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The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes. [ABSTRACT FROM AUTHOR]

Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome‐wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds. [ABSTRACT FROM AUTHOR]

A letter to the editor about male contraception is presented.

Determination of factors affecting sex ratio is important while considering application of sex ratio enrichment approach. Present study aimed to design a SYBR Green qPCR‐based method for measurement of primary sex ratio and to evaluate different factors (genetic group, sire, spermiogenic cycle and processing layer) affecting boar sperm sex ratio. The qPCR was based on relative copy number analysis of sex chromosome‐specific single copy gene fragments with an autosomal gene as reference and was evaluated using DNA dilution series from pigs with numerically normal karyotype. The sex ratio was estimated from genomic DNA samples isolated from boar semen collected from different genetic groups at different time points and different processing layers. The X chromosome frequencies of semen samples revealed significant effect of genetic group. However, significant variation was observed neither within same genetic group nor between ejaculates of different spermatogenic cycles. Among the processing techniques studied, swim‐up technique produced a significant X sperm enrichment in comparison to control whereas, Percoll density gradient failed to show any significant difference among layers. The lower layer in swim‐up technique was found to contain higher proportion of X sperms. The designed qPCR is found to be an easy, less time‐consuming method and does not require high end laboratory facilities or the specialized expertise. The lower layer of swim‐up processing has a scope for X sperm enrichment in boar semen with proper validation. [ABSTRACT FROM AUTHOR]

The present study in the 5’ upstream region of TLR4 gene revealed four Single Nucleotide Polymorphisms (SNPs) in Vrindavani and Tharparkar cattle. The polymorphic information content (PIC), heterozygosity and allelic diversity values were low to moderate for these SNPs. In Vrindavani cattle, one SNP was found to be in Hardy-Weinberg Equilibrium (HWE) and the remaining three were found to be in linkage disequilibrium (LD) as indicated statistically (P > 0.05). In Tharparkar cattle, two SNPs were found to be in HWE and were not in LD as indicated statistically (P > 0.05). These SNPs were used for construction of haplotypes. In-silico analysis of these SNPs predicted abolition of eight transcription factor binding sites and creation of eight new sites. The quantitative real time PCR analysis did not show any significant variation of gene expression among haplotypes. However, gene expression between breed was found to be significant (P < 0.05) which suggested that upstream region of bovine TLR4 gene has a crucial role in its expression. These findings in TLR4 gene offer essential evidence that can be useful in future research exploring its role in immunity. TLR4 can be used as a marker for selection for disease resistance in bovines. [ABSTRACT FROM AUTHOR]

This review deals with the various traditional and recent methods of sire evaluation. A sire evaluation is a method of prediction of sire's next-generation produced by breeding with specified females and creating their records in a specific environment. Breeding worth of progeny tested sires are obtained through sire index method that assigns ranking to each sire based on their genetic merit. Numerous sire indices are broadly classified in two type's viz., indices which are purely meant for ranking purposes and those which, besides, provide an estimate of the breeding worth of each sire. Sires can be evaluated in single or multiple herds. The statistical equations represent sire evaluation as linear or non-linear methods. Numerous methods can be incorporated as the advances are made in sire evaluation based on data structures, breeding approaches and selection methods. There are various approaches of sire evaluation such as Least Squares Method (LSM), Simple Regressed Least Squares (SRLS), Best Linear Unbiased Prediction (BLUP) and Derivative-Free Restricted Maximum Likelihood (DFREML) for single as well as multiple trait models which can be used to derive genetic worth of an individual. An efficient method of sire evaluation shows minimum within sire variance or error variance. [ABSTRACT FROM AUTHOR]

India is the highest milk producer of the world and crossbreeding to augment genetic potential of native breeds, has played an important role to achieve this feat. The present study with five microsatellite DNA loci BM1818, BM1443, BM1905, BM1258 and MB026 associated with Somatic Cell Score (SCS) and milk production, was aimed at finding variation in 76 crossbred cows. PCR amplified products were resolved on MetaPhore® agrose. The number of alleles for BM1443, BM1905, BM1258 and MB026 were found to be 7 each while it was 8 in BM1818. The size of alleles ranges from 149-186 bp for BM1443, 178-204 bp for BM1905, 208-252 bp for MB026 and 252-296 bp for BM1818. The data on polymorphism information content, heterozygosity, number of effective alleles of these short tandem repeat loci shows that BM1443 was having lowest and BM1818 was having maximum variability. Microsatellite BM1818 was not found to be associated with SCS in this population. Means of SCS of genotypes 178/192 and 188/188 for marker BM1905, genotypes 228/252 and 238/ 252 for marker MB026, genotype 120/110 for marker BM1258 and genotypes 182/154 and 178/154 for marker BM1443 were found to be higher. Only two markers viz. BM1818 and BM1443 was found to be significantly associated with 305 days milk yield. [ABSTRACT FROM AUTHOR]

