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Pedigree analysis is required to assess the genetic diversity and population structure of a close breeding population in order to effectively manage the breeding program and keep inbreeding under acceptable limits. Saanen x Beetal is a crossbred population of goats, reared at National Dairy Research Institute (NDRI) Karnal for the last five decades. This germplasm has been acclimated to a tropical climate and has a higher milk potential and prolificacy. Objective of this study was to elucidate the genetic diversity, population structure, and inbreeding in the flock of the Saanen x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 2603 animals from the year 1971–2021. Animals born between 2014–2017 were considered as a reference cohort. Results revealed that the average generation interval was 3.44 years for the complete pedigree. The average inbreeding coefficient and the average relatedness were 4.20% and 6.87%, respectively, for the complete pedigree and 10.78% and 10.80%, for the reference population. Higher inbreeding coefficient and average relatedness in the reference cohort demonstrated impact of enclosed gene pool and demands immediate intervention for managing diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 and 3 for the complete pedigree and reference cohort, respectively, which illustrates the fact that very few ancestors were responsible for genetic diversity in the flock, which results in the decline of effective population size. Effective number of founders (fe), ancestors (fa), and founder genome equivalents (fg) were 15, 7, and 3.11, respectively. The (fe/fa) ratio in the reference population was 2.14 indicating the occurrence of the bottleneck effect in the flock. We observed that inbreeding was non-significant for all reproductive traits except for age at first service and age at first kidding. To lessen inbreeding and augment genetic diversity in the flock, the stratified breeding plan needs to be followed, where, mate sele ction would be based on relatedness. Furthermore, introduction of unrelated Saanen and Beetal crosses will help alleviate the inbreeding accumulation.

Production and reproduction traits in Nili-Ravi buffaloes maintained at the ICAR-Central Institute for Research on Buffaloes, Sub-campus, Nabha, Punjab, were analysed to study the impact of Number of pregnancies (parity) and season of birth on performance. The least squares method was used to elucidate the effect of parity and season of calving on production and reproduction traits. The overall least squares means of production traits, 305 days or less milk yield, total lactation milk yield, and lactation length were 2603.22±47.66 kg, 2691.82±56.20 kg, and 305.72±4.95 days, respectively, and reproduction traits age at service, age at calving, service period, calving interval and dry period were 1418.76±16.60 days, 1741.30±18.52 days, 163.52±7.33 days, 466.55±6.70 days and 157.11±4.18 days, respectively. The parity had shown significant effect on all studied production and reproduction traits. However, the season of calving impacted only dry period in Nili-Ravi buffaloes.

A lactation curve can reveal abundant information about the pattern and persistency of lactation in an individual dairy animal. Identifying buffalo with particular pattern and persistency of lactation milk yield can serve as additional selection criterion for a dairy herd. Wood’s incomplete gamma function fitted well to the monthly test-day milk, fat% and SNF% yields of Murrah buffaloes and can be used in prediction of milk and milk constituents yield with higher accuracy. We also report that exponential function (Wilminks model) also can be used in prediction of milk constituents in Murrah buffaloes when constant k is changed in the model from 0.05 to 0.06 or 0.07. Thus, these functions can be used to make breeding and management related decisions particularly selection of desired and persistent buffaloes and thus improving the production of the herd by culling non-desired type of Murrah buffaloes.

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (atK= 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Murrah is a predominant milch breed of buffalo in India with superior genetic potential for milk production. Estimation of genetic parameters for production and reproduction traits is prerequisite for making breeding plan and efficient management decisions. This work was undertaken to understand the influence on performance traits by various factors (genetic and non-genetic) along with assessment of genetic parameters in Murrah buffaloes. The genetic parameters were figured using mixed model least-squares analysis. The results revealed that season and period in which animals calved, affects the performance of Murrah breed and may be considered during its evaluation. The heritability estimates for first lactation 305 days/less milk yield (305FLMY), first lactation total milk yield (FLTMY), first Lactation Length (FLL1), Wet average (WA), Herd average (HA), Age at first calving (AFC1) and Age at first service (AFS1) were 0.39±0.10, 0.29±0.09, 0.14±0.09, 0.29±0.09, 0.3±0.11, 0.27±0.09 and 0.22±0.09, respectively. The phenotypic and genetic correlation amid 305FLMY and majority of another production trait were positive and significant. Thus, it may be concluded that appropriate estimation of genetic parameters leads to robust selection for performance traits for genetic improvement in Murrah buffalo.

