using cross population extended haplotype homozygosity (XP-EHH) methodology for inter-population comparison of short-statured cattle with tall cohort. Genes harboured under CNVRs and sweep windows were annotated using GALLO, with functional mining from literature databases. In short-statured cattle, 41,913 CNVs were concatenated into 10,075 CNVRs, with 8.01% genomic coverage. A total of 25 genes were found to be common across two analyses i.e., unique (non-overlapping) CN regions in 70% short-statured individuals and scan of selection signature. Key genes across the analyses included IGF1R (cell proliferation), FGFR3 (skeletal growth), SOX6 (body size), EXT2/LGR4 (bone density), PRKCD (developmental regulation), ADAMTSL2 (extracellular matrix integrity), SLC25A6 (glucose metabolism), and SDHA (energy supply). Unique non-overlapping copy number regions (e.g., 78 regions found in 100% of dwarf individuals) harbored several genes, including ARL13B (osteogenesis), AXIN2 (bone remodeling), CCND2 (myogenesis), and TNNT1 (muscle contraction). This comprehensive CNV map and scan for signatures of selection unveil stature-associated genomic variants, informing conservation strategies for threatened short-statured breeds by enhancing their socio-economic value through targeted breeding. The findings underscore CNVs as pivotal drivers of phenotypic diversity in cattle populations, with implications for livestock genomics and sustainable agriculture.

India harbours considerable diversity among its indigenous pig populations, with distinct breeds distributed across the north-eastern hill states, the Gangetic plains, coastal western India, and island territories. These populations represent the product of long-term co-evolution with local environments, agricultural practices, and cultural systems, and contain alleles associated with thermal tolerance, feed-use efficiency under low-input conditions, disease resistance, and reproductive resilience that are not readily found in the commercial exotic breeds that dominate global industrial pork production. Despite this intrinsic and strategic value, India's indigenous pig breeds remain incompletely characterised, unevenly documented, and subject to progressive genetic erosion driven by uncontrolled crossbreeding with introduced exotic stocks. This narrative review synthesises the contemporary body of knowledge concerning India's registered indigenous pig breeds — principally Ghungroo, Doom, Niang Megha, Manipuri, Tenyi Vo, Agonda Goan, and Nicobari — with respect to their phenotypic attributes, productive characteristics, population status, and molecular diversity. It further examines the smallholder and tribal production systems within which these breeds are embedded, evaluates conservation and genetic improvement strategies, and considers the emerging role of genomic tools in accelerating breed characterisation and conservation management. The review critically engages with the national and international policy frameworks governing animal genetic resource management in India, identifying structural gaps and proposing directions for improved coordination between research institutions, government agencies, and farming communities. Major knowledge gaps identified include the absence of validated genomic reference panels for Indian indigenous pig breeds, a paucity of genetic parameter estimates for most breeds, and insufficient integration of community-based conservation approaches into formal breed management programmes. The review concludes with recommendations for a more integrated and community-responsive approach to the conservation and genetic improvement of India's indigenous pig heritage.

Long non-coding RNAs (lncRNAs) are emerging as important regulators of inflammatory and immune signaling, yet their contribution to bovine subclinical mastitis remains poorly defined. Here, we characterized the lncRNA expression landscape associated with disease in milk somatic cells of healthy and subclinical mastitic Vrindavani cattle. We identified 11,403 high-confidence lncRNAs, of which 104 were differentially expressed in subclinical mastitis (adjusted P < 0.05; |log2FC| ≥ 1), with the vast majority upregulated in mastitic samples. Predicted cis- and trans-associated target analyses identified 637 non-redundant genes, and KEGG analysis identified 8 significantly enriched cis-associated pathways and 152 significantly enriched trans-associated pathways (adjusted P < 0.05), predominantly enriched for immune and inflammation-related pathways. These findings prioritized a subset of mastitis-associated lncRNAs for subsequent methylation and interaction-network analyses. A subset of these lncRNAs further overlapped differentially methylated regions (DMRs), suggesting a potential association between lncRNA expression changes and DNA methylation alterations. Integration of lncRNA–miRNA and miRNA–mRNA interactions identified lncRNA–miRNA–mRNA interaction networks involving DMR-associated lncRNAs. Among the prioritized candidates, MSTRG.28878.1 showed overlap with a hypomethylated promoter-associated DMR, increased expression, and multiple connections within the predicted interaction network. Together, these findings identify candidate lncRNAs, methylation-associated loci, and predicted molecular interactions associated with bovine subclinical mastitis and provide a resource for future functional investigation of candidate non-coding RNA-associated mechanisms in disease.