Classical Swine Fever (CSF) is a contagious viral disease of pigs which is endemic in several parts of the world, including India. Prophylactic vaccination using live attenuated vaccine is the preferred method of control. However, there is significant inter-individual variation in the antibody response to vaccination. In this study, we measured the E2 antibody blocking percentage after 21 days of CSF vaccination in a mixed pig population consisting of Landrace, indigenous Ghurrah pigs, and their crossbreds. A Genome Wide Association Study (GWAS) carried out using single-SNP and haplotype based methods detected a 1.6 Mb region on SSC2 (28.92−30.52 Mb) as significantly associated with antibody response to CSF vaccination. The significant region and 1 Mb flanking sequences encompass 3 genes – EIF3M, DNAJC24 and ARL14EP, which code for proteins involved in Pestivirus replication and host immune response system. Our results combined with previous studies on immune response of pigs present this region as a suitable candidate for future functional investigations. [ABSTRACT FROM AUTHOR]

A total of 129 crossbred cows were selected to explore the genotypic and expression profiling of partial TNF-α gene and its association with mastitis susceptibility. Two exon spanning region of TNF-α gene (221 bp and 239 bp) were amplified by Polymerase Chain Reaction (PCR). The different genotypic analysis by SSCP revealed that 221 bp fragment was monomorphic, whereas 239 bp was polymorphic. Association studies revealed that AA genotypes of 239 bp were more prevalent in mastitis group and the mRNA expression of TNF-α was significantly (P < 0.05) higher in AA genotypic animals compare to AB and BB. This suggested that genotypes AB and BB may be used as candidate markers for mastitis resistance selection in dairy cattle. [ABSTRACT FROM AUTHOR]

Aim: The present study was undertaken to identify whether single nucleotide polymorphism (SNP) rs109231409 located on mannose-binding lectins 1 (MBL1) gene was associated with mastitis tolerance/susceptibility. Materials and Methods: After grouping 100 Vrindavani crossbred cattle as mastitis positive and negative animals, they were genotyped using polymerase chain reaction (PCR)-restriction fragment length polymorphisms method. Gene and genotype frequencies of different patterns were estimated by standard procedure (POPGENE version 1.32, (University of Alberta, Canada) and statistical analysis was carried out by logistic regression methods using STATA 12 software (StataCorp LP, USA). Results: The 588 bp fragment of MBL1 gene was amplified using PCR. PCR product was digested with ApaI restriction enzyme showed two distinct genotypes viz., GG (311 bp and 272 bp fragments) and GA (588 bp, 311 bp and 277 bp fragments). The gene, genotype frequencies, average heterozygosity, polymorphic information content and X2values for the locus rs109231409 was ascertained. Conclusions: No significant association between SNP "rs109231409" with mastitis tolerance was found. Although there is a lack of association, further studies have to be undertaken in a large population in order to validate the impact of rs109231409 (g.855G >A) on mastitis tolerance. [ABSTRACT FROM AUTHOR]

Epigenetics refers to the study of heritable phenotypic changes without alterations in the DNA sequence. Advanced studies in epigenetic molecular mechanisms and their biological functions have relied on various model systems including bacteria, fungi, plants, insects, and mammals. The fruit fly Drosophila melanogaster has been an established model organism in the study of genetics and developmental biology. Many regulatory pathways are conserved in Drosophila compared to mammals, rendering it a powerful model to study epigenetic mechanisms. In this review, we outline the various epigenetic mechanisms and their importance in Drosophila chiefly focussing on the predominant epigenetic variations such as DNA methylation, histone modifications like H3K18 acetylation, H3K27 and H4K20 methylation, H3S10 phosphorylation, H2K118 ubiquitylation, H4 sumoylation, RNA associated silencing, polycomb proteins, PEV (position effect variegation), TPE (Telomeric position effect), and dosage compensation. All these types of epigenetic mechanisms can be studied precisely in Drosophila by inducing various mutations in the genome. Advanced studies in Drosophila epigenetics helps to understand genomic imprinting, neurological memory, circadian rhythms, aging, and carcinogenesis. [ABSTRACT FROM AUTHOR]

• The study aimed to elucidate genetic diversity and selective sweeps in 82 Sahiwal cattle using ddRAD data. • A declining trend in the effective population size (74 in most recent generation) observed in the population which necessitates a breeding plan to maintain a sufficiently large Ne. The genomic inbreeding coefficients ranged from −0.0289 to 0.0725. • The LD estimates revealed a minimum of 114,800 SNP markers and at least 14,350 informative markers necessary for GWAS analysis and genomic selection studies, respectively. • We found 146 regions undergoing selective sweeps using five distinct statistical tests and these regions, located in non-overlapping. • We identified various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK) , as well as production traits (NRXN1, PLCE1, GHR). The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (F HOM , F UNI , F ROH , and F GROM), ranged from −0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075–35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population. [ABSTRACT FROM AUTHOR]