Milk serves as a mode of protection to neonate through transferring the host defense proteins from mother to offspring. It also guards the mammary gland against various types of infections. Along with the presence of six vital proteins, bovine milk (whey) contains a massive class of minor proteins, not all of which have been comprehensively reported. In this study, we performed an LC-MS/MS-based ultra-deep identification of the milk whey proteome of Indian zebu (Sahiwal) cattle. Three independent search engines that are Comet, Tandem, and Mascot-based analysis resulted in the discovery of over 6,210 non-redundant proteins commonly identified. Genome-wise mapping revealed that chromosome 1 showed a minimum expression of 14 proteins, whereas chromosome 19 expressed 250 maximum proteins in milk whey. These results demonstrate that milk proteome in Sahiwal cattle is quite complicated, and minor milk fractions play a significant role in host defense.

Stanniocalcin-1 (STC1) is secreted by the variety of tissues having a major role in the regulation of calcium ions in the involuting mammary gland. The present work aims to sequence and structural characterization as well as expression profiling of STC1 gene in buffalo. Polymorphism identified in the 3-untranslated region (UTR) was analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) genotyping in riverine and swamp buffaloes. Expression profiling of STC1 was performed in different lactation stages of mammary gland and peripheral blood mononuclear cells to study the impact of 3'-UTR polymorphism on its expression. Different polymorphic sites were detected in the entire coding and noncoding regions of riverine and swamp buffaloes, including two INDELs. An identified polymorphic nucleotide locus A324G, having target sites for two miRNAs, namely bta-miR-2382 and bta-miR-1343, reported in cattle, was genotyped by PCR-RFLP to reveal variable allelic distribution among swamp and riverine buffaloes. Gene expression profiling across buffalo mammary tissues representing different lactation stages showed maximum expression of the STC1 gene in the involuting mammary gland. Ruminants' specific genetic variation has been observed in STC1 and its implication in buffalo mammary gland involution as well as coregulation of gene expression through miRNA binding in the 3'-UTR is suggested.

In this study, we have sequence characterized and analyzed the polymorphism in buffalo NOD1 (nucleotide-binding oligomerization domain 1) gene as well as its expression analysis. Full-length sequence analysis of NOD1 revealed this gene in buffalo being conserved with respect to the domain structures, similar to other species. Alternate splice variants having exon3 skipping also identified for the first time in the gene expressed in buffalo-purified peripheral blood mononuclear cells (PBMCs). Phylogenetically ruminant species were found to be clustering together and buffalo displaying maximum similarity with cattle. Sequencing of NOD1 across 12 Indian buffalo breeds identified 23 polymorphic sites within coding region, among which 16 were synonymous and 7 changes found to be non-synonymous. Four SNPs (single nucleotide polymorphisms) of them were genotyped in 393 animals belonging to 12 riverine, swamp and hybrid (riverine × swamp) buffalo populations of diverse phenotypes and utilities, showing variable allelic frequencies. Principal component analysis revealed, riverine and swamp buffaloes being distinctly placed with the distribution of breeds within the group based on the geographical isolation. Further, quantitative real-time PCR detected NOD1 expression in multiple tissues with PBMCs and lungs showing highest expression among the tissues examined. Structural analysis based on the translated amino acid sequence of buffalo NOD1 identified four protein interaction motifs LxxLL important for ligand binding. Molecular interaction analysis of iE-DAP and NOD1-LRR and their complex stability and binding-free energy studies indicated variable binding energies in buffalo and cattle NOD1. Overall, the study reveals unique structural features in buffalo NOD1, important for species-specific ligand interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1534-2) contains supplementary material, which is available to authorized users.