Goats offer unique social, economic and biological benefits compared to other livestock species and are often referred to as the “poor man’s cow”. This study aimed to examine the polymorphism of six gene loci, namely IGF1, GH1, GH2, MSTN, IGFBP3 and GDF9, in Rohilkhandi goats using PCR-RFLP and assessed their association with various growth traits like body weight measured from birth to 48 months of age. Polymorphism was detected only in IGF1, GH1 and MSTN, whereas GH2, IGFBP3 and GDF9 were monomorphic in this population. Body weight, as an indicator of growth traits, increased significantly from 2.17 ± 0.04 kg at birth to 28.55 ± 0.32 kg at 48 months of age. Association analysis showed that IGF1 genotypes were related to body weight across all age points (p < 0.05, p < 0.01 and p < 0.001), with the BB genotype exhibiting higher mean body weights. GH1 genotypes showed effects only at 9 and 15 months and MSTN exhibited genotype-body weight associations at multiple ages across the growth period (p < 0.05, p < 0.01 and p < 0.001), with the AA genotype consistently showed higher body weight than BB. Although the study was based on a modest sample of female goats from a single herd, the consistent trends observed across age points provide a valuable initial indication of genotype-growth relationships in Rohilkhandi goats. The patterns detected for IGF1 and MSTN highlight their potential biological relevance for growth performance. Building on this foundation, future multi-herd studies with larger and more diverse populations will be important for confirming these promising signals and refining their usefulness for genetic improvement programs.

The study evaluated the influences of lemon grass essential oil (LGEO) and gallic acid (GA) supplementations on inflammation response, systemic immunity, gut health and performance in early weanling piglets. Thirty-two piglets were separated from parity-matched sows at the age of 3 weeks and randomly divided into four different supplementation groups: basal ration (control), LGEO, GA and LGEO + GA in basal diet. The inflammation response was monitored by measuring serum calprotectin level and neutrophil and lymphocyte ratio in blood, systemic immunity was evaluated by measuring serum immunoglobulin A (IgA) and immunoglobulin G (IgG), gut health was assessed by measuring amylase, lipase and ghrelin in serum, fecal microbial populations and diarrhea incidence and performance was evaluated on the basis of growth and mortality until day 21 post-weaning. The fecal Lactobacillus and Bifidobacterium counts were significantly increased in LGEO, GA and LGEO+GA groups while fecal coliform count was markedly dropped in LGEO and LGEO+GA groups. The GA supplementation markedly improved serum albumin and IgA concentrations, and attenuated calprotectin, ghrelin, globulin, amylase levels. The GA + LGEO supplementation significantly improved serum albumin level in early weanling piglets. Only one piglet died due to pneumonia in LGEO+GA group. In LGEO group, the diarrhea incidence was lowest among the supplementation groups and mean body weight was significantly higher on day 21 of weaning as compared to the control group. Taken together, it is concluded that the dietary supplementation of LGEO to early weaning pigs in a commercial swine production farm may be effective in improving growth performance and gut health.

Introduction Breed-specific characterization of uterine hemodynamics is essential for improving reproductive monitoring and management in indigenous Bos indicus cattle; however, systematic Doppler reference data across the estrous cycle remain limited. This study aimed to evaluate cyclic changes in middle uterine artery (MUA) blood flow and its association with luteal function in Tharparkar cows using transrectal spectral Doppler ultrasonography. Methods Ten clinically normal, cyclic Tharparkar cows (parity 1-3) were examined at three-day intervals from estrus (D0) to the subsequent estrus (D21). Doppler parameters including resistance index (RI), pulsatility index (PI), time-averaged maximum velocity (TMAX), vessel diameter, and calculated blood flow volume (BFV) were recorded. Follicular dynamics, corpus luteum (CL) size, and serum progesterone (P4) concentrations were assessed concurrently. Results Reproductive characteristics were consistent with Bos indicus physiology, with a mean preovulatory follicle diameter of 13.14 +/- 0.31 mm, luteal phase length of 16.10 +/- 0.23 days, and estrous cycle length of 20.50 +/- 0.30 days. CL size showed a strong positive correlation with serum P4 concentrations (r = 0.86, P < 0.05), confirming functional luteal competence. All Doppler indices exhibited significant cyclic variation across the estrous cycle (P < 0.05). RI and PI were lowest at estrus, increased during early luteal development, peaked during the mid-luteal phase (D9-D12), and declined toward the subsequent estrus. RI showed positive correlations with serum P4 (r = 0.73, P < 0.05) and CL size (r = 0.52, P < 0.05). In contrast, TMAX, BFV, and MUA diameter displayed reciprocal trends, with maximum values at estrus and minimum values during the mid-luteal phase. BFV correlated positively with TMAX (r = 0.84, P < 0.05) and vessel diameter (r = 0.70, P < 0.05), and negatively with RI (r = -0.58, P < 0.05) and P4 (r = -0.65, P < 0.05). Discussion This study establishes novel, breed-specific uterine artery Doppler reference profiles for Tharparkar cows, demonstrating distinctive cyclic vascular regulation closely linked to luteal function. These findings support Doppler ultrasonography as a functional tool for estrus confirmation, luteal assessment, and fertility monitoring in indigenous cattle.