• Leptin increases the expression of its own receptor and signaling transducer, JAK2. • Leptin reduces Gs to Gi protein ratio in receptor- and JAK-2-dependent manner. • It also decreases the expression of BK Caα and BK Caβ channel subunits. • These findings collectively suggest that leptin would exert an inhibitory influence on against-induced uterine relaxation in late pregnancy. Obesity can have a significant impact on pregnancy outcomes by compromising the ability of the uterus to relax, which increases the likelihood of conditions such as preterm labor. One of the key pathways responsible for uterine relaxation is the β-adrenergic signaling pathway, and it is well-documented that obesity, often linked to a high-fat diet, can disrupt this pathway within the uterine environment. Hyperleptinemia is a significant feature of pregnancy as well as obesity. However, the effect of leptin on β-adrenergic signaling pathway has not been studied. In the present study, we studied the effects of leptin on transcriptions of the major proteins defining the β-adrenergic signaling pathway in pregnant rat uterus. Leptin treatment at a supraphysiological concentration to pregnant rat uterine strips increased the mRNA and protein expressions of Gs protein but not the mRNA of β 2 - and β 3 -adrenoceptors. It also enhanced the expression of Gi-protein, but not the Gq protein. Nevertheless, the mRNA ratio of Gs to Gi protein experienced a significant decrease. Further, leptin reduced the transcription of BK Caα and BK Caβ channel subunits. In leptin-stimulated tissues, there was also an increase in the expression of leptin receptor and JAK-2. In conclusion, leptin decreases the ratio of Gs to Gi proteins and BK Caα and BK Caβ channel subunits suggesting hyperleptinemia is a likely factor inducing uterine relaxant dysfunction in obesity. [ABSTRACT FROM AUTHOR]

• The review highlights the potential applications of genomic techniques in conservation purposes as well as discusses few case studies regarding the applications of conservation genomics in livestock and wildlife species. • Advancements in next-generation sequencing (NGS) technologies has generated a massive amount of data that is more fine-scaled and accurate and has thus resulted in more and more species becoming "genome enabled" • The conservation genetics-based "one gene, many individuals" strategy has given way to a conservation genomics-based "few individuals, several genes" approach. Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field. [ABSTRACT FROM AUTHOR]

The present study examined the variability of MHC class II DRB exon 2 gene using restriction fragment length polymorphism analysis of PCR-amplified fragments PCR-(RFLP), and its association with Haemonchus contortus infestation in Salem Black and Tellicherry goat population. Animals were naturally exposed to mixed infestation of endoparasites, predominantly Haemonchus contortus. Pooled fecal coproculture and larval identification showed predominant presence of haemonchus (L3) larva. Fecal egg count (FEC) and packed cell volume (PCV) were used as indicator traits. All the three studied loci, TaqI, BsaI, and BsaHI, were polymorphic having two alleles and three genotypes. The loci showed low to moderate values of polymorphic information content in both breeds. The mean fecal egg count estimates were 477.12 ± 34.14 and 730.42 ± 41.19 eggs per gram of feces for Salem Black and Tellicherry goats, respectively. The mean PCV values were within the normal range in both breeds; however, they showed negative correlation with FEC values. There was variation among genotypes in mean values of FEC and PCV for all loci; however, the effect of genotypes on indicator traits was found to be statistically nonsignificant (P ≤ 0.05). [ABSTRACT FROM AUTHOR]

Milk β-casein has attracted extensive research interest in the dairy industry and animal breeding as a source of high-quality protein for human diet; however, adverse health effects have been ascribed to A1 β-casein variant consumption. A study was conducted to genotype the polymorphism in milk β-casein gene and examines the potential association between β-casein genotypes and milk production and reproduction traits in population of Frieswal cows. β-Casein A1/A2 genotype had significant effect (P ≤ 0.05) on several production traits including Total Milk Yield (TMY) (P ≤ 0.05), Milk Milk yield 300 days (MY300) (P ≤ 0.05), Lactation Length (LL) (P ≤ 0.01) and Peak Yield (PY) (P ≤ 0.01). β-Casein A1A1 genotype cows had significantly lower TMY, MY300, PY and DP as compared to A1A2 and A2A2 genotypes. A1A2 genotype had highest TMY, MY300, PY and DP; however, A2A2 and A1A2 genotypes were not significantly different from each other. The results pointed towards the superiority of A2 β-casein variant for several production traits in crossbreds. Further, with higher price of A2 milk, the inclusion of β-casein A1/A2 genotype in the selection of crossbreds offers higher profitability from dairy enterprise as well as provides a nutritional wellness product for consumers. [ABSTRACT FROM AUTHOR]

