Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes.

The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.

Advancing mastitis assessment in dairy bovines via short milking tube thermography: A seasonal perspective.

In India, where dairy production leads globally, infrared thermography (IRT) and short milking tube thermography specifically are vital for managing mastitis. Therefore, the present study focuses on thermal imaging of the udder and short milking tube (SMT) of the milking machine during the peak milking process of Sahiwal cows and Murrah buffaloes during winter, summer, rainy and autumn seasons to identify sub-clinical (SCM) and clinical mastitis (CM) cases using the Darvi DTL007 camera. The udder health was assessed using the California Mastitis Test, Somatic Cell Count (SCC) and IRT throughout the year. Log10SCC and thermogram analysis revealed a difference (p < 0.01) between healthy, SCM, and CM cases during different seasons in both breeds. Further results showed an increase (p < 0.01) in SMT thermograms of SCM and CM cases compared to healthy quarters in Sahiwal cows during winter, summer, rainy, and autumn were 4.26 and 7.51, 2.37 and 4.47, 2.20 and 3.64, 2.90 and 4.94 ºC, respectively and for Murrah buffaloes were 3.56 and 5.55, 2.70 and 3.81, 1.72 and 3.10, 3.14 and 4.42ºC, respectively. The highest degree of increase in milking udder skin surface temperature and SMT of SCM and CM cases compared to healthy quarters was observed during the winter and the least during the rainy season. Thus, regardless of the seasons examined in this study, SMT thermograms effectively assessed SCM and CM.

Influence of additive and maternal effects on production and reproduction traits in Murrah buffaloes: Insights from Bayesian analysis.

The aim of this research was to assess genetic parameters for first lactation production and reproduction traits in Murrah buffaloes by employing additive and maternal effects. Data on pedigree and specific traits of 640 Murrah buffaloes were gathered from 1997 to 2020. These traits encompassed first lactation milk yield (FLMY), 305-day first lactation milk yield (305FLMY), first lactation length (FLL), first lactation peak yield (FPY), first service period (FSP), first calving interval (FCI) and first dry period (FDP). Genetic evaluations employed six univariate animal models, accounting for both direct and maternal effects, facilitated by THRGIBBS1F90 and POSTGIBBSF90 programs. Fixed factors included in the analysis were period of calving, season of calving and age at first calving. The Bayesian estimates for direct heritability, derived from the most suitable model, were as follows: FLMY: 0.28 ± 0.01, 305FLMY: 0.30 ± 0.01, FLL: 0.19 ± 0.01, FPY: 0.18 ± 0.01, FSP: 0.12 ± 0.01, FCI: 0.14 ± 0.01 and FDP: 0.12 ± 0.01. Maternal effects were found significant, ranging from 5% to 10%, in first lactation traits under Model 2 and Model 5. Additionally, positive and significant genetic and phenotypic correlations were observed among the studied traits. In conclusion, selection based on 305-day first lactation milk yield suggests potential for genetic enhancement in Murrah buffaloes, advocating its inclusion in breeding programmes to bolster early performance. Also, consideration of maternal influences is necessary for genetic progress of animals.

Impact of age at first calving on fertility and production performance in Murrah buffalo.

The present study analyses the effect of age at first calving (AFC) on future fertility and productivity in Murrah buffaloes. The data of 314 buffalo heifers of animal farm section, ICAR-CIRB, Hisar were collected over a period of 9 years from 2010 to 2018. The buffalo heifers were categorized into six groups according to the AFC named as 30-35, 36-41, 42-47, 48-53, 54-59 and 60-65 months. The influence of AFC on standard lactation milk (SLMY), peak yield (PY), days in milk (DIM), calving to first service, service per conception, calving to conception interval (CCI) and calving interval till fifth lactation were studied. The study revealed poor productive traits in buffalo heifers calved at younger age (30-35 months) during first parity. The productive value positively corresponded with increase in AFC. During successive lactations, higher mean milk yield (SLMY and PY) was found in groups with 36-41, 42-47 and 48-53 months. The mean number of services per conception was lower in buffalo heifers with 36-41 and 42-47 months following first calving till fifth lactation. Similarly, the said groups had lower mean calving to first service, CCI and CI up to fifth lactation. The survival rate was higher in heifers with AFC 36-41, 42-47, 48-53 and 54-59 months than with AFC 30-35 and 60-65 months. The buffalo heifers with 36-41 and 42-47 months of AFC had higher survival rate and better productive and reproductive traits till fifth parity in the current study. The study concluded that a minimum ideal AFC of 36-41 months yielded the highest productive gain.

