Population-wide genetic analysis of Ovar-DQA1 and DQA2 loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate

Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.

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.

Cross-population genetic analysis revealed genetic variation and selection in the Ovar-DRB1 gene of Indian sheep breeds

In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.

Explicating the genetic diversity and population structure of Saanen × Beetal goats using pedigree analysis

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 × Beetal is a crossbred population of goats, reared at the 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. The objective of this study was to elucidate the genetic diversity, population structure, and inbreeding in the flock of the Saanen × Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal, for 2603 animals from the year 1971 to 2021. Animals born between 2014 and 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 the impact of the 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 numbers 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 selection would be based on relatedness. Furthermore, the introduction of unrelated Saanen and Beetal crosses will help alleviate the inbreeding accumulation.

Estimation of genetic parameters and genetic change of first parity reproductive traits in Alpine × Beetal goats

The study of reproductive traits is crucial for improving genetic potential of goats because of their significant utility in meat production. Hence, genetic analysis was conducted for reproductive traits on Alpine × Beetal goats using animal model for first parity data. Information on 1462 reproductive records were collected over five decades from ICAR-National Dairy Research Institute, Karnal, Haryana (1971-2021). Single-trait and multi-trait animal models were used for genetic analysis. Estimates of (co)variance components and genetic parameters were obtained using Gibbs Sampler for Animal Model due to non-normal distribution of data. Six single-trait animal models (including or excluding maternal and environmental effects) were fitted and best models were determined based on Deviance Convergence Criterion values. The prolificacy for the A × B goats for first parity data was 32%, having 68% single births, 31% twins and 1% triplets/quadruplets. The least squares mean for age at first service (AFS), age at first kidding (AFK), service period (SP), dry period (DP), gestation length (GL), kidding interval (KI), litter weight (LW), number of kids born (NKB) and number of females kids born (NFKB) in first parity were 546.15 ± 4.10 days, 679.05 ± 4.07 days, 226.51 ± 4.02 days, 67.96 ± 2.76 days, 150.74 ± 0.13 days, 362.53 ± 3.35 days, 3.99 ± 0.04 kg, 1.32 ± 0.02 and 0.64 ± 0.02, respectively. The heritability estimates obtained from best model for AFS, AFK, GL, KI, SP, and DP were 0.12 ± 0.00, 0.10 ± 0.00, 0.09 ± 0.01, 0.03 ± 0.00, 0.04 ± 0.00, and 0.05 ± 0.00, respectively. For NKB, NFKB and LW, heritability estimates were 0.16 ± 0.01, 0.03 ± 0.03, and 0.04 ± 0.00, respectively. These results imply lower heritability estimates for reproductive traits, and hence meagre scope for selection for further improvement. Maternal effects contributed significantly for traits such as GL, NKB and NFKB. Genetic correlation for number of female kids born was negative with SP and DP which is favourable. Furthermore, genetic correlation was negative for dry period and litter weight which is favourable as number of kids born and litter weight are traits of direct economic importance. Results reveal high genetic potential of this breed for meat industry owing to high prolificacy, provided consistent efforts are made for the genetic improvement of this germplasm.

Performance evaluation of Marwari lambs for growth traits and impact of inbreeding

This study aimed at the performance evaluation of a closed flock of Marwari sheep and also to study the effect of accumulated inbreeding on the growth traits using a linear mixed model methodology. The data generated for 39 years (1981 to 2020) on Marwari sheep maintained at ICAR-Central Sheep & Wool Research Institute, Arid Region Campus (CSWRI, ARC), Bikaner, Rajasthan, India were used for analysis on growth traits. The overall least-squares means (LSM) of live weights at birth (BWT), weaning (3MWT), 6 months (6MWT), 9 months (9MWT) and 12 months (12MWT) were observed to be 3.02 ± 0.01, 14.30 ± 0.04, 20.12 ± 0.05, 23.68 ± 0.06 and 26.39 ± 0.07 kg, respectively. Overall LSM for average daily gain from birth to 3 months (ADG1), 3 to 6 months (ADG2) and 6 to 12 months (ADG3) were 125.44 ± 0.40, 67.37 ± 0.40 and 35.83 ± 0.29 g/day, respectively. Kleiber ratio (KR) from birth to 3 months (KR1), 3 to 6 months (KR2), and 6 to 12 months (KR3) were 16.78 ± 0.02, 6.58 ± 0.04 and 3.05 ± 0.02, respectively. Results revealed a 4.36, 25.83, 36.33, 31.50 and 28.99% improvement in the live weights since the inception of the improvement programme. This is also reflected by a significant effect of sire on all the growth traits. The estimate of inbreeding in the flock was 1.55%. Highly inbred animals were 5.13% (>5% Fi). The study revealed the non-significant effect of inbreeding level on all growth traits except for BWT and KR3. For BWT, inbreeding classes had variation; however, a negative effect was not seen. The inbreeding class (>5% Fi) was reduced by 0.05 units for KR3 as against its preceding class. Dam's age at lambing and weight influenced the birth weight and subsequent weights. The study concluded that the selection programme of Marwari sheep is in the right direction; however, regular monitoring of inbreeding is necessary and factors affecting growth must be monitored to attain better growth rates in the nucleus.

