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Background: Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. Results: Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. Conclusion: The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale. [ABSTRACT FROM AUTHOR]

Lumpy skin disease (LSD) is a notifiable re-emerging transboundary viral disease of bovines that inflicts heavy losses in affected livestock farms. Genetic variations contribute substantially to the inter-individual differences in the immune response against disease agents. The present study aimed to evaluate the genetic basis of differential immune response in Vrindavani cattle by comparing the hematological, biochemical and cytokine genes' expression profiles of LSD-affected and unaffected animals. After 21 days of the outbreak at the farm, the animals were grouped as affected (those who developed symptoms) and unaffected/healthy (those who did not). Standard hematological and biochemical parameters were evaluated in both the groups. Expression profiling of important Th1 (IL2, INFG and GMCSF) and Th2 (IL4, IL6 and IL10) cytokines was also performed via a relative quantification approach using real-time PCR. Erythrogram and leucogram analyses revealed significant differences in total leucocyte count (TLC: 14.18 ± 0.74 versus 11.38 ± 0.68 x103/µL), hemoglobin (Hb: 8.66 ± 0.42 versus 10.84 ± 0.17 g%) and percentage of neutrophils (46.40 ± 1.98 versus 35.40 ± 2.11%), lymphocytes (49.40 ± 1.99 versus 62.40 ± 1.86) and monocytes (4.20 ± 0.37 versus 2.40 ± 0.40) between the affected and healthy animals, respectively. The production of liver enzymes (SGOT and SGPT) was significantly higher in affected animals (74.18 ± 4.76 and 59.51 ± 2.75) when compared to the healthy counterparts (65.95 ± 9.18 and 39.21 ± 3.31). The expression profiling of Th1 and Th2 cytokines revealed significant differences between the two groups, except IL10. The expression of IL2, GMCSF and IL6 were upregulated in healthy animals while that of INFG, IL4 and IL10 were upregulated in LSD-affected animals. The highest abundance was observed for IL2 transcripts in healthy animals among all assessed cytokines with log2fold change of 1.61 as compared to affected counterparts. Overall, the immune response in healthy animals (after exposure to LSD virus) was predominated by the expression of Th1 cell proliferation and there was an increased production of pro-inflammatory cytokines as compared to the affected counterparts. The results revealed that the effective immune response to LSD in cattle consists of changes in hematological and biochemical parameters and altered expression profile of cytokines with enhanced phagocytosis and lymphocyte recruitment. Furthermore, optimal expression of Th1 cytokines is required for maintaining optimal health against infectious insult with LSD virus in cattle. [ABSTRACT FROM AUTHOR]

Keywords: Correlation; heritability; maternal; model; trait; variance; ; ; ; ; ; EN Correlation heritability maternal model trait variance ZH 7948 7955 8 11/21/22 20221220 NES 221220 Introduction Livestock rearing plays a major part in ensuring nutritional security of masses in developing countries (Randolph et al. [14]). Similarly, Wang et al. ([21]) reported moderate heritability (0.40) for fiber diameter and low heritability estimate (0.19) for staple length at yearling stage in Inner Mongolia White Cashmere goats. In concurrence to our study, Di et al. ([4]) reported moderate direct additive heritability estimate of 0.22 for yearling fiber diameter in Chinese superfine Merino sheep on fitting multi-trait animal model. Higher heritability estimates, when compared to the present study, have been reported by Hanford, Van Vleck, and Snowder ([9]) in Rambouillet sheep and Jafari and Hashemi ([10]) in Makuie sheep. [Extracted from the article]

The improvement in imputation accuracy diminished across different methods of selecting SNPs with increased panel density. 5 O'Brien, A.C., Judge, M.M., Fair, S. & Berry, D.P. (2019) High imputation accuracy from informative low-to-medium density single nucleotide polymorphism genotypes is achievable in sheep1. Genomic technologies have not penetrated enough in livestock, especially in developing nations where animals from a particular breed/population cannot be concurrently genotyped mainly due to financial constraints. [Extracted from the article]