Estimation of direct and maternal covariance along with genetic and phenotypic trends of reproduction traits in Murrah buffalo.

The research utilized data from 662 Murrah buffaloes meticulously recorded over 24 years (1996-2019) from historical pedigree sheets maintained at the buffalo farm of the Department of Livestock Production and Management (LPM) at Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar. A series of six univariate animal models were employed to calculate estimates of (co)variance components and heritability for first lactation reproduction traits. Among these models, Model 2 was identified as the best fit for age at first calving (AFC) and calving interval (CI), while Model 1 proved optimal for service period (SP) and conception rate (CR). The heritability estimates for AFC, SP, CR and CI across the models were ranged between 0.11 and 0.32, 0.01 and 0.03, 0.05 and 0.06, and 0.01 and 0.06, respectively. Maternal effects (m2 ) were observed in AFC and CI, ranging from 0.10 to 0.20 and 0.01 to 0.03, respectively. Across all three traits, there was a consistent negative genetic correlation (-0.75 to -0.92) between direct additive and maternal effects. The breeding values for AFC, SP, CR and CI varied within specific ranges from -32.85 to 44.33 days, -15.61 to 28.42 days, -7.41 to 6.48% and -20.64 to 35.79 days, respectively. Significantly, Spearman's rank correlation analysis revealed highly significant relationships (p < .01) between the breeding values of different models, indicating strong and consistent associations within these traits. These findings underscore the stable and reliable connections observed within the breeding values for these essential reproductive traits across the various models used in the study. The majority of reproductive traits showed favourable negative trends, indicating a positive outcome. A decrease in AFC, SP and CI suggests an extended economic life for the animals. Additionally, the upward trends in CR reflect positive indications of effective management practices and skilled operational procedures.

Genomic clues of association between clinical mastitis and SNPs identified by ddRAD sequencing in Murrah buffaloes.

The total milk production of India is 209.96 MT out of which 45% is contributed by the indigenous buffalo and due to their high producing virtue, the prevalence of mastitis is 5-20%. Despite the increasing level of technological advancement, mastitis is still an issue of concern for dairy industry in India as well as across the world. Therefore, the present study aimed to identify the SNPs and associate them with the incidence of clinical mastitis in Murrah buffalo using the ddRAD sequencing approach taking mastitis incidence data of 96 Murrah buffaloes. A total of 246 million quality controlled reads were obtained with an average alignment rate of 99.01% and at a read depth of 10, quality controlled SNPs obtained were 18,056. The logistic regression model was used and a total of seven SNPs were found significantly associated (p < 0.001) with mastitis incidence and seven genes were identified viz., NCBP1, FOXN3, TPK1, XYLT2, CPXM2, HERC1, and OPCML. The majority of them were having tumor suppressing action, related to immunogenetics or glycolytic and energy production. Conclusively, the SNPs identified in this study may be useful for future studies on mastitis incidence in Murrah buffalo and the SNP associations can be further validated.

Sustainable multi-trait selection index based on production, reproduction, and health traits for genetic improvement of Murrah buffaloes.

Selection of Murrah buffaloes based on production, reproduction, and health traits play an important role in sustainable genetic improvement. With the aim to construct an index comprising of production, reproduction and health traits of Murrah buffaloes, the production and reproduction data during a 50-year span (1971-2020) and for health traits data of 27 years (1994-2020) were analyzed. Various three, four, five, and six trait combinations of production, reproduction, and health traits were explored for construction of performance indices. The income and expenditure method was used to calculate relative economic values (REV) for traits under consideration. A total of 37 performance indices were constructed using a multi-trait combination of production, reproduction, and health traits. Out of 37 indices, the (ADMY-PY-DO-AFC-FF) based index was identified as the best, with 78%, 2%, and 20% weightage given to production, reproduction, and female fertility, respectively. Furthermore, when REVs of traits were increased by 25% and 50%, there was no change observed in the relative importance of traits in the best index, indicating that the index was robust to substantial increases in economic values. Therefore, it is recommended that the above constructed composite selection index can be employed in selection of female buffaloes to achieve sustainable genetic gain.