Interferon Gamma Receptor (IFNGR) genes play an important role in the immune response against mycobacteria by regulating the proinflammatory cytokine Interferon Gamma (IFNG) alongwith subsequent mycobactericidal milieu and are potential strong candidates for investigating genetic basis of disease resistance. Present investigation was aimed at exploring the association of one SNP in IFNGR1 gene and two SNPs in IFNGR2 gene with susceptibility/resistance against bovine tuberculosis infection in cattle. All the three SNPs under investigation (rs109049057, rs109579937 and rs110689128) revealed polymorphism. SNP loci rs109049057 was found to be significantly (P < 0.01) associated with susceptibility to bovine tuberculosis in cattle in our case control population. The SNP was non-synonymous, suggesting its functional role in the immune response against bovine tuberculosis. [ABSTRACT FROM AUTHOR]

Lysophosphatidic acid (LPA) is known to increase uterine contraction in the estrus cycle and early pregnancy, however, the effect of LPA in late pregnant uterus and its mechanisms are not clear. In the present study, we show the LPA receptor subtypes expressed and the mechanism of LPA-induced contractions in late pregnant mouse uterus. We determined the relative mRNA expression of LPA receptor genes by quantitative PCR and elicited log concentration-response curves to oleoyl-L-α-LPA by performing tension experiments in the presence and absence of nonselective and selective receptor antagonists and inhibitors of the TXA2 pathway. LPA1 was the most highly expressed receptor subtype in the late pregnant mouse uterus and LPA1/2/3 agonist (Oleoyl-L-α LPA) elicited increased contractions in this tissue that had lesser efficacy compared to oxytocin. LPA1/3 antagonist, Ki-16425, and a potent LPA1 antagonist (AM-095) significantly inhibited the LPA-induced contractions. Further, the nonselective COX inhibitor, indomethacin, and potent thromboxane A2 synthase inhibitor, furegrelate significantly impaired LPA-induced contractions. Moreover, selective thromboxane receptor (TP) antagonist, SQ-29548, and Rho kinase inhibitor, Y-27632 almost eliminated LPA-induced uterine contractions. LPA1 stimulation elicits contractions in the late pregnant mouse uterus using the contractile prostanoid, TXA2 and may be targeted to induce labor in uterine dysfunctions/ dystocia. • LPA1 is the highest expressed receptor in late pregnant mouse uterus. • Oleoyl-L-α-LPA elicits a concentration-dependent increase in contractions in the late-pregnant uterus. • Oleoyl-L-α-LPA-induced contractions are comparable to PGF2α-induced contractions. • Oleoyl-L-α-LPA-induced uterine contractions are mediated by LPA1 receptor. • Oleoyl-L-α-LPA-activated uterine contractions are mediated by thromboxane A2 pathway. [ABSTRACT FROM AUTHOR]

Contents: Developing alternate therapies for bovine endometritis is important in the context of drug residues in the milk and emergence of antimicrobial resistant bacteria. In this regard, we studied the immunomodulatory effect of curcumin 30 µM, on lipopolysaccharide‐ (LPS) and/or flagellin (100 ng/ml each)‐induced prostaglandin E2 (PGE2) and proinflammatory cytokines (PIC) using primary bubaline endometrial stromal cells. After 24 hr treatment, the supernatant was assayed for PGE2 while cells were used for relative quantification of cytokines like IL‐1β, IL‐6, IL‐8 and TNF α transcripts using a control group as calibrator. LPS was found to possess potent stimulatory effect on PGE2 production, whereas the flagellin was not as potent as LPS in stimulating the PGE2 production either per se or in combination with LPS. LPS markedly up‐regulated the transcripts of IL‐8 and IL‐6 as compared to IL‐1β and TNF α in the bubaline endometrial stromal cells. Except for IL‐8, flagellin did not up‐regulate other PICs. There was no additive effect between LPS and flagellin on the up‐regulation of inflammatory cytokines. Curcumin inhibited the LPS‐induced up‐regulation of PIC with strong down‐regulation of IL‐8. The inhibitory effects of curcumin on the inflammatory mediators suggest a potential in the treatment of bovine endometritis. [ABSTRACT FROM AUTHOR]

Contents: Transition proteins (TNPs) are essential in chromatin condensation during spermiogenesis, and hence, they are the candidate genes for identifying sperm motility markers. Coding and in silico predicted promoter regions of these genes were investigated in crossbred and purebred cattle, and also, their mRNA quantification was done to explore its use as a diagnostic tool of infertility. PCR‐SSCP analysis revealed two band patterns in fragment III of TNP1 and fragment II of TNP2 gene. Sequence analysis revealed a deletion of "G" nucleotide in 3′UTR region of TNP1 and C>T SNP in intronic region of TNP2 gene. Least square analysis of variance did not reveal any significant influence of nucleotide deletion on any sperm motility parameters in both crossbred and purebred cattle. However, C>T SNP had a significant effect on initial progressive motility (p < 0.05) in purebred cattle and post‐thaw motility in overall cattle population. RT‐qPCR analysis did not reveal any significant variation in TNP1 and TNP2 gene expression among poorly motile and good quality spermatozoa of Vrindavani bulls. [ABSTRACT FROM AUTHOR]

