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This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of northeast India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia. [ABSTRACT FROM AUTHOR]

Abstract: Genetic structure of Banni buffaloes vis-à-vis four other river buffalo breeds of Western India was assessed using short tandem repeat markers. The total number of alleles varied between 115 and 127 across five buffalo breeds. The mean estimates of global F-statistics over all loci were 0.330 for F IT, 0.145 for F ST and 0.216 for F IS respectively. Analysis of molecular variance revealed that 14.33% of the total genetic variation was being explained by between breed differences. The phylogenetic tree constructed using chord distance estimates revealed the distinctness of Banni and Jaffarabadi buffaloes from other river buffalo breeds of the region. Multi dimensional scaling display of pair-wise F ST values revealed the close proximity of Mehsana, Surti and Murrah buffaloes while Banni and Jaffarabadi buffaloes were placed separately. The results of principal components analysis based on pair-wise chord distance estimates between individual animals were consistent with the observation based on multidimensional scaling (MDS) analysis. This genetic structure was further supported by Bayesian clustering analysis which revealed three inferred clusters with Banni and Jaffarabadi forming separate clusters each while the remaining three breeds viz. Mehsana, Surti and Murrah together formed a single cluster. The results of the present study thus revealed the genetic uniqueness of Banni buffalo among other buffalo breeds of the region. [Copyright &y& Elsevier]

Abstract: In the present study, microsatellite data on 24 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Marathwada buffaloes, a Central Indian population maintained under low input system. Sufficient allelic diversity was observed with a total of 109 alleles across different loci. The genetic diversity analysis of Marathwada buffaloes displayed moderate level of within breed variability in terms of mean number of alleles per locus (4.48) and heterozygosity values (Ho=0.532, He=0.624). The studied Indian buffalo population showed considerable heterozygote deficiency (F IS =0.138) and deviation from HWE at many investigated loci. Three quantitative tests viz. sign test, standardized difference test and Wilcoxon sign rank test and a qualitative test for mode shift distortion of allelic frequencies were employed to evaluate mutation drift equilibrium under three different models of microsatellite evolution. The population was found to deviate significantly under IAM and TPM, while it was reverse under SMM. The qualitative test for mode shift supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Marathwada buffaloes. [Copyright &y& Elsevier]

• The research explores new bio-dielectric i.e Calophyllum inophyllum (polanga). • 3 productivity & process quality aspects (MRR,TWR,REWR,SR,SH,ROC/RUC) are assessed. • Significant improvement in output responses were found in the comparison process. • Environmental impact with aerosol emission rate for PBD is lower by 17.33% in comparison to HC dielectric. • Current study will be more helpful in opening path for more in-depth research in GREEN EDM. In a global scenario, energy conservation with eco-sustainable manufacturing is a major challenge for engineers. Motivation and stringent implementation of sustainable manufacturing practices is one significant way to insure the green environment for future. Alarming needs at present is innovative green methods of non-conventional manufacturing processes to be globally competitive. So, in the present investigation, authors have assessed the operational feasibility of transesterified Calophyllum Inophyllum (Polanga) based non-edible oil as possible alternative bio-dielectric for EDM applications and compared the response patterns of the new bio-dielectric fluid with hydrocarbon based EDM oil. OFAT (one factor at a time) design algorithm was utilized using peak current, duty cycle, pulse-on time, and gap voltage as control parameters to evaluate the response pattern for material removal rate, electrode wear rate, relative electrode wear ratio, surface texture and aerosol emission rate. The study confirms that Polanga bio-dielectric contributes to higher productivity and better process quality parameters like enhancement in mean MRR by 0.86 times, better surface finish by 16.64%, surface hardness by 6.46% as well as refined microstructure quality as compared to traditional hydrocarbon dielectric. Assessment of environmental impact through aerosol emission rate confirms 17.33% reduction with Polanga bio-dielectric use. Results and performance evaluation reveal that new bio-dielectric fluid can be a primary dielectric choice for green EDM replacing conventional hydrocarbon, water and synthetic based dielectric fluids. Findings also confirms that it can greatly contribute for establishing a family of vegetable-based bio dielectrics in the area of green manufacturing thus removing obstacles like reduction of toxic emissions, operator's health hazards, fire hazards and enhancement of environmental sustainability in future. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome. [ABSTRACT FROM AUTHOR]

The present study was aimed to elucidate the host–virus interactions using RNA‐Seq analysis at 1 h and 8 h of post‐infection of sheeppox virus (SPPV) in lamb testis cell. The differentially expressed genes (DEGs) and the underlying mechanisms linked to the host immune responses were obtained. The protein–protein interaction (PPI) network analysis and ingenuity pathway analysis (IPA) illustrated the interaction between the DEGs and their involvement in cell signalling responses. Highly connected hubs viz. AURKA, CHEK1, CCNB2, CDC6 and MAPK14 were identified through PPI network analysis. IPA analysis showed that IL‐6‐ and ERK5‐mediated signalling pathways were highly enriched at both time points. The TP53 gene was identified to be the leading upstream regulator that directly responded to SPPV infection, resulting in downregulation at both time points. The study provides an overview of how the lamb testis genes and their underlying mechanisms link to growth and immune response during SPPV infection. [ABSTRACT FROM AUTHOR]

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations. [ABSTRACT FROM AUTHOR]