Rumen microbial diversity, enteric methane emission and nutrient utilization of crossbred Karan-Fries cattle (Bos taurus) and Murrah buffalo (Bubalus bubalis) consuming varied roughage concentrate ratio.

Dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance. The goal of this study was to see how the roughage concentrate ratio 70:30 (Low concentrate; LC) vs 40:60 (High concentrate; HC) and the host species crossbred cattle vs buffalo affected rumen microbial diversity, enteric methane emissions and nutrient utilization. Dry matter intake (kg/d) and dry matter percent digestibility were considerably (p < 0.05) higher in the HC ration and buffalo compared to LC ration and crossbred cattle, respectively. Both dietary mix and host species had a substantial (p < 0.05) impact on intake of various nutrients, including organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Increased concentrate proportion in the ration improved nitrogen balance, resulting in increased average daily gain and considerably reduced methane (g/d) output (p < 0.05). Furthermore, 16S rRNA genes were sequenced using Oxford Nanopore Technology (ONT) and subsequently annotated using the Centrifuge workflow to uncover ruminal bacterial diversity. Firmicutes was considerably (p < 0.01) greater in the LC diet, whereas, Bacteroidetes was higher in the HC ration. Genus Prevotella dominated all rumen samples, and buffalo fed LC ration had significantly (p < 0.01) higher Oscillospira abundance. At the species level, simple sugar-utilizing bacteria such as Prevotella spp. and Selenomonas ruminantium predominated in the crossbred cattle, but fibrolytic bacteria such as Oscillospira guilliermondii were statistically (p < 0.01) more abundant in the buffalo. Overall, dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance, however, host species remained a major driving force to change ruminal community composition as compared to roughage concentrate ratio under similar environmental conditions.

Genetic analysis of milk and milk composition traits in Murrah buffaloes using Bayesian inference.

Accurate and unbiased assessment of genetic parameters of milk and milk composition traits play an important role in formulating breeding program for genetic improvement of Murrah buffaloes. In this study, data spread over 28 years were utilized to estimate genetic parameters of traits viz., 305 d milk yield (305MY), 305 d fat yield (305FY), 305 d solid not fat yield (305SNFY), milk fat percentage (fat%) and solid not fat percentage (SNF) percentage (SNF%) in Murrah buffaloes kept at ICAR-National Dairy Research Institute, Karnal. Bayesian multiple-trait analysis was done using animal model and Gibbs sampling to estimate (co)variance components. Posterior means of heritability and posterior standard deviation for 305MY, 305FY, 305SNFY, fat% and SNF% were 0.18 ± 0.05, 0.17 ± 0.05, 0.18 ± 0.05, 0.07 ± 0.03 and 0.15 ± 0.06 and posterior means of repeatability estimates along with posterior standard deviation for corresponding traits were 0.33 ± 0.04, 0.32 ± 0.04, 0.33 ± 0.04, 0.14 ± 0.02 and 0.30 ± 0.04, respectively. Estimates of genetic correlation varied from -0.080 (305MY and fat %) to 0.999 (305MY and 305SNFY). Permanent environmental correlations varied from -0.060 (305MY and SNF%) to 0.999 (305FY and 305SNFY). This study indicated that all considered traits except fat% have ample genetic variability which can be exploited for selection and genetic improvement of Murrah buffaloes.

Comparative analysis of various methods for estimating expected genetic gain of production and reproduction traits in Murrah buffaloes.