Optimization of test day for milk yield recording and sire evaluation in Murrah buffaloes

In the present study, random regression models (RRM) were used to estimate genetic parameters for test-day milk yield in Murrah buffaloes using Legendre polynomial function (LP), with the objective to find the best combination of "minimum test-day model," which would be essential and sufficient to evaluate the trait successfully. Data included for analysis were 10,615 first lactation monthly test-day milk yield records (5th, 35th, 65th, …, 305th) from 965 Murrah buffaloes for the period 1975-2018. Cubic to octic-order orthogonal polynomials with homogeneous residual variances were used for the estimation of genetic parameters. Random regression models with sixth-order were selected based on goodness of fit criteria like lower AIC, BIC and residual variance. Heritability estimates ranged from 0.079 (TD6) to 0.21(TD10). For both ends of lactation, the additive genetic and environmental variances were higher and ranged from 0.21 ± 0.12 (TD6) to 0.85 ± 0.35 kg² (TD1) and 3.74 ± 0.36 (TD11) to 1.36 ± 0.14 kg² (TD9), respectively. Between adjacent test-day records, genetic correlation estimates ranged from 0.09 ± 0.31 (TD1 and TD2) to 0.97 ± 0.03 (TD3 and TD4; TD4 and TD5), but values gradually declined as the distance between test days increased. Negative genetic correlations were also obtained between TD1 with TD3 to TD9, TD2 with TD9 and TD10, and TD3 with TD10. On the basis of genetic correlations, models with 5 and/or 6 test-days combination were able to account for 86.1%-98.7% of variation along the lactation. Models with fourth and fifth-order LP functions were considered to account for variance with combinations of 5 and/or 6 test-day milk yields. The model with 6 test-day combinations had a higher rank correlation (0.93) with model using 11 monthly test-day milk yield records. On the basis of relative efficiency, the model with 6 monthly test day combinations with fifth-order was more efficient (maximum 99%) than the model using 11 monthly test-day milk yield records. Looking into the similar accuracy with the 11TD model, and the low resources requirement, we recommend the use of the "6 test-day combination model" for sire evaluation. These models may help in reducing the cost and time for data recording of milk yield.

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 h²_T1 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.

Estimation of genetic parameters for production and reproductive traits in Indian Karan-Fries cattle using multi-trait Bayesian approach

Estimates of variance components are needed for implementing genetic selection. This study was conducted to genetic parameters for production and reproductive traits on Indian Karan-Fries cattle using multi-trait repeatability animal model. Data collected from ICAR-National Dairy Research Institute, Karnal, India (from 1988 to 2019) were used. Single-trait and multi-trait repeatability animal models were used for parameter estimation. The posterior mean of Heritability estimates for 305-day milk yield (305-DMY), lactation milk yield (LMY), lactation length (LL) were 0.20 ± 0.03, 0.19 ± 0.03 and 0.06 ± 0.02, respectively. For age at first calving (AFC), calving interval (CI), and days open (DO), the posterior mean of heritability estimates were 0.24 ± 0.08, 0.06 ± 0.01, and 0.07 ± 0.02, respectively. The repeatability estimates for 305-DMY, LMY, LL, CI, and DO were 0.37 ± 0.02, 0.34 ± 0.02, 0.15 ± 0.02, 0.09 ± 0.02, and 0.12 ± 0.02, respectively. Genetic correlation between milk production traits (305-DMY, LMY, and LL) was positive and strong (> 0.80). However, the genetic correlation between milk production trait and AFC ranges from - 0.31 to 0.12. Unfavorable strong genetic correlations were observed between production and reproductive traits (CI and DO) with values ranged from 0.5 to 0.7. Phenotypic correlations among 305-DMY, LMY, and LL were generally positive and high. The moderate heritability estimates and potential genetic variation for 305-DMY, TMY, and AFC suggested that genetic gain can be obtained for these traits through genetic selection. Low heritability estimates found for LL, CI and DO, indicating that the possibility of changing these traits through genetic selection is small. High genetic correlation observed between productive and fertility traits were unfavorable. The existed strong genetic and phenotypic correlation estimates between CI and DO indicates that recording only one of them would be sufficient in the herd. As the multi-trait model showed slight improvements in the h² as well as r estimates for both productive and reproductive traits over univariate analysis, future selection with a multi-trait animal model applying Bayesian approach would be recommended.

