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The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development. [ABSTRACT FROM AUTHOR]

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle. [ABSTRACT FROM AUTHOR]

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

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

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]

The bovine TLR4 gene is an interesting candidate marker for mastitis resistance, since it is involved in neutrophil migration to and from the mammary gland during mastitis. TLR4 detects pathogen ligands, such as the Escherichia coli lipopolysaccharide (LPS) endotoxin and facilitates innate and adaptive immune responses. In the current study, a total of 130 crossbred cows (74 mastitis tolerant and 56 with clinical mastitis) kept at the Cattle and Buffalo Farm, IVRI, Izatnagar, were selected to explore the polymorphism in the co-receptor binding region 2 (CRBR2) fragment of the TLR4 gene. PCR-SSCP and sequence analysis showed two genotypes of the TLR4 gene's CRBR2 fragment, AA and AB, which were polymorphic in both the afflicted and tolerant groups. Sequencing revealed eight single nucleotide polymorphisms (SNPs) in allele A and ten SNPs in allele B. This genotype had no significant effect on the incidence of clinical mastitis according to the logistic regression model. Our study found insufficient evidence linking SNP variants in the CRBR2 region of the TLR4 gene to mastitis susceptibility in crossbred cattle. • A total of 130 crossbred cows were selected to explore the polymorphism in the CRBR2 fragment of the TLR4 gene. • No link found between the genotypes in the CRBR2 region of the TLR4 gene and clinical mastitis in crossbred cattle. • Sequencing results revealed eight single nucleotide polymorphisms (SNPs) in allele A and ten SNPs in allele B. [ABSTRACT FROM AUTHOR]

• 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]

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