The present study was conducted to assess the expected genetic gain for first lactation production and reproduction traits in Murrah buffaloes, in addition to optimization of progenies/sire. Data for period 1971-2020 were used from National Dairy Research Institute. Performance traits considered were 305 days milk yield (305DMY), average daily milk yield (ADMY), peak yield (PY), lactation length (LL), calving to first insemination interval (CFI), days open (DO), and calving interval (CI). Expected ΔG was estimated and compared by three different methods; method I involved heritability and selection differential; method II involved selection intensity, phenotypic standard deviation, and heritability; method III involved estimation of ΔG through four paths of inheritance. Initially, eleven progenies/sire were utilized for assessing expected ΔG by method III, and expected ΔG was found as 34.33, 0.12, 0.12 kg, 2.63, 1.51, 2.74, and 2.80 days/year for 305DMY, ADMY, PY, LL, CFI, DO, and CI, respectively. Additionally, there was a significant increase in expected ΔG on increasing progenies/sire from 6 to 11 while subsequent increase upto 16 had little effect on expected ΔG. These findings will be helpful in formulating breeding strategies worldwide in small buffalo herds to obtain sustainable ΔG in production and reproduction traits.

Comparative RNA isolation methods from fresh ejaculated spermatozoa in Sahiwal cattle (Bos indicus) and Murrah buffalo (Bubalus bubalis) bulls for high quality and enhanced RNA yield.

Sperm mRNA transcriptional profiling can be used to evaluate the fertility of breeding bulls. The aim of the study was to compare the modified RNA isolation methods for higher RNA yield and quality from freshly ejaculated sperm of cattle and buffalo bulls. Ten fresh ejaculates from each Sahiwal (n = 10 bulls × 10 ejaculates) and Murrah bulls (n = 10 bulls x 10 ejaculates) were used for RNA isolation. From the recovered live sperm, total sperm RNA was isolated by conventional methods (TRIzol, Double TRIzol), membrane-based methods combined with TRIzol (RNeasy + TRIzol) with the addition of ß-mercaptoethanol (BME) and Kit (RNeasy mini) methods in fresh semen. Among different isolation methods; the membrane-based modified methods combined with TRIzol (RNeasy + TRIzol) with the addition of ß-mercaptoethanol (BME) resulted significantly (p < .05) higher total RNA quantity (300-340 ng/µL) and better purity in different concentrations of spermatozoa viz., 30-40 million, 70-80 million and 300-400 million sperm. The study concluded that the inclusion of BME to the combined membrane-based methods with somatic cell lysis buffer solution was best for constant increased yield and purity of RNA isolation from Sahiwal cattle and Murrah buffalo bull sperm.

Effect of cryopreservation and capacitation on expression patterns of ATP synthesis associated genes in bubaline spermatozoa.

This study investigated the expression patterns of certain ATP synthesis associated genes (GAPDHS, PGK2, ENO4 and MDH2) in fresh and frozen-thawed bubaline spermatozoa vis-à-vis capacitation. Eight adult Murrah buffalo bulls, aged 5-7 years, were randomly selected from a bull farm and fresh semen was collected once a week for four weeks (n = 32) from the selected bulls. Simultaneously, frozen straws of the same bulls were collected (n = 32, four straws were pooled per sample). The samples were divided into four groups i.e., fresh non capacitated (control/group 1), fresh capacitated (group 2), frozen non capacitated (group 3) and frozen capacitated (group 4). In all groups mRNA extraction was done. The mRNA expression of GAPDHS was significantly higher in group 3 compared to the other groups, whereas the expression of ENO4 was significantly up-regulated in group 2 and 3 compared to the group 4. Similarly, the mRNA expression of PGK2 was significantly up-regulated in group 3 whereas in case of MDH2, it was significantly higher in group 2, 3 and 4 compared group 1. It can be concluded from our study that freezing and capacitation has a significant effect on the expression dynamics of the ATP synthesis-associated genes warranting necessary interventions in handling procedures to minimise the adverse effect of freezing on ATP synthesis process to ensure persistence of fertilizing ability of sperm.

Non-genetic effects and repeatability estimates of semen production traits in Murrah buffalo bulls.

