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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]

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

An inbred strain limits the segregating variance and provides more power and requires fewer experimental animals to produce good reproducibility. This study was undertaken with the aim to assess the impact of sex of offsprings and sex specific microsatellite variants on performance and fitness traits in F4 inbred Swiss albino mice. The phenomics of different performance and fitness traits were estimated on 506 F4 inbred mice population. Two 'X' chromosome specific microsatellite loci (DXMit187 and DxMit172) were used for PCR-Microsatellite genotyping of 102 F4 inbred population. PIC estimates showed that both the loci were informative for the population. In the current population, with the increasing level of "F" a declining trend was observed for Body weight at birth (BWB), Body weight at weaning (BWW), Litter size at weaning (LSW) and Litter weight at weaning (LWW). In F4 inbred population, BWW and ABW for males (17.32±0.32g and 30.81±0.31g) were significantly (p<0.05) higher than females (16.39±0.30g and 27.83±0.28g). The significant (p<0.05) impact of sex of offspring on performance traits revealed that less magnitude of inbreeding depression was observed in male as compared to female. There were 3 alleles and 5 genotypes at the DXMit172 locus, and 3 alleles and 4 genotypes at the DXMit187 locus. The highest and lowest allelic frequencies were found at DXMit172 locus for 142 (0.422) and 154 (0.226) alleles, respectively, and at DXMit187 locus for 126 (0.588) and 146 (0.093) alleles, respectively. Genotype 142/142 (0.382) and 154/148 (0.059) had the highest and lowest genotypic frequency at the DXMit172 locus, respectively, and at DXMit187 locus for 126/126 (0.588) and 146/146 (0.039) genotypes, respectively. In the current study, only the DXMit172 loci had significant genotypic associations with fitness traits (p<0.05). The average FIS based on X-specific microsatellite markers was 0.790 in the F4 inbred population. These results indicate that rate of inbreeding depression is more in females than in males. [ABSTRACT FROM AUTHOR]

The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS). [ABSTRACT FROM AUTHOR]

India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1 , PDE9A , PPBP , CXCL6 , RASSF6 , AFM , AFP , ALB , ANKRD17 , CNTNAP2 , GPC5 , MYLK3 , and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds. [ABSTRACT FROM AUTHOR]

The epithelial cells of the mammary gland secrete extracellular nanovesicles known as exosomes that carry and protect microRNAs and other various signaling biomolecules. Milk exosomes are stable during processing and remain protected from digestion in the gastrointestinal tract in order to reach specific target cells including peripheral tissues by crossing biological barriers. Milk exosomal microRNAs have their role as growth-promoting factor, in immunological programming, improving allergy tolerance and epigenetic controller of other mRNAs. However, in contrast, many translational evidence indicated that excessive consumption of bovine milk and continuous exposure of these exosomal microRNAs may be responsible for chronic inflammatory diseases of contemporary societies. Milk exosomes have potential preventive impact on necrotizing enterocolitis, ulcerative colitis, and inflammatory bowel diseases and may be targeted as preventive medicine or in therapeutic diets and also have potential as a nano-vehicle for drug delivery for chemotherapy. [ABSTRACT FROM AUTHOR]

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (F ST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield. [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 Indian Ghurrah pig has a mixture of European and Asian inheritance. • Analysis traced European admixture to the recent past. • Signs of interspecies introgression was detected in admixture analysis. • Ghurrah and Asian pigs show divergence in genomic regions governing teeth development. The evolution and domestication of pigs is a complex and ongoing process. Despite its rich biodiversity and proximity to the geographical origins of Sus scrofa domesticus, the place of Indian pigs in the global phylogeny is unclear. Using microarray-derived (porcine 60K SNP chip) genotypes of 11 Ghurrah pigs from North-Western India and a public dataset comprising 2113 pigs of 146 breeds, we determined the genomic ancestry of Ghurrah pigs and compared their genetic constitution to European and Asian breeds to ascertain signatures of divergent selection. Results showed that Ghurrah pigs contain genes of Asian and European ancestry with signs of inter-species introgression. Using Admixture LD – decay statistics, the European admixture event was dated to the recent past, coinciding with the start of cross-breeding efforts in India. The complex Asian ancestry pattern of the breed resembled that of wild boars of South – Central China and Thailand, possibly suggesting introgression from an Indian wild boar relative. Signatures of selection analysis showed the divergence of Ghurrah pigs from Asian and European breeds in genomic regions associated with odontogenesis, and nervous system processess, respectively. Our results present the first genomic characterization of an Indian pig breed using dense microarray-derived genotypes and highlight the importance of further genomic characterization of Indian domestic and wild pigs. Given the limited sample size available for this study, validation of the findings in a larger population is suggested. [ABSTRACT FROM AUTHOR]

The 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]