The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement. [ABSTRACT FROM AUTHOR]

Biological rhythmicity plays a critical role in the pathophysiology and overall survival of an organism. Period (Per), cryptochrome (Cry), Bmal1 and CLOCK are four important gene families that affect the circadian rhythms to considerable level. However, our understanding regarding the genetic basis of biological rhythmicity is still in its infancy. Biological rhythms are generated through underlying gene expression which is regulated by various control systems. The finely regulated gene expression modulates biological rhythms through various molecular and cell-signaling pathways (metabolic state, endocrine activity and neural excitability). Epigenetics through modifications of histone tags, chromatin remodeling, non-coding RNAs and other mechanisms plays an important role as regulators of gene expression controlling biological rhythmicity in the animal kingdom. MicroRNAs like miR328, miR383, miR192/194, miR122, miRNA-219 and miRNA-132 are some of the noteworthy miRNAs reported to be functionally related to circadian rhythmicity controlling various biological events. Besides miRNAs, histone modification enzyme systems, RNA binding proteins and sirtuins form important ways to regulate the expression of genes related to biological clock in living organisms. In this review, we have made an attempt to understand the epigenetic basis of biological rhythmicity in mammalian organisms and analyze the progress made to date. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate the efficiency of two Bovine SNP genotyping arrays (i.e., 50 K and HD) for breed clustering and stratification related studies in taurine and indicine breeds. The whole-genome SNP data at two densities were assembled into three datasets (A, B and C). Dataset A (N = 213) included 50 K genotypic data for five taurine (Holstein–Friesian, Guernsey, Brown Swiss, Angus and Jersey) and two indicine (Gir and Nellore) breeds. Dataset B (N = 241) included the same breeds with HD density data. Dataset C (N = 299) included 50 K SNP genotypic data for six taurine (Holstein–Friesian, Jersey, Guernsey, Brown Swiss, Angus and Hereford) and six indicine (Hariana, Kankrej, Brahman, Nellore, Sahiwal and Gir) breeds. The analysis was done using ADMIXTURE program (bioinformatics-based) and cross-validation errors and Principal Component Analysis (statistical analysis). The proportion of polymorphic markers and minor allele frequencies were assessed for each breed. The proportion of markers polymorphic was consistently higher in taurine breeds when compared with breeds from indicine group. Minor allele frequency estimates and ADMIXTURE results showed differential patterns for both the lineages. However, no significant increase in the accuracy of genomic clustering was found on moving from 50 K to HD density data. [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 present study was aimed to assess parameters related to genetic diversity, population structure and admixture in the Frieswal crossbred cattle of India. A total of three datasets were analyzed during this study. Dataset A (n = 80) consisted of data on two purebred populations, i.e., Shorthorn (n = 35) and Brahman (n = 25) and one crossbred strain Santa Gertrudis (n = 20). The dataset B (n = 71) consisted of data on three populations that included Holstein-Friesian (n = 30), Sahiwal (n = 27) and Frieswal (n = 14) cattle. The dataset C included data on all the six breeds under study. Dataset C was used to assess the indices of population structure and genetic diversity of different breeds prior to and after LD pruning. For Frieswal cattle strain, the proportion of polymorphic SNPs and MAF levels was 84.54% and 0.24, respectively. Frieswal strain maintained appreciable genetic diversity with observed heterozygosity measure of 0.414. PCA plots for three datasets depicted effective stratification of different breeds in the respective datasets. The genomic clustering levels of Sahiwal and Holstein-Friesian were found to be 98.45 and 99.89%, respectively, while the admixture of Frieswal was estimated to be about 61.5 and 38.5% from Holstein-Friesian and Sahiwal breeds, respectively. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWAS) are one of the best ways to look into the connection between single-nucleotide polymorphisms (SNPs) and the phenotypic performance. This study aimed to identify the genetic variants that significantly affect the important reproduction traits in Vrindavani cattle using genome-wide SNP chip array data. In this study, 96 randomly chosen Vrindavani cows were genotyped using the Illumina Bovine50K BeadChip platform. A linear regression model of the genome-wide association study was fitted in the PLINK program between genome-wide SNP markers and reproduction traits, including age at first calving (AFC), inter-calving period (ICP), dry days (DD), and service period (SP) across the first three lactations. Information on different QTLs and genes, overlapping or adjacent to genomic coordinates of significant SNPs, was also mined from relevant databases in order to identify the biological pathways associated with reproductive traits in bovine. The Bonferroni correction resulted in total 39 SNP markers present on different chromosomes being identified that significantly affected the variation in AFC (6 SNPs), ICP (7 SNPs), DD (9 SNPs), and SP (17 SNPs). Novel potential candidate genes associated with reproductive traits that were identified using the GWAS methodology included UMPS, ITGB5, ADAM2, UPK1B, TEX55, bta-mir-708, TMPO, TDRD5, MAPRE2, PTER, AP3B1, DPP8, PLAT, TXN2, NDUFAF1, TGFA, DTNA, RSU1, KCNQ1, ADAM32, and CHST8. The significant SNPs and genes associated with the reproductive traits and the enriched genes may be exploited as candidate biomarkers in animal improvement programs, especially for improved reproduction performance in bovines. [ABSTRACT FROM AUTHOR]