The objectives of this study were to determine the repeatability estimates and the effect of ejaculate, season, period, age, and bull on semen production traits in Murrah buffalo bulls maintained in an organized semen station. A data set comprising 54,268 ejaculates from 76 Murrah buffalo bulls collected across 12 years were analyzed. The analysis of variables included non-genetic factors as the fixed effects and bull as the random effect. The repeatability was estimated by the restricted maximum likelihood method (REML) using WOMBAT program. The overall least-squares means for semen volume, sperm concentration, total sperm/ejaculate, mass activity, individual motility, post-thaw motility, and frozen semen straws/ejaculate were 2.65 ml, 1222.04 million/ml, 3030.10 million, 2.64, 67.45%, 51.73%, and 128.80 doses. The repeatability estimates were 0.27, 0.25, 0.22, 0.28, 0.34, 0.27, and 0.23, respectively. The studied non-genetic factors influenced (P < 0.01) all seminal traits. Likewise, variation (P < 0.01) due to individual bull was also observed. The first ejaculate was superior in terms of ejaculate volume, sperm concentration, total sperm/ejaculate, and frozen semen straws than the second ejaculate. The south-west monsoon and summer seasons were the best seasons with better semen quality and frozen semen production. Compared to the remaining periods, during Period V (2014-2016), greater values for most seminal traits were found. Bulls above 8 years of age expressed higher semen production than the younger bulls below 4 years, whereas the best performance was observed in the age group of 12 years and above. The repeatability estimates were low to moderate ranging from 0.22 for total sperm/ejaculate to 0.34 for individual motility. A significant (P < 0.01) positive correlation was observed between the seminal traits except the negative correlation in semen volume and total sperm/ejaculate. It was concluded that all the non-genetic factors considered in this study exerted influence on studied seminal traits. Therefore, appropriate management practices can be applied to improve semen quality and quantity.

Genetic improvement of economic traits in Murrah buffalo using significant SNPs from genome-wide association study.

GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding has primarily focused on milk production, but its negative correlation with reproduction traits resulted in unfavorable decline of reproductive performance among buffaloes. A genome wide scan was performed on a total of 120 Murrah buffaloes genotyped by ddRAD sequencing for 13 traits related to female fertility, production, and growth. The identified 25 significant single nucleotide polymorphisms (SNPs) (P <1×106) are associated with age at first calving (AFC), age at first service (AFS), period from calving to 1st Artifical Insemination (AI), service period (SP) and 6 month body weight (6M). Fifteen genetic variants overlapped with different QTL regions of reported studies. Among the associated loci, outstanding candidate genes for fertility, including AQP1, TRNAE-CUC, NRIP1, CPNE4, and VOPP1, have effect in different fertility traits. AQP1 gene is expressed in ovulatory phase and various stages of pregnancy. TRNAE-CUC gene is associated with AFC and number . of calvings after 4 years of age. Glycogen content-associated gene CPNE4 regulates muscle glycogen and is upregulated during early pregnancy. NRIP1 generegulates ovulation, corpus luteum at pregnancy, and mammary gland development. The objective is to identify potential genomic regions and genetic variants associated with economic traits and to select the most significant SNP which have positive effect on all the traits.

Short milking tube thermogram analysis: an indicator of mastitis in Murrah buffaloes.

In the present study, thermal images of the short milking tube of the milking machine representing four udder quarters independently attached to a milking animal, along with pre-milking and post-milking udder and teat thermograms, were taken using a hand-held digital infrared thermal camera (DarviDTL007) during morning milking of lactating Murrah buffaloes (n = 132) to assess the mastitis status. California mastitis test (CMT) and somatic cell count (SCC) of milk samples were carried out to screen the udder quarters as healthy, subclinical (SCM), and clinical mastitis (CM). The thermograms revealed an increase (p < 0.05) of 2.19 and 3.72ºC in the mean values of short milking tube (SMT) surface temperature among SCM and CM quarters compared to healthy quarters, respectively. The mean values of udder skin surface temperature (USST) for pre-milking, milking, and post-milking of SCM and CM compared to healthy quarters showed an increase (p < 0.05) of 2.17, 1.96, and 1.61ºC and 3.11, 2.88, and 2.73ºC, respectively. Similarly, compared to healthy quarters, the mean values of teat skin surface temperature (TSST) for pre-milking and post-milking of SCM and CM showed an increase (p < 0.05) of 2.12 and 1.66ºC and 3.07 and 2.45ºC, respectively. Also, CMT and SCC results showed a strong positive correlation (r = 0.68-0.91, p < 0.01) with all the thermographic parameters. Thus, thermograms of SMT alone can be used as an efficient detection tool in assessing SCM among Murrah buffaloes.