Abstract: The present study investigates the mitochondrial DNA diversity in 154 Indian sheep from 19 breeds/populations from 3 different agroecological regions. A total of 37 haplotypes could be distinguished in Indian sheep. Overall values of nucleotide and haplotype diversities were 0.0017 and 0.60 respectively. The breeds of southern peninsular region showed high haplotype diversity (0.74). Two maternal lineages (haplogroups A and B) could be identified with haplogroup A predominating over haplogroup B. Network profile revealed a star burst phylogeny for haplogroup A. Signatures of recent population expansion were evident from unimodal patterns of mismatch distribution as well as significant negative values of Tajima''s D and Fu''s Fs tests. Apart from the maternal lineages A and B, no other known lineage was detected. [Copyright &y& Elsevier]

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: FIT = 0.144 ± 0.023, FIS = 0.071 ± 0.021, and FST = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals. [ABSTRACT FROM AUTHOR]

Abstract: Lactoferrin, an iron (Fe3+) binding glycoprotein, found in a variety of body secretions of mammals, is a potential candidate gene in dairy cattle breeding for increasing resistance against infections especially in the mammary gland. The present study was undertaken with the objective of examining the 5′ flanking region of bubaline (Bubalus bubalis) lactoferrin gene to gain insight into the polymorphism existing in this region across different buffalo breeds. The 5′ flanking region of lactoferrin gene was analyzed by single strand conformation polymorphism (SSCP) in five different Indian buffalo breeds, viz. Murrah, Jaffarabadi, Marathwada, Toda and Pandharpuri. A total of 10 distinct SSCP patterns were observed which further revealed 13 polymorphisms with 8 transitions, 4 transversions and one deletion mutation upon sequence analysis. A total of 1056 bp 5′flanking region of bubaline lactoferrin gene was sequenced which was found to have 96% homology with Bos taurus, 91% with Capra hircus, 95%, Bos indicus, 92% with Ovis aries, 57% with Sus scrofa and 28% with Homo sapiens. From the polymorphisms identified in the 1056 bp 5′ flanking region, polymorphism at nucleotide position −209 was found to lie within a potential SP1 transcription factor binding site, while SNP at −19 was found in the vicinity of the TATA box. Two SNPs identified at −57 and −61 positions were found to be present in the vicinity of putative estrogen response element. Another SNP at −636 position was found to be present in the vicinity of putative recognition sequence for IRF-1 which serves as a transcriptional activator for interferon genes and interferon inducible genes. The SNPs identified in the lactoferrin promoter region may serve as potential candidate genetic marker(s) in buffaloes for disease resistant traits. [Copyright &y& Elsevier]

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F ST , to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F ST methods, respectively. We found several candidate genes (e.g., NCR3 , ARID5A , HIST1H2BN , DEFB4 , DEFB7 , HSPA1L , HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping. • The combination of various statistical approaches could facilitate the wider spectrum of detection of both recent and ancient selection signatures. • The identified candidate genes provide insights into the adaptation and production performance of various cattle breeds. • Our observations can provide valuable knowledge for GWAS, genomic selection, implementing breeding schemes and conservation programmes. [ABSTRACT FROM AUTHOR]

The aim of the present study was to assess the population structure and admixture levels in the Vrindavani composite population in India by using Bovine50KSNP BeadChip data. Genotypic data were generated for randomly selected animals (n = 72) of Vrindavani population and the data for parental breeds i.e., Hariana (n = 10), Holstein-Friesian (n = 63), Jersey (n = 28) and Brown Swiss (n = 22) were retrieved from a public repository. The indices of population structure were calculated using PLINK software and R-program. The merged dataset was analysed for assessing admixture levels and population stratification using three different approaches i.e., principal component analysis (PCA), multi-dimensional scaling (MDS) approach and the model-based approach in STRUCTURE software. The average minor allele frequency (MAF) value for Vrindavani population was estimated to be 0.235. Vrindavani population was found to possess an average ancestry of 39.5, 22.9, 26.9, and 10.7% inheritance levels from Holstein Friesian, Jersey, Hariana and Brown Swiss cattle breeds, respectively. • We have got evidence of optimum applicability of Bovine 50 K SNP BeadChip data on crossbred population for admixture study • Admixture levels in Vrindavani crossbred population were calculated for the first time in the Indian context • The basic information generated in our study will help for characterization of other similar crossbreds of the country [ABSTRACT FROM AUTHOR]

The cost of SNP genotyping to screen different breeds and to estimate the exact proportion of ancestry level is quite high, which can be compensated through deriving a small panel of ancestry informative markers (AIMs). Hence, we carried out the present study to provide an insight into ancestry level inferred from a panel of informative markers in the crossbred Vrindavani population developed at ICAR-IVRI, India. We have performed a new method i.e., discriminant analysis of principal components (DAPC) for the first time on the dataset of Vrindavani cattle. To confirm our method, we had performed DAPC on two other well-known crossbred cattle, i.e., Frieswal and Beefmaster. Three sets of panels (500, 1000 and 2000 markers) were tested for clustering of individuals. Among all the panels, we found the panel (1000 markers) with DAPC based contribution method was of the smallest size and comparatively of the highest accuracy. • The present study was carried out to infer ancestry level from a panel of informative markers in the crossbred population • The 1000 markers panel selected through DAPC based contribution method was the smallest and comparatively accurate • The information generated in our study will pave the way for characterization of other crossbreds available in the country [ABSTRACT FROM AUTHOR]