Highlights • Tropical Indian goat breed tested for resistance/susceptibility to haemonchosis. • Indicator traits were faecal egg count, packed cell volume and dot ELISA. • Heritability of faecal egg count was low, and of PCV was moderate. • Two microsatellite loci were significantly associated with indicator traits. • Susceptible group showed up regulation of IFN-γ and down regulation of IL-10 mRNA. Abstract The present investigation was carried out with the objective to identify putative candidate genes / Quantitative trait loci for resistance / susceptibility towards Haemonchus infestation in tropical goat breed (Rohilkhandi goat) of India. The mean faecal egg count (FEC) and packed cell volume (PCV) of the population were 142.78 ± 22.54 epg (eggs per gram) and 31.73% ± 0.49, respectively. Grouping of animals as per dot ELISA test showed 41.33% (n = 124) positive and 58.66% (n = 176) negative for Haemonchus infestation. The microsatellite loci DYA and ODRB1.2 were significantly associated (P ≤ 0.05) to parasite resistance. The locus DYA showed significant association with log FEC and dot ELISA and the locus ODRB1.2 showed significant association with log FEC, PCV and dot ELISA at P ≤ 0.05. Real time expression profiling revealed that the susceptible group (high FEC group) had 11.1-fold more expression of IFNγ mRNA (Th 1 cytokine) and 0.11-fold lower expression of IL-10 mRNA (Th 2 cytokine), which was found to be statistically significant (P ≤ 0.05). [ABSTRACT FROM AUTHOR]

Lysophosphatidic acid (LPA) is a small ubiquitous lipid exerting diverse biological functions. Its role in reproduction in different species has created great interest in recent times. In the present study, we aimed to elucidate LPA signaling in nonpregnant buffalo uterus by in vitro studies. Standard techniques like real-time PCR (for mRNA expression of LPARs and COX-2 and iNOS), Western blot (for PPARγ protein expression), sandwich ELISA (for PGE2 and PGF2α assay) and histopathology (for assessment of endometrial architecture in culture) were used in this study. The buffalo uterine tissues were collected from the local slaughterhouse and were selected for the study on the basis of the presence of corpus luteum on the ovary (n = 5). The LPAR3 receptor was the highest expressed receptor as compared to LPAR1 and LPAR6 in non-pregnant uterine tissues after 6 h incubation in Dulbecco's Modified Eagle Medium (DMEM). 50 μM LPA increased the mRNA expressions of COX-2 and iNOS enzymes which were attenuated by the treatment of LPAR1/3 antagonist Ki16425. PPARγ antagonist GW9662 prevented the LPA-induced increase in iNOS mRNA expression but did not alter the COX-2 expression. LPA also enhanced the PGE 2 to PGF 2α ratio in uterine tissue homogenates which was inhibited by all the receptor antagonists as well as by the inhibitors of COX-2 and iNOS. LPA also increased the total nitrite level in tissue homogenates in LPAR1/3- and iNOS-dependent manner. Additionally, we demonstrate PPARγ mRNA and protein expressions in nonpregnant buffalo endometrium. In conclusion, the results of the present study suggest that LPA acts as a luteotropic factor during the estrus cycle in nonpregnant buffalo uterus by enhancing PGE2 to PGF2α ratio and NO level through multiple receptors. [ABSTRACT FROM AUTHOR]

New Findings: What is the central question of this study? Does the inhibition of the protein kinase casein kinase 2 (CK2) alter the uterine contractility? What is the main finding and its importance? Inhibition of CK2 impaired the spontaneous and oxytocin‐induced contractility in late pregnant mouse uterus. This finding suggests that CK2 is a novel pathway mediating oxytocin‐induced contractility in the uterus and thus opens up the possibility for this class of drugs to be developed as a new class of tocolytics. Abstract: The protein kinase casein kinase 2 (CK2) is a ubiquitously expressed serine or threonine kinase known to phosphorylate a number of substrates. The aim of this study was to assess the effect of CK2 inhibition on spontaneous and oxytocin‐induced uterine contractions in 19 day pregnant mice. The CK2 inhibitor CX‐4945 elicited a concentration‐dependent relaxation in late pregnant mouse uterus. CX‐4945 and another selective CK2 inhibitor, apigenin, also inhibited the oxytocin‐induced contractile response in late pregnant uterine tissue. Apigenin also blunted the prostaglandin F2α response, but CX‐4945 did not. Casein kinase 2 was located in the lipid raft fractions of the cell membrane, and disruption of lipid rafts was found to reverse its effect. The results of the present study suggest that CK2, located in lipid rafts of the cell membrane, is an active regulator of spontaneous and oxytocin‐induced uterine contractions in the late pregnant mouse. [ABSTRACT FROM AUTHOR]

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock. [ABSTRACT FROM AUTHOR]