Sodium dodecyl sulphate, N-octyl ß-D glucopyranoside and 4-methoxy phenyl ß-D glucopyranoside effect on post-thaw sperm motion and viability traits of Murrah buffalo (Bubalus bubalis) bulls.

Sodium Dodecyl Sulphate (SDS), N-Octyl ß-D Glucopyranoside (NOG), 4-Methoxy Phenyl ß-D Glucopyranoside (4-MPG) as ice recrystallization inhibitors were added to Tris Egg Yolk Glycerol (TEYG) semen extender for cryopreservation of semen of buffalo bulls. Post-thaw sperm motion and viability traits were evaluated. Pilot study involved six semen ejaculates (2 ejaculates/bull, from three bulls); second experiment was conducted using twenty seven semen ejaculates (9 ejaculates/bull, from 3 bulls) and in third experiment three semen ejaculates (one bull) were used. Eight concentrations of SDS (2, 1, 0.5, 0.25, 0.15, 0.125, 0.0625 and 0.0312%), twelve concentrations of NOG (33, 22, 11, 5.5, 2.5, 0.75, 0.5, 0.25, 0.125, 0.0625, 0.03125 and 0.0156 mM), and, eleven concentrations of 4-MPG (220, 165, 110, 55, 50, 25, 12.5, 6.25, 3.125, 1.56 and 0.78 mM) were supplemented in TEYG semen extender to evaluate the post-thaw sperm motility and viability traits. Computer Assisted Sperm Analysis (CASA) was used to measure the kinetic and functional parameters for sperm motion traits, Hypo Osmotic Swelling Test (HOST) for sperm plasma membrane integrity, Eosin Nigrosin staining for viability and Rose Bengal staining for sperm abnormalities for all the experiments except for pilot study where only Total Motility (TM) and Rapid Progressive Motility (RP) were evaluated. Three freezing protocols; i) Normal P24 (freezing rate of -30 °C min-1 from 4 °C to -15 °C; -40 °C min-1 from -15 °C to -60 °C; and -50 °C min-1 from -60 °C to -140 °C; and then plunged in liquid Nitrogen at -196 °C); ii) Moderate P25 (freezing rate of -30 °C min-1 from 4 °C to -15 °C; -50 °C min-1 from -15 °C to -60 °C; and -50 °C min-1 from -60 °C to -140 °C; and then plunged in liquid Nitrogen at -196 °C); and iii) Rapid P26 (freezing rate of -30 °C min-1 from 4 °C to -15 °C; -60 °C min-1 from -15 °C to -60 °C; and -50 °C min-1 from -60 °C to -140 °C; and then plunged in liquid Nitrogen at -196 °C) were evaluated using SDS 0.125% in TEYG semen extender. SDS ≤0.125%, NOG ≤0.0625 mM and 4-MPG ≤ 3.125 mM in TEYG buffalo semen extender improved significantly (p < .05) the kinetic and functional parameters as compared to the other Ice Recrystallization Inhibitors (IRIs) concentrations used for cryopreservation of buffalo bull semen in the pilot study. SDS 0.125% supplementation was the best IRI among all which resulted in improved kinetic and functional parameters of bull semen in second experiment. Conclusion was drawn that buffalo bull semen cryopreservation using sodium dodecyl sulphate, 0.125% as IRI in TEYG semen extender along with freezing protocol P 25 revealed optimum kinetic and functional parameters for post-thaw spermatozoa.

Changes in Whey Proteome between Mediterranean and Murrah Buffalo Colostrum and Mature Milk Reflect Their Pharmaceutical and Medicinal Value.

Milk represents an integrated meal for newborns; its whey protein is rich in many health beneficial components and proteins. The current study aimed to investigate the differences between colostrum and mature milk from Mediterranean and Murrah buffaloes using labeled proteomics and bioinformatics tools. In the current work, LC-MS/MS analysis led to identification of 780 proteins from which 638 were shared among three independent TMT experiments. The significantly changed proteins between the studied types were analyzed using gene ontology enrichment and KEGG pathways, and their interactions were generated using STRING database. Results indicated that immunological, muscular development and function, blood coagulation, heme related, neuronal, translation, metabolic process, and binding proteins were the main terms. Overall, colostrum showed higher levels of immunoglobulins, myosins, actin, neurofascin, syntaxins, thyroglobulins, and RNA-binding proteins, reflecting its importance in the development and activity of immunological, muscular, cardiac, neuronal, and thyroid systems, while lactoferrin and ferritin were increased in mature milk, highlighting its role in iron storage and hemoglobin formation.