Bovine herpesvirus-1 (BoHV-1) is a viral pathogen found in infected bull semen, which is transmitted to inseminated cows by artificial insemination. BoHV-1 infection can cause reproductive disorders leading to significant economic loss to cattle industry. To detect BoHV-1 in semen, in this study, a SYBR Green I based duplex real-time PCR was developed. The assay included primers from BoHV-1 glycoprotein C (gC) and bovine growth hormone (bGH) genes for simultaneous detection in single tube. The result was interpreted by analysing melting temperature ( T m ) peaks obtained after melt curve analysis of the amplified products at the end of reaction. The T m peaks for BoHV-1-gC indicated presence of BoHV-1 while the bGH peak indicated reaction without inhibition. The sensitivity of the assay was to detect ten BoHV-1 genome copies per reaction. The analytical sensitivity was to detect 0.21 TCID 50 infectious BoHV-1 in spiked semen. The assay was validated with 80 semen samples collected from breeding bulls. The diagnostic sensitivity and specificity of the assay was 100% with OIE recommended TaqMan probe based real-time PCR. [ABSTRACT FROM AUTHOR]

• We merged extracted datasets of 11 cattle breeds with our own generated Tharparkar genotypic data to obtain a final dataset of 284 animals. • The PCA indicates the partitioning between Exotic and Indigenous cattle breeds on the two PC axis. • We used several statistical tools (eight) to find out and verify more genomic footprints. • More number of short ROHs in Tharparkar shows a more historical relationship. • Combined analysis of all the methods may provide refined information about selective sweep regions in different methods. • We extracted out various candidate genes associated with economically important traits. In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, F ST , FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3 , CXCL5 , IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes. [ABSTRACT FROM AUTHOR]

In the present study, expression level of various ATP-binding cassette (ABC) viz.,ABCA1, ABCA7, ABCG1, ABCG2, andABCG5; associated transcription factors viz.,SREBF1,LXRα (NR1H3),PPARA, and Solute Carriers (SLC); or Glucose transporters (GLUT) viz.,SLC2A1(GLUT1), SLC2A4 (GLUT4), SLC2A8 (GLUT8), andSLC2A12 (GLUT12)superfamily of transporters were compared across physiological stages of buffalo mammary gland. The relative expression ofABCA1, andABCG1was significantly (p < 0.05) higher in mammary gland of heifer followed by involution and lactation stages. Similarly,ABCA7gene expression was highest in heifer mammary gland followed by lactation and involution stages.ABCG2gene expression was significantly (p < 0.05) high in lactating mammary gland in comparison to involution and heifer stages. On the other hand,ABCG5gene expression was highest in involuting mammary gland followed by lactation and involution stages. Additionally, the expression ofLXRαSREBF1, andPPARAwhich are known to regulate some of the ABC tranporters were also analyzed. The expression ofLXRα gene was high in involuting as compared to lactating mammary gland. In contrast,SREBF1andPPARAexpression was significantly (p < 0.05) high in lactating mammary gland. Among the several SLC transporters studied,SLC2A1, SLC2A4, andSLC2A8showed significant (p < 0.05) higher expression during lactation stage, whereasSLC2A12expression was greater during heifer stage suggestingSLC2A1, SLC2A4, andSLC2A8to be the major transporters associated with glucose uptake in buffalo mammary gland. The expression profile of (lactoferrin)LTF, known to be expressed at high level in mammary gland during involution was also studied. As expected, its expression was significantly (p < 0.05) higher during involution in comparison to lactating mammary gland.in buffaloes as well. The inclusion ofLTFas a control gene further provided the confidence in the buffalo mammary gland expression data generated in the present study. This study thus helped to provide information about the distinct expression pattern of various transporters and their regulators in buffalo mammary gland during different physiological states. [ABSTRACT FROM PUBLISHER]

Lactation is an important physiological process in dairy animals. During lactation, up to 85% of the body glucose is directed toward the mammary glands for milk synthesis. Studies related to lactation physiology are generally carried out on mammary biopsies, which may adversely affect animal health. In the present study, milk enriched MEC were used to study the expression pattern of GLUT1 and apoptotic genes (BAX and BCL2) across different stages of lactation in riverine buffalo in relation to milk yield. MEC were enriched from milk using cytokeratin-8 antibodies coated magnetic beads. Total RNA isolated from enriched MEC showed significant correlation (r2 = 0.92 ± 0.02) with the milk yield at different stages of lactation. GLUT1 expression pattern correlated with the milk yield as highest GLUT1 expression (4.68 ± 0.79) was observed during peak-lactation (90 days post-parturition), whereas low GLUT1 expression (1.01 ± 0.1, 15 d; 0.71 ± 0.03, 30 d) was observed during early lactation. The BAX/BCL2 ratio was high (1.02 ± 0.2, 15 d; 0.94 ± 0.06, 30 d) during the early phase of lactation, indicating high rate of apoptosis, whereas low BAX/BCL2 ratio (0.25 ± 0.03, 60 d; 0.42 ± 0.04, 90 d) was observed during mid-lactation coinciding with the increase in RNA concentration and milk yield. Highest BAX/BCL2 ratio (1.41 ± 0.3, 120 d; 4.02 ± 0.6, 240 d) was observed during late lactation i.e., 240 days, which was also reflected as decline in milk yield and RNA concentration. Also, BAX/BCL2 ratio in milk enriched MEC was in accordance with RNA concentration in MEC and milk yield at different phases of lactation. Our study showed that expression pattern of genes under study (GLUT1, BAX, and BCL2) in milk enriched MEC correlated well with important physiological properties such as milk yield in buffalo. [ABSTRACT FROM PUBLISHER]