• Haplotype structure was elucidated in Vrindavani cattle via sliding window approach. • Haplotype-based association analysis was undertaken with (re)production traits. • Haplotypes showed significant association with AFC, TLMY, PY, DD, ICP and SP. • Overlapping candidate genes revealed pathways affecting the (re)production performance. Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations. [ABSTRACT FROM AUTHOR]

• We elucidated putative CNVs and CNV regions in Vrindavani cattle using Bovine SNP50 genotyping data. • 252 putative CNVs were detected which further concatenated into 69 CNVRs. • Five CNVRs were significantly associated with 10 (re)production traits in Vrindavani population. • The study provides useful insights to establish the comprehensive CNV map of Vrindavani population for association studies. The present study was aimed to analyze the genome-wide copy number variations (CNVs) in Vrindavani composite cattle and concatenate them into CNV regions (CNVRs), and finally test the association of CNVRs with different production and reproduction traits. Genotypic data, generated on BovineSNP50 Beadchip (v3) array for 96 Vrindavani animals, was used to elucidate the CNVs at the genome level. Intensity data covering over 53,218 SNP genotypes on bovine genome was used. Algorithm based on Hidden Markov Model was employed in PennCNV program to detect, normalize and filter CNVs across the genome. 252 putative CNVs, detected via PennCNV program, in different individuals were concatenated into 71 CNV regions (CNVRs) using CNVRuler program. Association of CNVRs with important (re)production traits in Vrindavani animals was assessed using linear regression. Five CNVRs were found to be significantly associated with ten important (re)production traits. The genes harbored in these regions provided useful insights into the association of CNVRs with genes and ultimately the variation at phenotype level. Important genes that overlapped with CNVRs included WASHC4, HS6ST3, MBNL2, TOLLIP, PIDD1 and TSPAN4. Furthermore, the CNVRs were found to overlap with important QTLs available in AnimalQTL database which affect milk yield and composition along with reproduction and immune function traits. The copy number states of three enes were validated using digital droplet PCR technique. The results from the present study significantly enhance the understanding about CNVs in Vrindavani cattle and should help establish its CNV map. The study will also enable further investigation on association of these variants with important traits of economic interest including disease incidence. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate different animal models for their appropriateness to best fit the body weight data of Corriedale lambs at different ages and reared under temperate conditions. Data used in this study consisted of 24,907 body weight records on a total of 6162 lambs of Corriedale sheep population. The data pertained to body weight traits at different ages i.e., at birth (BW), weaning (WW), six months (SW), nine months (NW) and yearling age (YW). The (co)variance components of five traits were estimated using univariate analysis based on restricted maximum likelihood (REML) algorithm in WOMBAT program. Six different univariate animal models, with or without maternal genetic effect, maternal permanent environment effect and covariance between additive genetic and maternal genetic effects, were fitted on the body weight data of the Corriedale sheep population. All univariate animal models incorporated season (winter, spring) and period of lambing (8 periods, each of 5-year duration), and sex of lamb (male, female) as fixed effects. AIC, Log-likelihood and likelihood ratio test results were used to evaluate the best fit models for body weights at different ages. Model I, incorporating additive genetic effect of the individual as random effect, showed the minimum AIC estimate for BW. Model III showed the minimum AIC values for all other traits under consideration i.e., WW, SW, NW and YW. The direct additive genetic heritability for birth weight was 0.025 under the best fit model i.e., model I. The direct heritability estimates for WW, SW, NW and YW were 0.151, 0.216, 0.103 and 0.132, respectively under the best-fit models. Maternal genetic heritability ranged from 0.043 to 0.087 for different body weights, except BW for which model I was the best-fit. Most of the covariance and correlation estimates between direct additive genetic and maternal genetic effects were negative. Low estimates of heritability found in best-fit models in this research are suggestive of the less appropriateness of applying individual selection for this population as it may only result in slow progress for body weight traits in Corriedale sheep. Environmental factors played a significant role in generating the variation in body weight traits in Corriedale sheep. • In the present study, body weight at birth, weaning, six month, nine month and yearling age were evaluated in Corriedale sheep using six different animal models with or without the inclusion of different random effects. • Different mixed animal models were evaluated for their appropriateness in analysing the variation of different body weight traits in Corriedale sheep. • Model III incorporating direct additive genetic and maternal genetic effects along with covariance between them was best-fit for all traits except birth weight, for which model I was most appropriate. • Environmental factors played a significant role in generating the variation in body weight traits in Corriedale sheep. • Low estimates of heritability found in best-fit models in this research are suggestive of the reduced appropriateness of individual selection for this population. [ABSTRACT FROM AUTHOR]