Genomic selection (GS) has transformed modern animal breeding by enabling the prediction of genetic merit using dense genome-wide molecular markers rather than relying solely on pedigree and phenotypic information. Since its conceptual introduction in 2001, GS has become a cornerstone of genetic improvement programs in livestock species, particularly dairy cattle, and has subsequently expanded to beef cattle, sheep, goats, swine, poultry, and aquaculture. The integration of high-density single nucleotide polymorphism (SNP) genotyping with advanced statistical prediction models has substantially increased the accuracy of breeding value estimation, shortened generation intervals, and accelerated rates of genetic gain. Compared with conventional best linear unbiased prediction (BLUP) and marker-assisted selection (MAS), genomic selection captures the combined effects of thousands of loci distributed throughout the genome, making it highly effective for complex quantitative traits governed by many genes of small effect. Recent advances, including single-step genomic BLUP, Bayesian prediction methods, whole-genome sequence analysis, functional genomics, multi-omics integration, artificial intelligence, and precision livestock farming technologies, have further enhanced the scope and efficiency of genomic prediction. These innovations are facilitating simultaneous improvement in productivity, fertility, feed efficiency, disease resistance, animal welfare, and environmental sustainability. Moreover, genomic information is increasingly being integrated with genome editing technologies such as CRISPR to support precision breeding strategies. This review summarizes the historical evolution, fundamental principles, methodological developments, and practical applications of genomic selection in livestock breeding while highlighting emerging innovations and future research directions that are expected to shape next-generation animal improvement programs.

Heat stress significantly affects livestock production, particularly in tropical regions where temperatures often exceed animals' comfort zones. This study investigates the molecular mechanisms of heat stress tolerance in Jamunapari goats (Capra hircus) through transcriptomic analysis, gene co-expression network construction, and hub gene identification. Female goats (1-2 years old) were monitored during high Thermal Humidity Index (THI) in June and normal THI in March. Based on heat tolerance and physiological parameters, goats were classified into Thermo-Neutral (TNG) and Heat-Stress (EHSG) groups. Differential gene expression analysis revealed 133 upregulated genes and 501 downregulated genes in the EHSG group. Upregulated pathways included NF-kappa B signaling, MAPK signaling, and cytokine-cytokine receptor interactions, while downregulated genes were linked to IL-17 signaling and platelet activation. Notably, the small heat shock proteins (CRYAB) and aquaporins (AQP11) were significantly downregulated. Weighted Gene Co-expression Network Analysis (WGCNA) identified key gene modules associated with Iberia Heat Tolerance Coefficient and respiration rate. Hub genes such as TUFM, TOMM40, BCSL1, VCL, VASP, ITGB, and VWF were critical for adaptation to heat stress. These findings enhance our understanding of heat stress resilience, offering potential targets for breeding programs aimed at improving livestock tolerance to heat stress in tropical environments.

Classical Swine Fever (CSF) is one of the most important viral infections affecting swine. In the present study, the complete genome of the cell culture-adapted lapinized Indian Classical Swine Fever virus (CSFV) was cloned into the pBR322 vector using an improved method. The viral RNA was amplified by RT-LA PCR into two overlapping fragments of 6.5 kb and 5.8 kb sizes, and cloned separately into the pTZ57R/T vector. To generate CSFV full-length cDNA, the segments were fused utilising a restriction endonuclease region located within the overlapping region. The complete genome was then cloned into the pBR322 vector and designated as pBR/T7-CSFV. The recombinant plasmid was confirmed by PCR, restriction enzyme analysis, and nucleotide sequencing. The full-length cDNA backbone of CSFV can serve as a reverse genetics model with the T7 promoter and can be used for creating recombinant viruses and for developing a DIVA strategy for CSFV. This study describes a modified method for full-length amplification of an Indian CSFV isolate and cloning it into the pBR322 vector.

