Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India

The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.

Imputation accuracy for genomic selection using embryo biopsy samples in Gir

The aim of this study was to establish a platform for genomic selection of in vitro-fertilized (IVF) Gir embryos. Multiple displacement amplification (MDA)-based embryo biopsy samples were genotyped, and genomic estimated breeding values (GEBV) for milk yield (305MY) were calculated. The concordance of GEBV and accuracy between embryo biopsies and the respective liveborn were assessed. Imputation was performed using two panels (Z-Chip and Bovine HD, Illumina) based on a database of 73,110 lactating cow's database and pedigree files from 147,131 animals. Biopsied embryos had similar pregnancy rates (39% vs 40%), pregnancy loss rates (18% vs 20%), and pregnancy length compared to Control embryos. After genotyping, low call rate means were detected for biopsy samples compared to the respective calf samples (0.80 vs 0.98). Imputation presented 0.83 (Z-Chip) and 0.96 (HD) accuracy (CORRanim). Embryo GEBV accuracy levels were higher in BovineHD imputation (0.82) than Z-Chip imputation (0.55) or no imputation (0.62), and the correlation between embryo/calf pairs' accuracy was 0.85 for BovineHD imputation, 0.11 for Z-Chip imputation, and 0.02 for no imputation. GEVB estimates correlation between embryo/calf pairs was 0.87 for BovineHD imputation, 0.80 for Z-Chip imputation, and 0.41 before imputation. The call rate of embryo samples did not affect the correlation between embryo/calf pairs for accuracy and GEBV before and after BovineHD imputation. Embryos obtained on the same farm presented GEBV 305MY differences of up to 800 kg, emphasizing the expected impact of embryo genomic selection for the Gir breed.

Outstanding Gir oocyte donors: How does individual factor affect in vitro embryo production efficiency?

The oocyte donor plays a pivotal role in bovine in vitro embryo production (IVP) success. The individual factor affects blastocyst/oocyte ratio and determine the existence of outstanding performing animals. The aim of this study was to assess the extent of individual factor effect to IVP efficiency, in a population of Gir oocyte donors. Extreme (high or low IVP efficiency based on blastocyst/oocyte ratio) animals were selected out of a population of 250 oocyte donors (1,734 observations) to form high (>0.48, n = 40), average (0.17-0.48, n = 168), and low (<0.17, n = 42) efficiency donor groups. Cumulus-oocyte complex indicators (total number, IVF-grade number, and IVF-grade/total ratio) were lower (p < 0.05) in high efficiency donors. The number of blastocysts per OPU was analyzed for highest performing bull, and an increase (p < 0.05) in high efficiency donors and a decrease (p < 0.05) in low efficiency donors were noticed, compared to average efficiency donors. The number of pregnancies obtained per OPU was affected (p = 0.017) by donor's efficiency (low:0.60 ± 0.09 $$ 0.60\pm 0.09 $$ , average:1.17 ± 0.07 $$ 1.17\pm 0.07 $$ , high:2.57 ± 0.26 $$ 2.57\pm 0.26 $$ ), being 4.3-fold higher in high than in low efficiency donors. We conclude that producing embryos from high efficiency blastocyst/oocyte ratio donors increases blastocyst and pregnancy numbers by OPU, being an important indicator for donor selection in IVP programs.

Genetic and non-genetic factors affecting semen production and quality characteristics of Gir cattle breed under semi-arid climate

Aim

This study aims to evaluate genetic and non-genetic factors influencing semen production potential of Gir bulls.

Materials and Methods

Data on semen quantity (n=6911) and quality (n=466) available from January 2011 to December 2018 at BAIF's frozen semen station, Jind, Haryana, India, were utilized for the study. Factors, namely, season of collection, age at collection, and bull (random effect) were studied for their effect on quantitative and qualitative semen traits. Least square means for the traits were obtained using a general linear model. The effect of age within bull for repeatable traits was analyzed using a longitudinal model with age as the control variable. Multivariate analysis using mixed repeatability model equation was utilized to estimate bull effect correlation (genetic + permanent environmental correlation), phenotypic correlations, and repeatability.