Abstract: Due to evolutionary divergence, cattle (taurine, and indicine) and buffalo are speculated to have different responses to heat stress condition. Variation in candidate genes associated with a heat-shock response may provide an insight into the dissimilarity and suggest targets for intervention. The present work was undertaken to characterize one of the inducible heat shock protein genes promoter and coding regions in diverse breeds of Indian zebu cattle and buffaloes. The genomic DNA from a panel of 117 unrelated animals representing 14 diversified native cattle breeds and 6 buffalo breeds were utilized to determine the complete sequence and gene diversity of HSP70.1 gene. The coding region of HSP70.1 gene in Indian zebu cattle, Bos taurus and buffalo was similar in length (1926bp) encoding a HSP70 protein of 641 amino acids with a calculated molecular weight (Mw) of 70.26kDa. However buffalo had a longer 5′ and 3′ untranslated region (UTR) of 204 and 293 nucleotides respectively, in comparison to Indian zebu cattle and Bos taurus wherein length of 5′ and 3′-UTR was 172 and 286 nucleotides, respectively. The increased length of buffalo HSP70.1 gene compared to indicine and taurine gene was due to two insertions each in 5′ and 3′-UTR. Comparative sequence analysis of cattle (taurine and indicine) and buffalo HSP70.1 gene revealed a total of 54 gene variations (50 SNPs and 4 INDELs) among the three species in the HSP70.1 gene. The minor allele frequencies of these nucleotide variations varied from 0.03 to 0.5 with an average of 0.26. Among the 14 B. indicus cattle breeds studied, a total of 19 polymorphic sites were identified: 4 in the 5′-UTR and 15 in the coding region (of these 2 were non-synonymous). Analysis among buffalo breeds revealed 15 SNPs throughout the gene: 6 at the 5′ flanking region and 9 in the coding region. In bubaline 5′-UTR, 2 additional putative transcription factor binding sites (Elk-1 and C-Re1) were identified, other than three common sites (CP2, HSE and Pax-4) observed across all the analyzed animals. No polymorphism was found within the 3′-UTR of Indian cattle or buffalo as it was found to be monomorphic. The promoter sequences generated in 117 individuals showed a rich array of sequence elements known to be involved in transcription regulation. A total of 11 nucleotide changes were observed in the promoter sequence across the analyzed species, 3 of these changes were located within the potential transcription factor binding domains. We also identified 4 microsatellite markers within the buffalo HSP70.1 gene and 3 microsatellites within bovine HSP70.1. The present study identified several distinct changes across indicine, taurine and bubaline HSP70.1 genes that could further be evaluated as molecular markers for thermotolerance. [Copyright &y& Elsevier]

It is now a well-accepted notion that each new experimental design requires proper evaluation of internal control genes (ICGs) for accurate normalization of expression data. In riverine buffaloes, till date no appropriate ICG has been reported for studying transcriptional response under any of the physiological stressful condition. The objective here was to test 16 well-known reference genes from different functional categories that could serve as suitable ICG during heat stress studies in buffalo mammary tissue. Briefly, the mammary explants were exposed to 45°C for 1 h and subsequently allowed to recover at 37°C for different time points (2-24 h). Three software programs, geNorm, Normfinder and BestKeeper, were used to measure gene transcript stability. RPL22 was excluded because of weak amplification and unacceptable PCR efficiency. Except GAPDH, all other genes showed expression stability within the acceptable range (<1.5). RPL4, B2M, RPS23 and EEF1A1 genes were found to be most stably expressed while GAPDH and ACTB showed least stability. The BestKeeper analysis identified high correlation for RPL4 ( r = 0.953) and EEF1A1 ( r = 0.914) with BestKeeper index. Based on the present findings, it could be suggested that geometric average of RPL4, B2M, RPS23 and EEF1A1 would provide accurate normalization to transcriptional data of buffalo mammary explant in response to heat stress. [ABSTRACT FROM AUTHOR]

Abstract: The aim of the research reported herein was to evaluate the stability of 7 frequently used housekeeping genes including ACTB (β-actin), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ubiquitously expressed transcript protein (UXT), ribosomal protein S9 (RPS9), ribosomal protein S15 (RPS15), ribosomal protein S23 (RPS23) and hypoxanthine-guanine phosphoribosyl transferase (HPRT) in mammary epithelial cells (MECs) isolated from buffalo milk at different phases of lactation (15d, 30d, 45d, 60d, 120d and 240d relative to parturition) of three buffaloes. The expression of the genes varied considerably in different MECs samples analyzed. GAPDH showed the highest expression, whereas the expression of UXT was the lowest in MECs of buffalo during all stages of lactation. Microsoft excel based visual application i.e. geNORM and Normfinder were used to rank candidate reference genes based on expression stability. RPS9 and RPS23 were found to be the most stable genes during lactation in buffalo. Geometric mean of these genes can be used for normalization of real time PCR data in mammary epithelial cells during lactation. [Copyright &y& Elsevier]