• We analyzed the population diversity and selection signatures of the high altitude sheep breed Changthangi. • Changthangi was compared to three breed groups, namely European commercial, Indian, and breeds inhabiting plains. • Results revealed multiple functional regions on chromosomes 2, 3, 6 and 18 to be under selection in Changthangi. • The UCP gene family, associated with adaptation to cold and hypoxic conditions, was found to be under selection in Changthangi. Changthangi is a high-altitude sheep breed of India that is adapted to cold and hypoxic climate of Himalayas. In the present study, we analysed population structure of Changthangi and contrasted it with selected Indian and European commercial sheep breeds to detect genomic regions under positive selection. The Illumina OvineSNP50v1 genotype data on 292 animals from seven different sheep breeds i.e., Changthangi (n = 29), Garole (n = 26), Deccani (n = 24), Tibetan (n = 37), Rambouillet (n = 102) and Australian Merino (n = 50) was used. European Mouflon (n = 24) was used as an out-group for studying the stratification and phylogenetic lineage. While the principal component analysis (PCA) revealed Changthangi to cluster with Tibetan sheep; TREEMIX and ADMIXTURE results also detected the introgression of lowland Indian sheep inheritance in Changthangi. Changthangi sheep were compared with other breed groups as reference i.e., commercial (Australian Merino and Rambouillet), Indian (Deccani, Garole and Tibetan) and breeds inhabiting plains (Australian Merino, Rambouillet, Deccani and Garole). Genomic comparisons of Changthangi using cross population extended haplotype homozygosity (XP-EHH) showed multiple functional regions present on Ovis aries (Oar) chromosomes 2, 3, 6 and 18 to be under selection in Changthangi sheep. These regions were related with adaptation to climatic and hypoxic stressors, fleece characteristics and functioning of immune and reproductive systems. UCP genes, associated with adaptation to cold and hypoxic conditions, were the main loci under positive selection in Changthangi sheep population. The selection signals in Indian and European commercial sheep breeds were mainly associated with body weight and carcass traits. Furthermore, selection signals found in different comparisons were found to be part of different quantitative trait loci (QTLs) associated with important traits in different breed classes. The genes present in these regions are suitable candidates for future studies on the genetic mechanisms underlying high-altitude adaptation. [ABSTRACT FROM AUTHOR]