Results

The overall least square means of ejaculate volume, sperm concentration, total sperms, initial and post-thaw motility, hypo-osmotic swelling test, and acrosome integrity of frozen semen were 6.62±0.03 ml, 1.22±0.01 10⁹/ml, 8.09±0.05 10⁹/ejaculate, 75.78±0.001%, 55.92±0.0001%, 55.13±0.005%, and 71.08±0.001%, respectively. The season of the collection showed a significant effect on volume, concentration, total sperm, and initial motility. The performance of bulls was superior in summer season, followed by winter and monsoon. Increase in semen attributes during summer season was due to the effect of lower temperature on sensitive stages of spermatogenesis. Age at collection had a significant effect on all semen traits. Volume and total sperm count showed increasing trend while concentration showed a decreasing trend with an increase in age. Motility and quality traits did not show any particular pattern. Individual bulls showed differences in all the semen performance traits with age. The repeatability of the traits ranged from 0.04 (HOST) to 0.58 (acrosome integrity). Bull effect correlation ranged from -0.73 (initial motility and acrosome integrity) to 0.93 (HOST and acrosome integrity).

Conclusion

Individual bulls showed variation in traits measured over age. The result of the study could be utilized in suggesting suitable management plans to achieve the desired profit by improving semen quality in Gir bulls.

Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations

Background

Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis.

Results

We identified 46 previously reported alleles and no novel variants. Of note, 1/3 of the alleles were detected only in Zebu cattle. Comparison of the degree of genetic variability at the population and sequence levels with genetic distance in the three above mentioned breeds and nine previously reported breeds revealed that Zebu breeds had a gene diversity score higher than 0.86, a nucleotide diversity score higher than 0.06, and a mean number of pairwise differences greater than 16, being similar to those estimated for other cattle breeds. A neutrality test revealed that only Nellore-Brahman cattle showed the even gene frequency distribution expected under a balanced selection scenario. The F_ST index and the exact G test showed significant differences across all cattle populations (F_ST = 0.057; p <  0.001). Neighbor-joining trees and principal component analysis identified two major clusters: one comprising mainly European Taurine breeds and a second comprising Zebu breeds. This is consistent with the historical and geographical origin of these breeds. Some of these differences may be explained by variation of amino acid motifs at antigen-binding sites.

Conclusions

The results presented herein show that the historical divergence between Taurine and Zebu cattle breeds is a result of origin, selection, and adaptation events, which would explain the observed differences in BoLA-DRB3 gene diversity between the two major bovine types. This allelic information will be important for investigating the relationship between the major histocompatibility complex and disease, and contribute to an ongoing effort to catalog bovine MHC allele frequencies according to breed and location.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0618-7) contains supplementary material, which is available to authorized users.

Traditional versus molecular based detection of a rare occurrence of babesiosis in Gir calf and its therapeutic management

A 30-day old Gir calf was brought to Veterinary Polyclinic with symptoms of high fever, dullness, dyspnea, pale mucus membrane and haemoglobinuria. Blood sample was collected and microscopic examination of thin blood smear confirmed the case of acute babesiosis. It was further confirmed by polymerase chain reaction that amplified an approximately 410 bp portion of the ssu-rDNA of Babesia spp. The calf was managed with diminazene aceturate @5 mg/kg (Berenil) intramuscularly followed by supportive therapy including intravenous infusions. The present study reports a rare case of bovine babesiosis, its clinical variants, diagnosis, hematology and therapeutic management.

Prevalence of gastrointestinal parasites in bovines in and around Junagadh (Gujarat)

Coprological examination of 416 bovine faecal samples revealed the presence of parasitic stages of Toxocara vitulorum, strongyles, Strongyloides spp., Fasciola spp., amphistomes, coccidia (Eimeria spp. and Cryptosporidium spp.) and Buxtonella sulcata. About 42 % (n = 302) faecal samples from cattle and 36 % (n = 114) samples from buffaloes were positive for gastrointestinal (GI) parasitic infections. Both cattle (14.57 %) and buffalo (15.79 %) had the highest incidence of Buxtonella sulcata, respectively. The overall incidence of GI parasitic infections in young animals (below 1 year) was higher followed by older (more than 5 years) and adult animals (1-5 years) and the difference was statistically significant (p < 0.05). Non descriptive breeds of bovines showed more parasitic infections than pure breeds, the difference being statistically non-significant (p > 0.05). Season wise GI parasitic infections were recorded to be non-significantly (p > 0.05) higher in monsoon (48.38 %) followed by summer (39 %) and winter (34.61 %) in cattle. There was no significant variation of GI infections in buffaloes in relation to season though highest prevalence was documented in monsoon (44.89 %) followed by winter (35.71 %) and summer (24.32 %). Similarly, sex wise females recorded higher infection rates than males in bovines and the difference being statistically non-significant (p > 0.05).