A functional genomics approach was used to examine the immune response for transcriptional profiling of PBMC M. bovis infected cattle and healthy control cattle to stimulation with bovine tuberculin (purified protein derivative PPD-b). Total cellular RNA was extracted from non-challenged control and M. bovis challenged MDM for all animals at intervals of 6 h post-challenge, in response to in-vitro challenge with M. bovis (multiplicity of infection 2:1) and prepared for global gene expression analysis using the Agilent Bovine (V2) Gene Expression Microarray, 8 × 60 K. The pattern of expression of these genes in PPD bovine stimulated PBMC provides the first description of an M. bovis specific signature of infection that may provide insights into the molecular basis of the host response to infection. Analysis of these mapped reads showed 2450 genes (1291 up regulated and 1158 down regulated) 462 putative natural antisense transcripts (354 up-regulated and 108 down regulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). The results provided enrichment for genes involved top ten up regulated and down regulated panel of genes, including transcription factors proliferation of T and B lymphocytes. The highest differentially-expressed genes were associated to immune and inflammatory responses, immunity, differentiation, cell growth, apoptosis, cellular trafficking and regulation of lipolysis and thermogenesis. Microarray results were confirmed in infected cattle by RT qPCR to identify potential biomarkers TLR2, CD80, NFKB1, IL8, CXCL6 and ADORA3 of bovine tuberculosis. [ABSTRACT FROM AUTHOR]

Lysophosphatidic acid (LPA) is an important factor involved in embryo implantation and pregnancy establishment in humans and domestic livestock. LPA exerts its action through six G-protein-coupled receptors (LPA1-LPA6). We investigated the types of LPA receptors expressed in buffalo uterus and also their differential expression in the nonpregnant, and early-pregnant endometrium. The nonpregnant, and early-pregnant (<42 days) uteri were collected from the local slaughterhouse. RT-PCR experiments detected mRNAs of all the six LPA receptors (LPAR1-LPAR6) in both nonpregnant, and early-pregnant endometrial tissues. Their comparative profiling by real-time PCR revealed that the early pregnant endometrium expressed more mRNAs of LPAR1 and LPAR6. All the mRNA fragments were sequenced and submitted to Genbank, NCBI. Western blot studies also showed a similar expression pattern of these two receptor proteins, including higher expression of both LPA1 and LPA6 proteins during early pregnancy. And between these two receptors, LPA6 upregulation was more pronounced than LPA1. In immunohistochemistry, these receptors were found to be localized in the endometrial glandular epithelial cells of both types of uterus. Level of LPA was also higher in early pregnant endometrial tissues. In summary, our study demonstrated expression of all the six LPAR mRNAs in buffalo uterus, wherein the early-pregnant uterus did express comparatively higher mRNA as well as protein of LPA1 and LPA6, indicating their role in pregnancy. The more pronounced expression of LPA6 possibly indicates its greater contribution to mediating LPA signaling in early pregnancy (29–42 days) of buffalo. [ABSTRACT FROM AUTHOR]

In present investigation, differential expression of transcriptome after classical swine fever (CSF) vaccination has been explored at the cellular level in crossbred and indigenous (desi) piglets. RNA Sequencing by Expectation-Maximization (RSEM) package was used to quantify gene expression from RNA Sequencing data, and differentially expressed genes (DEGs) were identified using EBSeq, DESeq2, and edgeR softwares. After analysis, 5222, 6037, and 6210 common DEGs were identified in indigenous post-vaccinated verses pre-vaccinated, crossbred post-vaccinated verses pre-vaccinated, and post-vaccinated crossbred verses indigenous pigs, respectively. Functional annotation of these DEGs showed enrichment of antigen processing-cross presentation, B cell receptor signaling, T cell receptor signaling, NF-κB signaling, and TNF signaling pathways. The interaction network among the immune genes included more number of genes with greater connectivity in vaccinated crossbred than the indigenous piglets. Higher expression of IRF3, IL1β, TAP1, CSK, SLA2, SLADM, and NF-kB in crossbred piglets in comparison to indigenous explains the better humoral response observed in crossbred piglets. Here, we predicted that the processed CSFV antigen through the T cell receptor signaling cascade triggers the B cell receptor-signaling pathway to finally activate MAPK kinase and NF-κB signaling pathways in B cell. This activation results in expression of genes/transcription factors that lead to B cell ontogeny, auto immunity and immune response through antibody production. Further, immunologically important genes were validated by qRT-PCR. [ABSTRACT FROM AUTHOR]

Bovine tropical theileriosis is an important haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints of the livestock development programmes in India and Southeast Asia. Indigenous cattle ( Bos indicus ) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance to tropical theileriosis in indigenous cattle is not well documented. Recent studies incited an idea that differentially expressed genes in exotic and indigenous cattle play significant role in breed specific resistance to tropical theileriosis. The present study was designed to determine the global gene expression profile in peripheral blood mononuclear cells derived from indigenous (Tharparkar) and cross-bred cattle following in vitro infection of T . annulata (Parbhani strain). Two separate microarray experiments were carried out each for cross-bred and Tharparkar cattle. The cross-bred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were down-regulated and 485 were up-regulated. Their fold change varied from 2283.93 to − 4816.02. Tharparkar cattle showed 875 differentially expressed genes including 451 down-regulated and 424 up-regulated. The fold change varied from 94.93 to − 19.20. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level. Functional annotation study of DEGs confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. It is therefore, hypothesized that the different susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against T . annulata infection. [ABSTRACT FROM AUTHOR]