The present study was undertaken to identify the microRNAs (miRNAs) expressed in the mammary tissue of a bubaline heifer. Small RNAs were isolated from the mammary gland tissue and enriched for miRNA fraction. The linker-ligated small RNAs were reverse transcribed to synthesize cDNA and amplified by PCR. The PCR products were ligated to the pGEM-T Easy vector; cloned into DH5 alpha cells and sequenced. Sequencing of 40 clones, randomly chosen from this library, produced 115 concatemerized short sequences. The short sequences were checked for their matches with the help of refseq_rna database, EST database (NCBI) and Ensembl. The analysis was performed for more than 90% identity with miRNAs across different species in miRBase. Alignment of putative small RNA sequences with the bovine genome was attempted in GenBank (NCBI) and Ensembl using BLAST. The small RNA sequences with a partial matches within the bovine genome and/or with flanking sequences (upstream or downstream) were analyzed for hairpin structures using the Mfold web server. Reverse complements were also assessed for the homology search. miRNA sequences showing only a partial match with already reported sequences were considered as a putative bubaline miRNAs. Six developmentally important putative miRNA precursors were identified from this study using cloning and sequencing followed by the Bioinformatics approach. This study will help in the elucidation of pathways involving miRNAs in bubaline species at the heifer stage. [ABSTRACT FROM AUTHOR]

Pashmina is the fine undercoat of the Changthangi goats (Capra hircus) with Keratin-associated proteins (KAPs) as one of its main structural components. KAPs form a semi-rigid matrix in which the Keratin intermediate filaments (KIFs) are embedded. In the present study, an attempt was made to elucidate the polymorphism of KAP16.6 gene loci and its association with fiber yield and quality traits (fine yield, mean fiber diameter, mean fiber length, and guard hair percentage). A total of 103 animals of Changthangi goats were randomly selected and genomic DNA was isolated from blood samples. After amplification of the coding region of KAP16.6 (254 bp) gene, restriction digestion with HindIII enzyme (AAG/CTT) produced two polymorphic patterns in the Changthangi goats. The genotypic distribution of the designated genotypes A1A1 (0.0), A2A2 (0.379), and A1A2 (0.621) of KAP16.6 gene varied significantly (p <.01) from Hardy-Weinberg equilibrium. Missense mutation AGC (Serine) > AAC (Asparagine) was identified at KAP16.6 locus in Changthangi goats for the first time. The genetic variability parameters for the gene loci analyzed were: heterozygosity value 0.4283, PIC: 0.3366, effective allele no 1.7492 and Shannon index (I) of 0.6196. The estimated PIC value reflected median polymorphism exhibited by the Changthangi goat population under study for the selected gene. Statistical analysis further revealed a significant effect of KAP16.6 genotype on the fiber length (p <.05) whereas the effect was nonsignificant for other Pashmina production traits under study. The results from the present study have practical significance in the breeding plans for Changthangi goats in this region for improved production performance. [ABSTRACT FROM AUTHOR]

