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

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

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

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

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

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

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

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

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

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

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