Altered lipid metabolism in obesity causes pregnancy complications in humans and animals. Leptin levels increase in pregnancy, as well as obesity. However, the effect of obesity on uterine leptin receptors and its distal signaling is not clear. The present study aimed to understand the effect of increased fat on leptin signaling in rat uterus. Wistar female rats were fed with an HF diet (40% Fat, 17% Sucrose, 1.25% Cholesterol, 0.75% Cholic acid) for 6 weeks before the mating and during pregnancy. HF diet significantly increased the fat depots, liver weight, serum, and tissue cholesterol levels. It produced fatty degeneration in the liver and caused infiltration of inflammatory cells, cystic endometrial glands, and sub endometrial fibrosis of the uterus. In isometric tension experiments, leptin caused a significant increase in uterine contractions in high fat-fed animals compared to control animals. Analysis of receptor expressions revealed no significant difference between the groups. However, a significant decrease in the JAK2 and BKCaα mRNA expression was observed in the uterus of high fat-fed rats. No change in the BKCaβ, eNOS, iNOS, MLCP, and MLCK mRNA expressions was noticed in the HF group compared to the control. The findings of the present study suggest that the contractile response to leptin in the uterus of high fat-fed rats may be attributed to reduced signaling through JAK2 and, lowered expressions of BKCa channel α subunits. [ABSTRACT FROM AUTHOR]

Genomic DNA was isolated from the blood of 100 crossbred cattle (HF, Jersey, Brown Swiss x Hariana cattle). Exon 4 and intron 6 of lactoferrin (Lf) gene was characterized by PCR-SSCP. Two alleles of exon 4, namely E & F showing two genotypes EE and EF and two alleles of intron 6, namely A and B showing two genotypes AA and AB were found in studied population. Cloning and sequencing results revealed that in exon 4, there was one SNP in allele E and two SNPs in allele F, which changed amino acid isoleucine to valine. In intron 6 there was one SNP in allele A and three SNPs in allele B. Least square analysis for SCC and FLMY revealed that genotype AA was significantly associated with low SCC, while genotype AB was significantly associated with high SCC. However, genotype EE was significantly associated with FLMY as compared to genotype EF. [ABSTRACT FROM AUTHOR]

Background The aim of the present study was to assess the effect of seven days daidzein pretreatment in cecal ligation and puncture (CLP) model of sepsis. Methods We assessed the survival benefit of daidzein and its effect on lung injury in CLP-induced sepsis in mice and determined the bacterial load in peritoneal fluid, blood, and lung homogenates. Tumor necrosis factor a (TNF-a) and corticosterone levels were measured by enzyme-linked immunosorbent assay; relative mRNA expression was estimated by real-time polymerase chain reaction, and standard biochemical techniques were used to measure nitrite level, myeloperoxidase activity, and vascular permeability. Results Daidzein pretreatment for seven days at a dose of 1 mg/kg body weight subcutaneously increased the survival time of septic mice. Daidzein decreased the bacterial load in peritoneal fluid, blood, and lungs, reduced the tumor necrosis factor a and nitrite level in plasma, and partially suppressed lung injury by reducing vascular permeability and myeloperoxidase activity in septic mice. Further, it restored the relative mRNA expressions of inducible nitric oxide synthase, glucocorticoid receptor a, and glucocorticoid receptor β genes in septic lungs were restored by daidzein pretreatment. Conclusions Daidzein pretreatment for 7 d in sepsis increased the survival time in mice, which may be relate to decrease in bacterial load, anti-inflammatory effect, and protection from lung injury. [ABSTRACT FROM AUTHOR]

MicroRNAs are a class of small, endogenously produced, 18 to 24 nucleotides long in length. These are non-coding RNAs that regulate the gene expression at post-transcriptional level. They play important roles in animals and plants by controlling regulatory mechanisms, and likely influencing the output of many protein-coding genes. They generally bind to 3' UTR region of the target sequence which then leads to alterations in the gene expression. They also bind to other regions like coding sequence and 5' UTR but these are less efficient sites of interaction compared to 3'UTR. This alteration in gene expression is either due to repression of translation or mRNA degradation whereby the RNA interference pathway is initiated to eliminate the targeted sequences. Now a days, various computational or bioinformatics databases, tools, and algorithms have been developed to identify the target genes which will be further biologically validated using various techniques like reporter gene assay, qRT-PCR, microarray etc. [ABSTRACT FROM AUTHOR]