In this study, approximately 3.4 kb nucleotide sequence of caprine TLR7 (Toll-like receptor 7) gene was generated from twelve different Indian goat breeds belonging to different geographical regions. Goat TLR7 gene ORF (Open Reading Frame) was found to be 3141 nucleotides long coding for 1046 amino acids similar to sheep. The sequence analysis at nucleotide level revealed goat TLR7 having 99.5% homology with sheep, followed by other livestock species. Simple Modular Architecture Research Tool (SMART) was used for the structural analysis of goat TLR7 that showed the presence of 22 leucine rich repeats (LRRs) along with single Toll/interleukin-1 receptor (TIR) domains. TIR domain, when compared, was found to be similar in ruminant species, goat, sheep, cattle, and buffalo. The phylogenetic analysis also revealed grouping of all ruminant species together, goat being closer to sheep followed by cattle and buffalo. A total of 22 polymorphic sites were observed in TLR7 gene of 24 goats representing 12 different breeds, out of which 19 were present within the coding region and three in 3'UTR. Out of the seven nonsynonymous SNPs, two were in ectodomains and one in TIR domain. Overall our results indicate substantial variation within goat TLR7 gene, which could be exploited for association with disease susceptibility. [ABSTRACT FROM PUBLISHER]

The present study was undertaken to characterize the structure of S100A8 gene and its promoter in water buffalo and yak. Sequence data of 2.067 kb, 2.071 kb, and 2.052 kb with respect to complete S100A8 gene including 5' flanking region was generated in river buffalo, swamp buffalo, and yak, respectively. BLAST analysis of coding DNA sequences (CDS) of S100A8 gene revealed 95% homology of buffalo sequence with cattle, 85% with pig and horse, 83% with dog, 72-73% with murines, and around 79% with primates and humans. Phylogenetic analysis of predicted CDS revealed distinct clustering of murines, primates, and domestic animals with bovines and bubalines forming a subcluster among farm animals. In silico translation of predicted CDS revealed a sequence of 89 amino acids with 7 amino acid changes between cattle and buffalo and 2 changes between cattle and yak. The search for Pfam family revealed the N-terminal calcium binding domain and the noncanonical EF hand domain in the carboxy terminus, with more variations being observed in the N-terminal domain among different species. Two amino acid changes observed in carboxy terminal EF hand domain resulted in altered secondary structure of yak S100A8 protein. Analysis of S100A8 gene promoter revealed 14 putative motifs for transcriptional factor binding sites. Two putative motifs viz. C/EBP and v-Myb were found to be absent in swamp buffalo as compared to river buffalo and cattle. Differences in the structure of S100A8 protein and the transcriptional factor binding sites identified in the present study need to be analyzed further for their functional significance in yak and swamp buffalo respectively. [ABSTRACT FROM AUTHOR]

Abstract: This study involved cloning and sequencing of the coding regions of all 10 Toll-like receptor (TLR) genes of goat. Goat TLR 1–10 gene sequences revealed a high degree of nucleotide identity with sheep and cattle sequences (>90%) and 75–85% with pig, mouse and human sequences. At the amino acid level, 85–99% similarity was observed with sheep and cattle and 60–85% with pig, mouse and human. TLR9c DNA of goat showed the highest amino acid identity to that of sheep (99%) while TLR8 cDNA showed the lowest identity of 88.7% to that of sheep. Variations were seen in the number of leucine rich repeats (LRRs) of goat TLRs as compared to other ruminant species with maximum differences in the TLR3 gene. Phylogenetic analysis through molecular evolution and genetic analysis (MEGA) software and multi dimensional scaling revealed a high degree of conservation of goat TLRs with those from other species. However when the TIR domain of all the TLRs were compared, goat TLR7 TIR alone showed a high divergence of 19.3 as compared to sheep sequences. This is the first report of the full-length cDNA sequences of all the 10 TLR genes of goats which would be a useful tool for the study of evolutionary lineages and for phylogenetic analysis. [Copyright &y& Elsevier]

Abstract: This study examines the genetic profiles of seven sheep breeds/populations of the Northwestern semi arid zone of India based on microsatellite markers. The coarse wooled sheep viz., Jalauni, Sonadi, Muzzafarnagri, Patanwadi, Kheri, Malpura and Munjal were analyzed with 25 microsatellite markers to determine within breed variability, genetic differentiation and relationships among them. The mean number of alleles across all the populations ranged from 6.8 to 8.7, whereas the gene diversity varied from 0.657 to 0.744. These observations reveal a considerable amount of genetic diversity available within these seven breeds/populations. Significant positive within population inbreeding estimates (F IS) were observed for all the breeds/populations which suggested a deficiency in the number of heterozygotes. The relative magnitude of global genetic differentiation was 7.9% thereby implying moderate levels of discrimination among all populations. The pair-wise genetic distance (D A) and genetic differentiation (F ST) between these breeds/populations revealed Kheri and Malpura to be the closest, whilst the highest degree of genetic differentiation was found between Muzzafarnagri and Sonadi which was also supported by the tree topology. The generated information sheds light into the current genetic status and relationship between these sheep and can be utilized for their effective conservation and management. [ABSTRACT FROM AUTHOR]