The present study was carried out on 96 animals representing three distinct colour variants of Badri cattle to investigate the genetic diversity, population structure and substitution mutations in the genetic codons due to single nucleotide variations. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA (ddRAD) sequencing approach. A standardized bioinformatics pipeline was employed to identify single nucleotide polymorphisms (SNPs), initially detecting 7,168,552 SNPs through alignment with the Bos indicus reference genome assembly. Subsequent stringent quality filtration yielded 65,483 high-confidence SNPs for downstream analysis. Genetic diversity analysis of the Badri cattle population resulted in average values of 0.145, 0.088, and 0.091 for Shannon's diversity Index (I), Simpson's Diversity (h), and Simpson's Unbiased Diversity (uh), respectively. Genetic similarities between the black and brown, black and grey, and brown and grey Badri variants were found to be 0.9972, 0.9980 and 0.9970, respectively. Tajima's D diversity value was observed to be significant and positive for 99.29% of high-confidence SNPs (65,483). STRUCTURE analysis showed admixture among the three Badri colour variants, suggesting a lack of genetic differentiation. Annotation of high-confidence SNPs regarding genetic codon changes indicated maximum substitutions in the GGC with GGT (22 occurrences), followed by AAC to AGC (20 occurrences), GAA to TAA (19 occurrences) and CAA to CAG (19 occurrences). The study concludes there are genetic similarities among colour variants, lack of rare alleles, balancing selection, sudden population contraction and genetic codon substitutions within the Badri cattle population. Insights derived from SNP data analysis hold potential significance for conservation initiatives and breed improvement programs for indicine cattle. [ABSTRACT FROM AUTHOR]

In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs. 115 CNVRs were identified in 69 Landlly pig population. Approximately 75% detected CNVRs were novel for Landlly population. Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Comprehensive CNV map in the Indian porcine genome developed for the first time. [ABSTRACT FROM AUTHOR]

The present study was aimed at genetic characterization and diversity analysis of Pandharpuri buffalo population using the Food and Agriculture Organization (FAO) recommended bovine microsatellite markers. Genomic DNA was isolated from blood samples of 50 unrelated animals and a total of 23 microsatellite loci were amplified using polymerase chain reaction. Among 23 recommended microsatellite markers, 14 markers (BM2113, BM1818, CSSM66, HEL13, INRA037, ILSTS05, HAUT27, INRA023, INRA035, HEL5, ETH3, NRA063, MM12 and ETH10) were found to be highly polymorphic in Pandharpuri population. The amplified products were run on polyacrylamide gel electrophoresis (PAGE) apparatus along with a ladder; subsequently, the allele typing was done based on silver staining of the gel. The effective and observed number of alleles, heterozygosity (expected and unbiased) estimates and polymorphic information content (PIC) levels were estimated for each locus. A total of 87 alleles were secured for 14 polymorphic loci studied giving an overall average of 6.21 alleles per locus. The number of alleles ranged from 2 (INRA063) to 9 (BM1818 and HEL13). The mean effective number of alleles across all polymorphic loci was found to be 4.28. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.77 and 0.76, ranging from 0.50 (INRA063) to 0.88 (BM1818) and 0.50 (INRA063) to 0.88 (BM1818), respectively. The average PIC estimate across all polymorphic loci was 0.73 ranging from 0.373 (INRA063) to 0.864 (BM1818). In the present study, the characterization and diversity estimates are reported for Pandharpuri population. It was found to maintain optimum diversity based on 14 polymorphic microsatellite markers. [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]

Subclinical mastitis, generally caused by Staphylococcus aureus, has a global economic impact all over the world. Hence, it needs to be resolved on higher priority which may be attained via. selection of mastitis resistant animals or inclusion of mastitis resistant trait into herd apart from management care. Diverse hosts with various genetic make-ups encounter pathogens in a diverse manner which in turn leads to contradicting outcome of the disease. Identification of species-wise or breed-wise differential expressed genes in response to S. aureus through relative evaluation of transcripts may be useful for judging the immuno-competency of a species or breed toward mastitis. The present study was undertaken to examine the stimulant effect of S. aureus peptidoglycan (PGN) and lipoteichoic acid (LTA) on Peripheral blood mononuclear cells (PBMC) harvested from blood samples of crossbred cattle, Tharparkar cattle, and Murrah buffaloes. After 6 h of in vitro stimulation qRT-PCR was used to measure the relative mRNA expression of TLR-2, TNF-α, IL-8, IFN-γ and IL-10 genes in stimulated and un-stimulated PBMC. The selected genes revealed significant differences in the pattern of immune response among crossbred cattle, Tharparkar cattle and Murrah buffalo in spite of the same stimulant dose. [ABSTRACT FROM AUTHOR]