Bovine-specific microsatellite markers were used to assess the genetic variation in Belahi cattle. Both within-breed (Belahi) and between-breed (Sahiwal, Gir, Tharparkar, Rathi, Nagori, Mewati, Kankrej and Belahi breeds) diversity indices were estimated. Sixteen microsatellite loci were polymorphic with more than five alleles per locus. Mean allelic diversity was 9.31, with a total of 149 alleles. Polymorphism information content varied from 0.31 (TGLA227) to 0.87 (CSSM33) with an average of 0.71. Estimate of Nei’s gene diversity was 0.72 ± 0.15. The observed and expected heterozygosity at different loci were 0.69 ± 0.17 and 0.71 ± 0.15 and varied from 0.30 (TGLA227) to 0.88 (TGLA122) and 0.32 (TGLA227) to 0.88 (CSSM33), respectively. Within-population inbreeding estimates (FIS) for Belahi cattle was 0.0337, indicating an average deficiency of 3.37%. Belahi cattle revealed the presence of genetic diversity within population and there was no significant heterozygosity excess indicating the absence ...

Aim: The present study was performed to investigate the effect of genetic and non-genetic factors affecting milk fat yield and to estimate genetic parameters of monthly test day fat yields (MTDFY) and lactation 305-day fat yield (L305FY) in Murrah buffaloes. Materials and Methods: The data on total of 10381 MTDFY records comprising the first four lactations of 470 Murrah buffaloes calved from 1993 to 2014 were assessed. These buffaloes were sired by 75 bulls maintained in an organized farm at ICAR-National Dairy Research Institute, Karnal. Least squares maximum likelihood program was used to estimate genetic and non-genetic parameters. Heritability estimates were obtained using paternal half-sib correlation method. Genetic and phenotypic correlations among MTDFY, and 305-day fat yield were calculated from the analysis of variance and covariance matrix among sire groups. Results: The overall least squares mean of L305FY was found to be 175.74±4.12 kg. The least squares mean of overall MTDFY ranged from 3.33±0.14 kg (TD-11) to 7.06±0.17 kg (TD-3). The h 2 estimate of L305FY was found to be 0.33±0.16 in this study. The estimates of phenotypic and genetic correlations between 305-day fat yield and different MTDFY ranged from 0.32 to 0.48 and 0.51 to 0.99, respectively. Conclusions: In this study, all the genetic and non-genetic factors except age at the first calving group, significantly affected the traits under study. The estimates of phenotypic and genetic correlations of MTDFY with 305-day fat yield was generally higher in the MTDFY-5 of lactation suggesting that this TD yields could be used as the selection criteria for early evaluation and selection of Murrah buffaloes.

The objective of the present study was to identify the best fit lactation model in relation to bovine leptin gene and to assess lactation persistency based on lactation curve traits in crossbred Karan Fires cattle. Incomplete gamma (Wood) function and exponential (Wilmink) function tests were used to describe the characteristics of lactation curve in first lactation. Woods model showed a comparatively better fit. Different types of lactation curves depicted by these cattle using data spread over a period of 15 years (1994 to 2009) were grouped into desired and nondesired type of lactation curve. Subsequently, genotype profiling was done using PCR-RFLP. A single nucleotide polymorphism identified in exon-2 region of bovine leptin gene, was associated with desired type of lactation curve and animals having TT genotype showed better persistency of milk yield. The results validated in test population had shown positive relationship between leptin genotypes and lactation curve traits. The inference from work has a potential application in breeding program of the country, where it may give support to existing expected producingability (EPA) based selection methodology followed for selection of dairy animals, by adding leptin genotype as one additional selection criterion for early selection in crossbred dairy bulls and cattle.