Abstract: In the present study, 272 individuals of Tharparkar (THC), Rathi (RAC), Nagori (NAC), Mewati (MEC) cattle breeds from Rajasthan and Gir (GIC), Kankrej (KAC) from Gujarat states of India were evaluated for assignment accuracy of individuals to their respective source population by employing multilocus genotypic data generated using 25 bovine specific microsatellite markers. The high diversity indices and moderate yet significant genetic differentiation values (F ST) across the set of markers indicated their utility for assigning individual genotype to its population of origin with high statistical precision. Different assignment tests based on likelihood and genetic distance approach were implemented to evaluate the assignment accuracy. In direct approach, an overall high percentage of correct assignment was observed with two likelihood-based methods (Bayesian approach; 93.7%, and frequency method; 92.6%), whereas, distance based criteria produced relatively lower assignment accuracy that ranged from 78.7% to 90.1%. Individuals of THC, RAC, GIC and NAC breeds were assigned to their respective populations with high accuracy rate. The animals of KAC and MEC breeds, however exhibited least assignment percentage reflecting the presence of admixture in these two populations. Similarly with 10,000 simulation and rejecting population if probability is <0.01, Bayesian method yielded highest assignment scores (95.6%) while frequency based approach resulted in 92.6% correct assignment. With distance based criteria the assignment accuracy ranged from 80.6% to 93.0%. The analysis indicated superiority of Bayesian method over frequency and distance distance based methods for assigning individuals to their source populations. RAC and GIC individuals displayed 100% accurate assignment while NAC and THC exhibited 97.3% and 95.7% of correct assignment with Bayesian criterion. Minimum assignment success rate was observed for KAC (92.9%) and MEC (93.7%) breeds. The overall high assignment accuracy observed for THC, RAC, GIC and NAC reflected their genetic structure as discrete cattle breeds. [Copyright &y& Elsevier]

• Transcriptomic analysis of LTCs at immediate early infection of SPPV WS & SPPV VS. • Most DEGs are involved in various cellular pathways at 0.5h of SPPV-VS infection. • RICTOR and STAT3 identified as top upstream regulators in SPPV-VS & WS, respectively. • qRT-PCR confirms the up-regulation of CD40, FAS, NFKB2 & RICTOR genes in infected LTCs. • Dysregulation of DEGs involve in viral entry, replication & host cell defense. This study explored the transcriptome of lamb testis cells infected with sheeppox virus (SPPV) wild strain (WS) and vaccine strain (VS) at an immediate-early time. Most of the differentially expressed genes (DEGs) and differentially expressed highly connected (DEHC) gene network were found to be involved in SPPV-VS infection compared to SPPV-WS. Further, the signaling pathways were mostly involved in SPPV-VS infection than SPPV-WS. SPPV modulates the expression of several important host proteins such as CD40, FAS, ITGβ1, ITGα1, Pak1, Pak2, CD14, ILK leading to viral attachment and entry; immune-related DEGs such as MAPK, JNK, ERK, NFKB, IKB, PI3K, STAT which provide optimal cellular condition for early viral protein expression; and FOXO3, ATF, CDKNA1, TCF, SRF, BDNF which help in inducing apoptosis and MPTP, BAD and Tp53 inhibits apoptosis or cell death at the immediate-early time. The results captured the specific genes and enabled to understand distinct pathogenic mechanisms employed by VS and WS of SPPV. [ABSTRACT FROM AUTHOR]

Abstract: The pituitary specific transcription factor (Pit-1) controls the expression of prolactin, thyrotropin, and growth hormone genes and is considered as an important candidate gene for several quantitative traits. The study was aimed to reveal the distribution pattern of known variants at Pit-1/HinfI locus in 16 distinct Indian native cattle (Bos indicus) breeds. PCR-RFLP analysis of 1350 bp fragment revealed the predominance of BB genotype and B allele with a mean frequency of 0.881 and 0.937, respectively, irrespective of utility type (dairy, dual, draft), geographical region (northern, central and southern) and coat colour (red/brown and grey/white). AB genotype was the next most frequent with a mean frequency of 0.119. Interestingly, only a single individual out of 723 screened was observed to have AA genotype. The significantly low frequency of A allele observed in present study differs from Bos taurine breeds. Chi square test showed non-significant (P >0.05) difference in pattern of variant distribution, regardless of the geographical location, agroclimatic regions and coat colour. However, significant differences (P <0.05) were observed between utility type categories (dual vs draft and dairy vs draft). This study further validates the utility of PCR-RFLP as efficient means of exploring the distribution pattern of known variants at important candidate genes in Indian zebu cattle for future breeding plans. [Copyright &y& Elsevier]

• We have identified genes by GWAS which are involved in well-established MAPK and PI3K-AKT signalling pathways, affecting biochemical process of coat colour production. • Due to introduction of exotic blood to continue the process of development of Vrindavani cattle, a very low F ST value was observed suggesting outbreeding of the population. • This work provides a preliminary information to carry forward researches on genomic basis of coat colour patterns in crossbred cattle Coat colour and various patterns are the hallmarked qualitative traits studied in cattle as well as other livestock; however, variation in this trait is resultant of interactions and epistasis of a set of genes rather than being a product of a single gene. In this study, GWAS has been conducted from 50K SNP genotype data, with a stratified approach on Vrindavani cattle (n=48). The study was conducted in two sets of an experiment wherein set I treats all the solid colours (n=18) as controls and rest spotted or patchy types as cases (n=30), and set II treats brown and brown with white spots as controls (n=15), and rest as cases (n=33). After quality check (MAF>0.01, genotyping rate>90%, and H-W equilibrium at p≤ 0.001) of genotype data, 37247 SNPs were further used for accomplishing Genome-Wide Association Study (GWAS) with coat colour. The distinct phenotypes were classified into four different sub-groups that are solid black, black with white patches, solid brown, and brown with white patches along with greyish white. The allele frequency difference was checked in all sub-groups. The GWAS was conducted in PLINK v1.7 and for graphical representation R was used. Two SNPs in set I and 20 in set II were found to be significantly associated with coat colour in Vrindavani cattle. A ±500 Kb genome scan around the significant SNPs revealed gene BDNF for SNP DIAS-217 in set I and FGF18 for SNP ARS-BFGL-NGS-105192, and CACNA2D1 , and HGF for SNP BTB-01885061 in set II, are present around these SNPs. In KEGG-based pathway enrichment analysis, all the above-mentioned genes were found to be involved in well-established MAPK and PI3K-AKT signalling pathways, affecting the biochemical process of coat colour production. Genome-wide F ST values were low to moderate across the genome, however few associated SNPs had moderate to high F ST values indicating their power in differentiating the subgroups according to coat colour phenotype. This study provides a preliminary report of markers and genes involved in coat colour expression and revealed that the reported genes around the associated SNPs are involved in brown with white spotting phenotype. However, further researches in this field are essential for a more conclusive result. [ABSTRACT FROM AUTHOR]