Short-term effect of foot-and-mouth disease (FMD) vaccination on the milk yield in the Deoni and crossbred cows

Biannual vaccination of the cattle with inactivated foot-and-mouth disease (FMD) vaccine is the control strategy in endemic countries. Reduction in the milk yield is one of the main reasons for poor compliance of the cattle owners to FMD vaccination. As it can adversely affect the herd immunity, the present study aimed to quantify the losses in the milk yield post-FMD vaccination. Retrospective data on the milk yield (kg) recordings, days in milk, parity, and age at vaccination of the Deoni and crossbred cows were collected from 10 days before (-10) to 10 days after (+10) FMD vaccination (dpv). Days in milk were categorized into three stages of lactation for Deoni and crossbred cows. Age (month) was categorized into four classes. Least squares means of the milk yield were generated after adjusting for year, age, parity, and stage of lactation. Based on exploratory data analysis, the corrected milk yield records from -2 to +2 dpv for 5 years comprising 614 data points on Deoni cows (n=54) and 488 data points on crossbred cows (n=55) were used for the final analysis. Because of the correlated errors on the corrected milk yield, linear mixed model ANOVA was done by fitting dpv as fixed effect and cow as random effect, and the results revealed the effect of dpv was non-significant (P>0.05) in either breed. With respect to dpv 0, a marginal reduction of 90 g in the corrected milk yield in the Deoni cow was recorded on dpv 1, while the reduction was about 360 g on dpv 0 as compared dpv -1 in the crossbred cow. It was concluded that FMD vaccination caused a transient non-significant reduction in the milk yield in the Deoni and crossbred cows.

Farmer's participatory approach for breed improvement in Malpura sheep

The objective of the study was to propose a model for a community-based breeding programme (CBBP) in Malpura sheep. The study was carried out for nine years (2012-2018) in 31 villages covering 77 flocks. The average flock size was 54.39 ± 0.65. The study revealed that the Malpura sheep is a long-day breeder with 72.1% of lambing during August to January. The higher concentration of lambing in this period is to avoid the stress of harsh summer and scarcity of feed. The disposal pattern of male lambs was stringent due to selection. Only 3.1% of male lambs reach to adult stage. For females, the replacement rate was 34.11%. The live weights (kg) from 8,263 lambs were 3.34 ± 0.01, 14.61 ± 0.04, 20.48 ± 0.07 and 30.01 ± 0.16, for birth, three-, six- and 12-month age, respectively. Non-genetic factors such as sex, season and year of birth and flock significantly influenced growth. The heritability was 0.20 ± 0.03, 0.20 ± 0.008, 0.23 ± 0.004 and 0.17 ± 0.009 for birth, three-, six- and 12-month weight, respectively. This indicated scope for genetic improvement, given a systematic breeding programme, is in place. The present model followed by sheep breeders is highly dependent upon the Government aided Central Sheep and Wool Research Institute (CSWRI) for supply of breeding rams, data collection and health care. Alternate self-sustainable model of CBBP is proposed wherein a breeder's organization leads the way to establish a ram-rearing centre (RRC), teams of experts for ram selection, data collection and market linkage. CSWRI will continue to assist for selection decisions and real-time data entry using a cloud-based "Avimegh" platform. The early selection of 5% male lambs at weaning and rearing them at RRC until final selection at 12-month will provide unbiased selection of rams under CBBP. The surplus rams will be sold by RRC for profit. Several key measures such as micro-finance, co-ordination between stakeholders, market linkage and technical input for data collection and selection have been suggested to make the CBBP self-sustainable.

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Reference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree-based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single-Step approach (SSGBLUP) using both. For a scenario with no-selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single-Step approach to obtain accurate and unbiased prediction of GEBV.