Estimation of genetic parameters of growth traits for direct and maternal effects in Murrah buffalo.

An understanding of genetic principles and environmental factors affecting the growth traits is essential to implement optimal breeding and selection programs. Early growth is an indicator of future success in production and reproduction status of dairy animals. In this study, a total of 18,989 records of body weight were used to estimate genetic parameters of body weight at birth (BW), 3 months (3BW), 6 months (6BW), 9 months (9BW),12 months (12BW), 18 months (18BW), 24 months (24 BW), 30 months (3BW), and 36 months (36BW) in Murrah buffalo at ICAR-NDRI Karnal, Haryana, for the period 1974-2019. The genetic parameters were estimated using the average information restricted maximum likelihood (AIREML) procedure by excluding or including maternal effects. Six analytical models were fitted in order to optimize the model for each trait. The most appropriate univariate model was selected based on the log likelihood ratio test (LRT). Influencing factors like calf sex, period of birth, season of birth, and dam's parity were investigated. The results showed that the maternal genetic effects, in addition to direct additive effects, were important for unbiased and accurate genetic parameter estimates of growth traits in Murrah buffaloes. Total heritability estimates h2T1 for BW, 3BW, 6BW, 9BW, 12BW, 18BW, 24BW, 30BW, and 36BW were 0.25, 0.04, 0.14, 0.16, 0.10, 0.15, 0.21, 0.24, and 0.23, respectively. Maternal effect was significant for birth weight and accounted for 13% variation through maternal genetic and 5% variability through maternal permanent environmental effect. Maternal genetic effect was also important for other traits. However, it interfered with the estimates of variance ratios in live weight traits owing to large and negative covariance between direct and maternal genetic effects. Direct genetic correlations between body weight traits were positive and high ranging from 0.10 to 0.94. Results revealed that the Murrah herd has a sizable genetic variability for growth traits and hence, there is sufficient scope for selection for achieving better growth rate if selection in this direction is applied. Owing to higher positive genetic correlation of 6BW with later ages, the scope of indirect selection for optimum growth in later ages can be aimed at by selecting animals for their higher 6-month live weight.

Genetic analysis of skin measurements and its relation with milk production in Murrah buffaloes reared under tropical conditions of Chhattisgarh plains.

The experiment was conducted at ABIS Buffalo Dairy Farm, Rajnandgaon, on 300 milking Murrah buffaloes. In buffaloes, the information on body measurements, skin thickness, and their associations with milk yield and interrelationship among them is scanty. Hence, the present study was designed to establish the relationship of skin thickness with milk production in Murrah buffaloes. The data was statistically analyzed using R statistical software. The average skin thickness of the neck, chest, abdomen, rump, hind quarter, udder, and flank regions were 6.27 ± 0.11, 6.13 ± 0.13, 7.28 ± 0.14, 9.78 ± 0.15, 8.00 ± 0.12, 4.14 ± 0.09, and 8.53 ± 0.12 mm, respectively. In this study, the skinfold thickness of the neck and chest regions had a highly significant effect (P < 0.01) on the total lactation milk yield of Murrah buffaloes whereas skin thickness of other regions under study had no significant effect on total lactation milk yield. The results of the study revealed that parity and stage of lactation had a significant effect (P < 0.05) on the skinfold thickness of all the seven regions of Murrah buffalo under investigation. The study indicated that except for the udder region the correlation of all skin thickness with TMY was found to be negative and significant. The genetic correlations between milk yield and skin thickness of the neck, abdomen, and udder were low to medium. The heritability estimate for different skinfold thicknesses and milk yield in this study was low to medium. These results could facilitate further exploration in the use of skinfold thickness for management precision and can be useful in the selection of better animals under field conditions.

Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo.

Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.