Haptoglobin (Hp) protein has high affinity for hemoglobin (Hb) binding during intravascular hemolysis and scavenges the hemoglobin induced free radicals. Earlier reports indicate about uniqueness of Hp molecule in human and cattle, but in other animals, it is not much studied. In this paper, we characterized buffalo Hp molecule and determined its molecular structure, evolutionary importance, and tissue expression. Comparative analysis and predicted domain structure indicated that the buffalo Hp has an internal duplicated region in α-chain only similar to an alternate Hp2 allele in human. This duplicated part encoded for an extra complement control protein CCP domain. Phylogenetic analysis revealed that buffalo and other ruminants were found to group together separated from all other non-ruminants, including human. The key amino acid residues involved in Hp and Hb as well as Hp and macrophage scavenger receptor, CD163 interactions in buffalo, depicted a significant variation in comparison to other non-ruminant species. Constitutive expression of Hp was also confirmed across all the vital tissues of buffalo, for the first time. Results revealed that buffalo Hp is both structurally and functionally conserved, having internal duplication in α-chain similar to human Hp2 and other ruminant species, which might have evolved separately as a convergent evolutionary process. Furthermore, the presence of extra Hp CCP domain possibly in all ruminants may have an effect during dimerization of molecule in these species.

A genetic study was conducted to elucidate the effect of alpha-Lactalbumin (α-LA) gene polymorphism on milk production traits involving total milk yield and daily milk yield during first lactation in two breeds of water buffaloes namely, Murrah and Bhadawari. Single strand conformation polymorphism (SSCP) was carried out to explore genetic polymorphism present at this locus. For this study, exon 1 region of α-LA was analyzed. Finally, polymorphism data was associated with milk production traits by employing least square analysis. In Murrah buffalo, five genotypes such as AB, BB, BC, CC and CD and four alleles A, B, C and D were detected whereas in Bhadawari buffalo two genotypes namely, AB and BC and three alleles namely, A, B and C were found. Genotypes showed significant effects (p≤0.05) on total milk yield and daily milk yield in Bhadawari buffalo but had non-significant effects on these traits in Murrah buffalo. (Asian-Aust. J. Anim. Sci. 2006. Vol 19, No. 3 : 305-308)

Phenotypic characterization and body biometric in 13 traits (height at withers, body length, chest girth, paunch girth, ear length, tail length, length of tail up to switch, face length, face width, horn length, circumference of horn at base, distances between pin bone and hip bone) were recorded in 233 adult Gojri buffaloes from Punjab and Himachal Pradesh states of India. Traits were analysed by using varimax rotated principal component analysis (PCA) with Kaiser Normalization to explain body conformation. PCA revealed four components which explained about 70.9% of the total variation. First component described the general body conformation and explained 31.5% of total variation. It was represented by significant positive high loading of height at wither, body length, heart girth, face length and face width. The communality ranged from 0.83 (hip bone distance) to 0.45 (horn length) and unique factors ranged from 0.16 to 0.55 for all these 13 different biometric traits. Present study suggests that first principal component can be used in the evaluation and comparison of body conformation in buffaloes and thus provides an opportunity to distinguish between early and late maturing to adult, based on a small group of biometric traits to explain body conformation in adult buffaloes.

Present study was aimed to discover the single nucleotide variation present in exon 40 region of the Fatty Acid Synthase (FASN) gene. FASN plays a central role in de novo lipogenesis in mammals and variation in this enzyme may affect economic traits including fatty acid composition of buffalo milk. A total of 80 DNA samples in two riverine buffalo breeds namely, Gojri and Chhattisgarhi were screened using Restriction Fragment Length Polymorphism (RFLP). FASN gene was found to be polymorphic with an adenine to guanine transition. Three types of genotypes, viz. AA, AG and GG were observed in the studied breeds. Allele A was found to be more frequent than G allele. All the genotypes showed almost the same frequency across the breeds, indicating that there is absence of selection for FASN gene in lesser known buffalo breeds of India. The study will augment the information available and can be applied in future studies to determine the role of bovine FASN gene as a candidate gene marker for a milk-fat content.