• The Indian Ghurrah pig has a mixture of European and Asian inheritance. • Analysis traced European admixture to the recent past. • Signs of interspecies introgression was detected in admixture analysis. • Ghurrah and Asian pigs show divergence in genomic regions governing teeth development. The evolution and domestication of pigs is a complex and ongoing process. Despite its rich biodiversity and proximity to the geographical origins of Sus scrofa domesticus, the place of Indian pigs in the global phylogeny is unclear. Using microarray-derived (porcine 60K SNP chip) genotypes of 11 Ghurrah pigs from North-Western India and a public dataset comprising 2113 pigs of 146 breeds, we determined the genomic ancestry of Ghurrah pigs and compared their genetic constitution to European and Asian breeds to ascertain signatures of divergent selection. Results showed that Ghurrah pigs contain genes of Asian and European ancestry with signs of inter-species introgression. Using Admixture LD – decay statistics, the European admixture event was dated to the recent past, coinciding with the start of cross-breeding efforts in India. The complex Asian ancestry pattern of the breed resembled that of wild boars of South – Central China and Thailand, possibly suggesting introgression from an Indian wild boar relative. Signatures of selection analysis showed the divergence of Ghurrah pigs from Asian and European breeds in genomic regions associated with odontogenesis, and nervous system processess, respectively. Our results present the first genomic characterization of an Indian pig breed using dense microarray-derived genotypes and highlight the importance of further genomic characterization of Indian domestic and wild pigs. Given the limited sample size available for this study, validation of the findings in a larger population is suggested. [ABSTRACT FROM AUTHOR]

The adipokine, leptin exerts inhibitory effect on both spontaneous and oxytocin-induced contractions in myometrium. However, the mechanisms involved in leptin-induced effect are not clear. In the present study, we studied the altered characteristics of uterine contractions in the presence of leptin and the possible mechanisms of its effect in late pregnant (18.5 day) mouse uterus. We conducted functional, biochemical and molecular biology studies to demonstrate the mechanism of leptin-induced response. Leptin exerted an inhibitory response (E max 40.5 ± 3.99%) on basal uterine contractions. The extent of inhibition was less than that obtained with known uterine relaxants, salbutamol (E max 103 ± 8.66%) and BRL-37344 (E max 84.79 ± 8.12%). Leptin-induced uterine response was inhibited by leptin receptor antagonist SHLA and JAK-STAT pathway inhibitor, AG-490. The relaxant response was also subdued by NO-cGMP-PK-G pathway blockers L-NAME, 1400W, ODQ and KT-5823. Further, leptin enhanced the levels of NO and cGMP in uterine tissues. Also, SHLA, AG-490 and a combination of 1400 W and L-NAME prevented leptin-induced increase in NO. Similar effect was observed on cGMP levels in presence of leptin and SHLA. However, leptin did not influence CaCl 2 -induced response in potassium-depolarized tissues. We also detected leptin receptor protein in late pregnant mouse uterus located in endometrial luminal epithelium and myometrial layers. Real-time PCR studies revealed significantly higher expression of short forms of the receptor (ObRa and ObRc) in comparison to the long form (ObRb). In conclusion, the results of the present study suggest that leptin inhibits mouse uterine contraction by stimulating short forms of the leptin receptors and activating NO pathway in a JAK-STAT-dependent manner. [ABSTRACT FROM AUTHOR]

A total of 9 SNPs located in TFRC and ACK1 genes of SSC13q41 genomic region were examined for their association with the adhesion pattern of native Indian pigs using local isolate of diarrhoeagenic E. coli. Phenotypic evaluation of adhesion pattern of 150 pigs revealed 116 animals positive for adhesion, whereas 34 animals had non-adhesive phenotype. Among the adhesive animals, 6, 87 and 23 pigs were strongly adhesive, weakly adhesive and adhesive, respectively. PCR–RFLP study revealed 8 polymorphic SNPs with low to moderate PIC ranging from 7.39 to 37.25% and low to high heterozygosities (8–70%). The loci g.291 C > T, rs81218930 C > T, rs318751568 C > T of TFRC and g.93222 C > A g.94600 C > T of ACK1 showed significant departure from HWE. The genotypic frequencies of the SNPs as well as the haplotypes did not differ significantly (P > 0.05) across the adhesion patterns except one SNP (ACK1-g.107371 A > C). Among the g.107371 A > C genotypes observed, CA was associated with non-adhesive phenotype. Furthermore, TFRC mRNA expression levels were found to be significantly (P < 0.05) different among various adhesive phenotypes, whereas that of ACK1 was significantly (P < 0.05) different between non-adhesive and adhesive groups. The significant association of SNP (ACK1-g.107371 A > C), which was also previously reported to influence ETECF4 mediated diarrhoea susceptibility, implicates its wider application in genetic control of piglet diarrhoea. Furthermore, the up-regulation of TFRC gene expression in adhesive group supports its proposed role in activation of immune cells against E. coli and intracellular iron transport. [ABSTRACT FROM AUTHOR]