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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]

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

• 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 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]

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]

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 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]

• Indian pig breeds were found to be evolutionarily closer to Chinese than European pig breeds. • · Genetic diversity in Indian and Chinese breeds was found to be lower than European breeds. • In Indian pigs genes for adaptation to tropical climate and low input scavenging system were under positive selection. In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25–25.25 Mb region of SSC18, 123.25–124 Mb region of SSC15 and 118.75–119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16 , FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction. [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]