In the present study, to analyze the genomic ROH fragments, haplotypes, inbreeding coefficient and effective population size (Ne), SNP50K data of 72 Vrindavani crossbred cattle strain were obtained. After a quality check, 24,449 biallelic SNPs were retained, which were in HWE, MAF > 0.01 and genotyping rate >95%. A total of 385 ROH were found, and chromosome 25 was mostly covered with 50.86%, while chromosome one was least with 12.42%. We classified ROH into <10Mb, 10-15Mb, 15-20Mb, >20Mb categories and observed a 3% inbreeding coefficient for the population in >20Mb category. Inbreeding from an excess of homozygosity was found to be 6% in the population. Ne was also estimated through Ne Estimator and SNeP and in the recent generation, it was found to be 40 for a census size of 464 cattle. The Ne/Nc ratio was found to be 0.086 and a decreasing trend of Ne was observed for over five generations. 45.95% of the autosomal genome was covered with haplotypic structure with highest total block length in chromosome one and lowest in 28. From all the observations made in this study, it can be concluded that Vrindavani is an admixed cattle strain but have an unstable population structure in the current period. [ABSTRACT FROM AUTHOR]

The Cashmere (Pashmina) fiber attracts great demand worldwide for its fineness. To identify and determine the role of Insulin-like Growth Factor-1 (IGF-1) gene polymorphism on Pashmina fiber traits (quality and quantity), exon IV, and part of intron IV of the IGF-1 gene of Changthangi goats were analyzed. 103 Changthangi goats of either sex were divided into two groups, the high producers and low producers of Pashmina. Upon restriction digestion with HaeIII, three genotypes were identified, i.e., A1A1 (0.253), A2A2 (0.320), and A1A2 (0.427). These genotypes did not vary significantly (p >.05) from Hardy–Weinberg Equilibrium. DNA sequence analysis revealed G > C transversion in intron-IV of IGF-1 gene at the HaeIII restriction site. The SNP effect of two alleles on mean Cashmere fiber diameter of down fibers (MFD) was statistically significant (p <.05) and the average finest fiber diameter was 13.46 µ for genotype A2A2. The mean genetic variability parameters for the gene analyzed were heterozygosity value (0.4977), PIC Value (0.3738), Effective allele no (1.9908),and Shannon index I (0.6908). The significant association of IGF-1 gene polymorphism and fiber finesse can be exploited in breeding programmes to improve the production and quality of Pashmina fiber in goat populations. [ABSTRACT FROM AUTHOR]

Selection of the most appropriate animal model for the estimation of genetic parameters for body weight was carried out using restricted maximum likelihood (REML) procedure at birth and thereafter at 3, 6, and 8 weeks of age in Landlly pigs. Six different models were fitted for each trait; by inclusion or exclusion of maternal additive genetic effect, maternal permanent environmental effect, and covariance between direct and maternal additive genetic effects. Records on 1968 piglets, born in 4 parities of 131 gilts/sows, sired by 68 boars during a period of 5 years from 2014 to 2018 were used. In order to determine the most appropriate model, Log likelihood values, log the likelihood ratio test and Akaike’s information criterion were used. A model including direct additive genetic and maternal permanent environmental effects fitted best to data for birth weight. The best model explaining W3, W6, and W8 included direct additive genetic, maternal genetic and maternal permanent environmental effect with direct and maternal genetic covariance. Total heritability estimates for the body weights were low to moderate across best models. [ABSTRACT FROM AUTHOR]