Immune response against subclinical haemonchosis in Himalayan hill goats

Haemonchosis commonly occurs as chronic and subclinical infection in small ruminants, and understanding of immunological response against subclinical haemonchosis is of paramount importance for designing and implementing effective control strategies. The present study was designed to evaluate immunological response during subclinical haemonchosis, experimentally established in goats. Sixteen 5-6 month-old helminth naive kids were randomly allocated into one of two groups, infected and uninfected; the infected group being infected per os with 250 Haemonchus contortus larvae per kg body weight. Faecal, blood and serum samples were collected every third day up to 30 days post-infection (DPI), thereafter weekly up to 58 DPI to record changes in faecal egg count (FEC), haemoglobin (Hb), packed cell volume (PCV), peripheral eosinophil percentage and immunological parameters, such as macrophage cytokine interleukin-12 (IL-12), Th1 cytokine (IFN-γ), Th2 cytokines (IL-4, 13, 25, 33) and immunoglobulins (IgG and IgE). Pre-patent period of H. contortus in the present study was 18 days and eggs per gram (EPG) peaked on 30 DPI. The total reduction in body weight gain in the infected group was 26 g per day when compared with uninfected animals. Hb (7.35 ± 0.34 g/dL in infected animals compared with 9.76 ± 0.67 in control animals) and PCV levels (22 ± 1.54 g/dL in infected animals compared with 29.2 ± 1.27 in control animals) decreased significantly up to 44 DPI in infected group (P = 0.000). IL-4, IL-13, IL-33, IgG and IgE showed significant increase in infected animals at different periods. IFN-γ, IL-12 and IL-25 did not show any significant changes barring a steep rise of IFN-γ on 27 DPI. A positive correlation was observed between IgE and IL-4 in subclinical haemonchosis. Of particular note was that all the major cytokines, such as IFN-γ (P = 0.000), IL-4 (P = 0.000), IL-13 (P = 0.009), and both IgG (P = 0.000) and IgE (P = 0.003), were observed at the lowest concentration on 24 DPI. The effect of infection was found to be significant on cytokines with a strong interaction with time. Taken together, the data suggest that Th2 immune response is predominating in subclinical haemonchosis. The economic loss in term of body weight gain due to subclinical haemonchosis was considerable.

Kinetics of Interferon gamma and Interleukin-21 response following foot and mouth disease virus infection

Foot and mouth disease (FMD) is one of the most contagious diseases of cloven footed animals causing significant economic impediment in livestock production system. The immune response to FMD virus (FMDV) infection is regulated by a complex interplay between various cells, cytokines and other immune components. Based on the well established role of Interferon-gamma (IFN-γ) and Interleukin-21 (IL-21) in viral infections, this study aimed to determine expression level of these cytokines in clinically infected adults and calves; and the results were compared with those in the subclinically infected animals up to 120 days post outbreak (DPO) in a vaccinated cattle herd. The expression level of IFN-γ and IL-21 was assayed on 0, 7, 14, 28, 60, 90, and 120 DPO by enzyme linked immunosorbent assay (ELISA) with simultaneous assessment of FMDV structural protein-antibody titer against serotype 'O' by liquid phase blocking ELISA (LPBE) and nonstructural protein-antibody, a differential marker of infection, using r3AB3 indirect ELISA (r3AB3 I-ELISA). Although, the peak expression of IFN-γ was observed on 14 DPO across all categories of animals, the clinically infected animals registered a significant increase in IFN-γ level as compared to the subclinically infected population possibly due to the difference in the extent of virus replication and inflammation. The IL-21 level increased significantly during 14-28 DPO and highest expression was noticed on 28 DPO. The increase in the expression level of IFN-γ and IL-21 at 28 DPO correlated with the increase in antibody titer as determined by LPBE suggesting the role of these cytokines in augmenting immune response to FMDV infection.

Genetic diversity of Cahi DRB and DQB genes of caprine MHC class II in Sirohi goat

The objective of this study was to assess the genetic diversity of the Sirohi goat for DQB and DQB1 loci, and to study their association with antibody response induced by the Peste des petits ruminants (PPR) vaccine. A total of 360 Sirohi kids were studied using single stranded confirmation polymorphism (SSCP) followed by polymerase chain reaction sequence-based typing (PCR-SBT) for DQB and DQB1 diversities. The competitive enzyme-linked immuno-sorbent assay (C-ELISA) was used to evaluate immune response post-PPR vaccination. Study revealed rich diversity of major histocompatibility complex (MHC) region in goat. A total of 18 DQB and 15 DQB1 alleles were obtained which were new. Alleles DRB*0104 and DQB1*0101 were the most common. The approach of SSCP combined with PCR-SBT reflects cost-effective and most powerful approach to decipher the genetic diversity in complex MHC region. Study revealed variation in DQB and DQB1 genes in Sirohi flock along with high Wu-Kabat index. A total of 16 of the 89 amino acid residue sites in DQB and 19 of 86 residue sites in DQB1 had more than three amino acid substitutions. Positive evolutionary selection was evident in Sirohi for MHC region. Nonsignificant association of DQB and DQB1 genotypes with PPR virus (PPRV) vaccine response revealed complexity of the phenotype and importance of other factors for vaccine response. Rich diversity of DQB and DQB1 genes reflects the fitness of the population and importance of this locus for future selection programmes.