• Combination of MAF-LD with Delta, F ST & FIFS methods enabled the selection of SNPs for breed purity. • 582 SNPs accurately assigned individuals to their respective breeds. • 63 Tharparkar-specific SNPs annotate to candidate genes of important phenotypic traits. Tharparkar cattle breed is widely known for its superior milch quality and hardiness attributes. This study aimed to develop an ultra-low density breed-specific single nucleotide polymorphism (SNP) genotype panel to accurately quantify Tharparkar populations in biological samples. In this study, we selected and genotyped 72 Tharparkar animals randomly from Cattle & Buffalo Farm of IVRI, India. This Bovine SNP50 BeadChip genotypic datum was merged with the online data from six indigenous cattle breeds and five taurine breeds. Here, we used a combination of pre-selection statistics and the MAF-LD method developed in our laboratory to analyze the genotypic data obtained from 317 individuals of 12 distinct breeds to identify breed-informative SNPs for the selection of Tharparkar cattle. This methodology identified 63 unique Tharparkar-specific SNPs near intermediate gene frequencies. We report several informative SNPs in genes/QTL regions affecting phenotypes or production traits that might differentiate the Tharparkar breed. [ABSTRACT FROM AUTHOR]

• The natural and artificial selection are expected to impose pressure on specific genomic regions and leave footprints called as "selection signatures" • We identified selective sweep regions based on Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) • Highlighted candidate genes related to adaptation and production traits Knowledge about genetic diversity and selection signatures are very essential for the management and sustainable utilization of sheep genetic resources in India. In this study, we performed a comprehensive genome-wide analysis of genetic diversity and selection signatures using SNP data. A total of 79 animals from three Indian sheep breeds: Changthangi (n = 29), Deccani (n = 24), and Garole (n = 26) genotyped with Illumina Ovine SNP50 BeadChip were included in this study. The average minor allele frequency was 0.284 with a standard deviation of 0.129. The overall mean observed (H O) and expected heterozygosity (H E) were 0.369±0.141 and 0.373±0.118, respectively. The proportion of polymorphic SNPs (P N) ranged from 0.84 (Garole) to 0.93 (Changthangi). The average pairwise genetic distance (D) ranged from 0.301 (Garole) to 0.313 (Changthangi). We identified a total of 9244 ROH segments and the genomic inbreeding coefficients ranged from 0.0673 (Deccani) to 0.1779 (Garole). Two different statistical approaches (ROH and iHS) revealed selection signatures in 37 genomic regions mapping to 188 genes across 16 of the 26 autosomes in three sheep breeds. The selective sweeps provide new insights into the local adaptation and production potential of three Indian sheep breeds. Some notable candidate genes include the TRPM8 gene involved in cold adaptation, JADE2, PLEKHB2, SPP2, TSHR, and UBE2B genes associated with meat quality traits, and the PPP3CA gene associated with fecundity. [ABSTRACT FROM AUTHOR]

Japanese encephalitis (JE) is a mosquito-borne flaviviral zoonotic disease and is one of the major causes of encephalitis in children. Swine, being an amplifier host of Japanese encephalitis virus (JEV), play an important role in its epidemiology. Therefore, early detection of either JEV or antibodies against JEV in swine is a feasible alternative for initiating necessary measures to prevent the spread of infection to humans. Since IgM antibodies appear early in swine sera, recombinant NS1 protein based indirect IgM ELISA was developed in the present study with the objective to know the recent infection of swine population with JEV. The relative diagnostic sensitivity and specificity of the developed ELISA was 95.34% and 98.6%, respectively. The developed ELISA was found to have excellent reproducibility on inter-laboratory and inter-institutional validation studies. A total of 3,027 field swine sera samples were screened using the developed ELISA and 488 samples were found positive for IgM against JEV with an overall sero-positivity of 16.12% in swine population of India. The highest sero-positivity was observed in swine population of Eastern zone of India which coincided with the maximum number of human JE cases reported from this zone during the same period. Further, antibody kinetics study revealed that the IgM antibodies against NS1 protein of JEV started appearing in swine sera at day 5 and disappeared completely by day 40. The IgG antibodies started appearing at day 7, and remained for more than 365 days indicating the suitability of IgM ELISA to know the recent infection of JEV. The developed IgM ELISA can be readily incorporated into surveillance programs for detection of JEV activity in swine population so that outbreaks in humans can be prevented by taking suitable preventive measures. • Indirect IgM ELISA was developed and validated to know the recent infection of JE virus in swine. • Screening of 3,027 field swine sera samples revealed overall sero-positivity of 16.12% in swine population of India. • Highest sero-positivity in swine population of Eastern zone of India coincided with the maximum number of human cases reported from the same zone. • Antibody kinetics study reinforced the suitability of IgM ELISA for predicting recent infection in swine. [ABSTRACT FROM AUTHOR]