• Association of bovine MHC class I (BoLA-A) exons 2–3 and 4–5 allelic variants with immune response to B. abortus S19 is reported in the present study. • The association analysis of various BoLA-A alleles with the immune response revealed that calves with certain defined genotypes induced significantly higher cell-mediated immune responses in terms of lymphocyte proliferation, lymphocyte mediated cytotoxicity and nitrite production. • It is assumed that allelic variants of BoLA-A (exons 2–3 and 4–5) were associated with the differential immune response of calves to B. abortus S19 vaccination. In the present study, we analyzed the immune response of calves to Brucella abortus strain 19 vaccine (S19) and its association with MHC class I (BoLA-A) alleles (exons 2–3 and 4–5). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for typing of BoLA-A exon 2–3 with Dde I and Taq I restriction enzymes; and exon 4–5 with Hinf I in 45 crossbred calves. The PCR-RFLP analysis revealed five BoLA-A alleles each for exon 2–3 (A10/A19, A19, A18/19, A18 and A31) and exon 4–5 (A, B, C, D and E). Immune response against B. abortus S19 was assessed at the 4th week post vaccination; antibody response by standard tube agglutination test (STAT) and cell-mediated immunity by lymphocyte proliferation and lymphocyte-mediated cytotoxicity assays. Further, the macrophage function in terms of nitrite production was also analyzed. The association analysis of various BoLA-A alleles with the elicitation of immune response revealed that calves with certain defined genotypes induced significantly higher cell-mediated immune response in terms of lymphocyte proliferation with higher stimulation indices (S.I.) of 1.59 (BoLA-A19), 1.49 (A18/19) and 1.52 (Hinf I-D); lymphocyte mediated cytotoxicity (55.52 % in A19) and nitrite production (43.40 μM in A31). It is assumed that allelic variants of BoLA-A (exons 2–3 and 4–5) were associated with the differential immune response of calves to B. abortus S19 vaccination. Therefore, further studies on association analysis of MHC class-I genes in large number of cattle may generate more information and might be useful for adapting the alternative approach of exploring genetic resistance in the cattle herd against bovine brucellosis. [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]

A male Golden retriever dog was presented with history of profuse bleeding from right nostril with mild hard swelling over the right nares. Transmissible veneral tumor (TVT) in nasal cavity was diagnosed after cytological examination of nasal discharge with numerous discrete spherical nuclei with chromatin granules and multiple cytoplasmic vacuolizations. Treatment with Vincristine sulfate resulted in complete resolution and recovery. [ABSTRACT FROM AUTHOR]

The present study was undertaken to characterize the distinct immune response in indigenous Ghurrah and exotic Landrace pigs by challenging monocyte-derived macrophages (MDMs) with CSF virus under in-vitro conditions and assessing the variations in the transcriptome profile at 48 h post-infection (hpi). RNA-sequencing was carried out in infected and non-infected MDMs of Ghurrah (n = 3) and Landrace (n = 3) piglets prior- as well as post-stimulation. MDMs of Ghurrah showed greater immune regulation in response to CSF infection with 518 significantly differentially expressed genes (DEG) in infected versus non-infected MDMs, as compared to only 31 DEGs in Landrace MDMs. In Landrace, the principal regulators of inflammation (IL1α , IL1β and TNF) were upregulated in infected cells while in Ghurrah, these were downregulated. Overall, macrophages from indigenous Ghurrah showed more immunological dysregulation in response to virulent CSF virus infection as compared to the exotic Landrace pigs. • The present study aimed to characterize the distinct immune response in indigenous Ghurrah and exotic Landrace pigs against CSF vaccination. • Monocyte-derived macrophages (MDMs) were stimulated with CSF virus under in-vitro conditions. • The variations in the transcriptome profile via RNA-Seq approach were assessed in stimulated cells at 48 h post-infection. • MDMs of Ghurrah showed greater immune regulation in response to CSF infection with 518 significantly differentially expressed genes in infected versus non-infected MDMs, as compared to only 31 DEGs in Landrace MDMs. • In Landrace, the principal regulators of inflammation (IL1α, IL1β and TNF) were upregulated in infected cells while in Ghurrah, these were downregulated. • Macrophages from indigenous Ghurrah showed more immunological dysregulation in response to virulent CSF virus infection as compared to the exotic Landrace pigs. [ABSTRACT FROM AUTHOR]