Genetic appraisal of serological response post vaccination against enterotoxaemia (ET) in Malpura and Avikalin sheep

Enterotoxaemia (ET) is a fatal enteric disease of small ruminants attributable to a toxigenic type of Clostridium perfringens. The key strategy for prevention of ET is the management and vaccination. Present study aimed at identifying the sources of variation for ET vaccine response especially against epsilon toxin in 173 sheep that included 83 Avikalin and 90 Malpura lambs raised at the institute flock in the semi-arid region of India. The mean age at vaccination was 90 days. Sera were tested by blocking ELISA. Study showed significant variability for response to ET vaccine. 5.2% animals had + positivity, 20.8% animals had ++ positivity, 51.4% animals had +++ positivity and 22.5% animals had ++++ positivity. Amongst environmental determinants, breed, season, sex and age at vaccination proved to be non-significant sources of variation (P > 0.05). MHC genotypes with DRB1 gene and DQA2 genes also revealed non-significant association with ET vaccine response; however, a trend of decreasing PI values with increasing ranks was observed. Study revealed strong response of epsilon toxin along with complexity of the ET vaccine response as phenotype to be explained by genetic and non-genetic factors. The importance of better management practices and vaccination is suggested for preventive measures.

The expression of IL6 and 21 in crossbred calves upregulated by inactivated trivalent FMD vaccine

Foot and mouth disease (FMD) is an economically important disease and a whole-virus inactivated trivalent virus vaccine is the mainstay for controlling the disease in India. The protective humoral immune response to FMD vaccination is a complex, but, tightly regulated process mediated by the interplay of interleukins (IL). Based on the specific role of IL6 and 21 in adaptive immune response, we hypothesized that inactivated trivalent FMD vaccine would stimulate IL6 and 21 expression in the circulating lymphocytes. The expressions of IL6 and 21 were assayed on 0, 28, 60, 90, and 120 d post-vaccination (DPV) by quantitative PCR (qPCR) with simultaneous assessment of FMDV antibody titer by liquid phase blocking ELISA. The results revealed that the peak expression of IL6 and 21 was on DPV 28 which correlated well with the FMDV antibody titer and plummeted to the prevaccination titer level by 60 DPV. As IL21 is the final effector of antibody production as compared to IL6, we investigated the expression of IL21 in calves that had protective titer (>1.8) with the unprotected group (<1.8). Expression of IL21 on 28 DPV was numerically higher in the protected than that of the unprotected group of calves.

Association of BoLA DRB3 alleles with variability in immune response among the crossbred cattle vaccinated for foot-and-mouth disease (FMD)

Polymorphism of bovine leukocyte antigen (BoLA) DRB3 gene is being intensively investigated for potential association with economically important diseases of cattle. Accordingly, we investigated the association of DRB3 Exon 2 polymorphism as evidenced by the variation in the binding pockets with variability in immune response to inactivated trivalent (O, A and Asia1) foot and mouth disease virus (FMDV) vaccine in a closed population of crossbred cattle. Antibody titer of ≥ 1.8 was set as the cut off value to distinguish the protected (≥ 1.8) and unprotected (<1.8) animals. Eleven different alleles of over 3% frequency were detected in the population. We found that DRB3 alleles 0201, 0801 and 1501 always ranked high for protective immune response whereas alleles 0701, 1103 and 1101 consistently ranked low for unprotected immune response for all the three serotypes. Rank correlation of DRB3 alleles among the three serotypes was positive, high in magnitude and statistically significant (P<0.05). Logistic regression analysis revealed that odds of protection from the vaccine were highest for all the three serotypes if allele (∗)1501 was present and strengthened the results of allele ranking. Predicted amino acid substitution in the peptide binding pockets revealed that all the important sites had high Wu-Kabat index. Similarly, specific residues in pockets were crucial for immune response to FMD vaccine. There were specific substitutions in un-protected alleles such as absence of acidic amino acids substituted by basic amino acid at β71, presence of non-polar cysteine or basic histidine at β30 and presence of polar tyrosine at β37. From the observations, we hypothesize that the substitutions lead to unique conformational changes in the protein products of the studied alleles that would associate with the protective or unprotective antibody response to FMDV vaccine. The knowledge has potential implications in future selection programs if integrated with the complete BoLA haplotype details and production traits of the herd.