• Owing to developments in high-throughput technologies, the genome-wide detection of selection signatures has become more common in recent years • Various statistical methods have been developed for the identification of selection signatures based on site frequency spectrum, linkage disequilibrium, reduced local variability, and population differentiation. • In future, the advanced Machine Learning enabled neural networks can also be applied in livestock populations to handle large &complex data sets efficiently and to improve the accuracy of detection of selection signals. • In this review, we have discussed the results of significant studies done in the recent years. Livestock populations have been consistently improving in terms of performance and productivity by selective breeding over the centuries. These selection strategies are expected to leave footprints in the genome that are identified as selection signatures. Due to advances in high-throughput technologies, the genome-wide detection of selection signatures has become more widespread in recent years. Such studies provide insights into the domestication and evolutionary processes that resulted in a huge number of livestock breeds able to live in diverse environments and production systems. Furthermore, these studies facilitate the identification of candidate genes under selection that are associated with economically important traits in livestock populations. Various statistical methods have been developed for the detection of selection signatures based on site frequency spectrum, linkage disequilibrium, reduced local variability, and population differentiation. The objectives of this review are to give a comprehensive overview of the general concept, various methodologies, and bioinformatics tools currently available for the detection of selective sweeps and to summarize the results of recent selection signature studies carried out in various livestock species. [ABSTRACT FROM AUTHOR]

• The IRF7 and RIG1/DDX58 was activated in PBMCs of indigenous pigs at 7dpv. • LAMB1 was downregulated with lower copies of CSF viruses in MDMs of indigenous pig. • Proinflammatory genes were repressed in MDMs of indigenous than crossbred pig. The genetic basis of differential host immune response vis-à-vis transcriptome profile was explored in PBMCs of indigenous (Ghurrah) and crossbred pigs after classical swine fever vaccination and in monocyte derived macrophages (MDMs) challenged with virulent classical swine fever (CSF) virus. The humoral immune response (E2 antibody) was higher (74.87%) in crossbred than indigenous pigs (58.20%) at 21st days post vaccination (21dpv). The rate of reduction of ratio of CD4+/CD8+ was higher in crossbred pigs than indigenous pigs at 7th days post vaccination (7dpv). The immune genes IFIT1, IFIT5, RELA, NFKB2, TNF and LAT2 were up regulated at 7dpv in RNA seq data set and was in concordance during qRT-PCR validation. The Laminin Subunit Beta 1 (LAMB1) was significantly (p ≤ 0.05) down-regulated in MDMs of indigenous pigs and consequently a significantly (p ≤ 0.01) higher copy number of virulent CSF virus was evidenced in macrophages of crossbred pigs than indigenous pigs. Activation of LXR:RXR pathway at 60 h post infection (60hpi) in MDMs of indigenous versus crossbred pigs inhibited nuclear translocation of NF-κB, resulted into transrepression of proinflammatory genes. But it helped in maintenance of HDL level by lowering down cholesterol/LDL level in MDMs of indigenous pigs. The key immune genes (TLR2, TLR4, IL10, IL8, CD86, CD54, CASP1) of TREM1 signaling pathway were upregulated at 7dpv in PBMCs but those genes were downregulated at 60hpi in MDMs indigenous pigs. Using qRT-PCR, the validation of differentially expressed, immunologically important genes (LAMB1, OAS1, TLR 4, TLR8 and CD86) in MDMs revealed that expression of these genes were in concordance with RNA-seq data. [ABSTRACT FROM AUTHOR]

• An indirect ELISA using recombinant NS1 protein to detect anti-JEV IgG antibody in swine. • Developed ELISA validated in 10 different laboratories revealing excellent reproducibility. • Screening of 3628 swine Serum samples revealed sero-positivity of 32.22% against JE virus. • Developed ELISA can be used in surveillance programs for detection of JEV activity in swine population thereby aiding in prevention of outbreaks in humans. Japanese encephalitis virus (JEV) causes severe neurological disease in humans, especially among children. The disease is endemic in several South Asian countries including India. Swine play a major role as amplifier host for JEV and act as a source of infection to humans through mosquito bite. Early detection of either virus or antibodies in swine will aid to undertake control measures to prevent virus spread to humans. Swine seldom show symptoms of JEV infection and the viraemic phase lasts for a short period of 3 to 4 days indicating the potential of detection of antibodies, which remain for relatively longer period, as a suitable alternative. Cost effective and sensitive assays for the detection of JEV antibodies in swine are not available indigenously. Hence, we have developed a recombinant nonstructural protein 1 (rNS1) based enzyme linked immunosorbent assay for the detection of IgG antibodies against JEV in swine. The test is robust, highly sensitive (91%), specific (97%), reproducible and affordable. Field validation of the assay was done by screening 3628 swine Serum samples collected from different parts of India. The overall sero-positivity was found to be 32.22%. The developed ELISA can be readily incorporated into surveillance programs for detection of Japanese encephalitis virus activity in swine population thereby aiding in prediction of outbreaks in humans. [ABSTRACT FROM AUTHOR]