Fecundity-related genes, such as GDF9, play a critical role in regulating ovulation, fertilisation and early embryonic development. This study aimed to elucidate the functional role of GDF9 in caprine granulosa cells by employing CRISPR/Cas9-mediated gene editing. The CRISPR/Cas9 system, incorporating single guide RNA (sgRNA) and Cas9 endonuclease, was used to specifically disrupt the GDF9 gene. Successful GDF9 knockout was confirmed via the T7 Endonuclease I (T7E1) cleavage assay. Subsequent analyses assessed the impact of GDF9 disruption on the expression of GDF9 and its associated receptors-BMPR-1A, BMPR-1B and BMPR-II. Additionally, the study examined the modulatory effects of fibroblast growth factor 2 (FGF2) on receptor expression. FGF2 treatment led to increased mRNA expression of BMPR-1A, BMPR-1B and BMPR-II in wild-type granulosa cells. Furthermore, follicle-stimulating hormone receptor (FSHR) levels were significantly upregulated, whereas luteinising hormone receptor (LHR) expression decreased following FGF2 stimulation in wild-type cells. In contrast, GDF9-knockout cells showed elevated expression of both FSHR and LHR. The study also investigated the impact of GDF9 deletion on the expression of key steroidogenic genes, particularly StAR. The combined presence of GDF9 and FGF2 synergistically enhanced StAR expression. Cellular responses to FGF2 included a downregulation of CASPASE 3, indicating reduced apoptosis and an upregulation of PCNA, suggesting increased cell proliferation. In conclusion, this study provides novel insights into the regulatory role of GDF9 in ovarian granulosa cell function and highlights the utility of CRISPR/Cas9 technology for functional genomics in caprine species. The findings have significant implications for enhancing reproductive performance through targeted gene modulation.

The present study was aimed to investigate the relationship between diarrhoea-associated polymorphisms and pre-weaning growth rates in an organized Landlly herd. A total of 250 piglets were genotyped for 10 shortlisted SNPs and assessed for pre-weaning growth rates, with body weights recorded from birth to the 6th week of age. Seven out of the 10 SNPs were found to be polymorphic in the target population, with the MUC 4-g.8227 G>C locus significantly affecting growth rates of the 2nd to 4th week piglets whereas, the MUC 20-g.191 affected growth rates at the 4th week of age. These findings suggest that the g.8227C>G and g.191C>T SNP polymorphisms are associated with both growth performance and diarrhoea in piglets, recommending that a balanced approach should be maintained between health status and growth performance in piglet selection programs.

Small ruminants, especially goats, are highly valued for their meat, milk and fibre. The introduction of prolific breeds can boost productivity, offer farmers additional income and contribute to food security. This study aimed to examine the polymorphism of eight fragments of different genes related to reproductive efficiency in fifty Rohilkhandi goats using PCR-RFLP and to analyse the association of these variants with various reproductive traits. The gene fragments analysed were FecB, FecXG, FecXI, FecXB, FecXH, GDF9, MSTN and IGF1. Genetic polymorphism was detected in the MSTN and IGF1 gene fragments out of the eight analysed. The reproductive traits evaluated included the age of the doe at 1st kidding, average kidding interval, average litter size, kidding per year, kids per year and weight of doe at 1st kidding etc., with a mean value of 546.98 ± 10.52 days, 316.65 ± 6.21 days, 1.32 ± 0.05, 1.17 ± 0.02, 1.54 ± 0.06 and 16.09 ± 0.15 kg, respectively. The mixed-model analysis revealed that MSTN genotypes significantly influenced (p < 0.05) ADK, BWDK, KPY and approached significance (p = 0.05) for LS, while IGF1 genotypes significantly affected (p < 0.05) traits ADK and BWDK. These findings suggest that polymorphisms in the MSTN and IGF1 genes may directly or indirectly influence reproductive performance in Rohilkhandi goats. This first genomic investigation in the breed provides preliminary evidence of such associations and underscores the need for larger, multi-breed studies to validate these results and identify reliable molecular markers for use in marker-assisted selection to improve fecundity and productivity in indigenous goats.