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.

Comparative genetic analysis of frequentist and Bayesian approach for reproduction, production and life time traits showing favourable association of age at first calving in Tharparkar cattle

OBJECTIVE

The present study was aimed primarily for estimating various genetic parameters (heritability, genetic correlations) of reproduction (age at first calving [AFC], first service period [FSP]); production (first lactation milk, solid-not fat, and fat yield) and lifetime traits (lifetime milk yield, productive life [PL], herd life [HL]) in Tharparkar cattle to check the association of reproduction traits with lifetime traits through two different methods (Frequentist and Bayesian) for comparative purpose.

METHODS

Animal breeding data of Tharparkar cattle (n = 964) collected from Livestock farm unit of ICAR-NDRI Karnal for the period 1990 through 2019 were analyzed using a Frequentist least squares maximum likelihood method (LSML; Harvey, 1990) and a multitrait Bayesian-Gibbs sampler approach (MTGSAM) for genetic correlations estimation of all the traits. Estimated breeding values of sires was obtained by BLUP and Bayesian analysis for the production traits.

RESULTS

Heritability estimates of most of the traits were medium to high with the LSML (0.20±0.44 to 0.49±0.71) and Bayesian approach (0.24±0.009 to 0.61±0.017), respectively. However, more reliable estimates were obtained using the Bayesian technique. A higher heritability estimate was obtained for AFC (0.61±0.017) followed by first lactation fat yield, first lactation solid-not fat yield, FSP, first lactation milk yield (FLMY), PL (0.60±0.013, 0.60±0.006, 0.57±0.024, 0.57±0.020, 0.42±0.025); while a lower estimate for HL (0.38±0.034) by MTGSAM approach. Genetic and phenotypic correlations were negative for AFC-PL, AFC-HL, FSP-PL, and FSP-HL (-0.59±0.19, -0.59±0.24, -0.38±0.101 and -0.34±0.076) by the multi-trait Bayesian analysis.

CONCLUSION

Breed and traits of economic importance are important for selection decisions to ensure genetic gain in cattle breeding programs. Favourable genetic and phenotypic correlations of AFC with production and lifetime traits compared to that of FSP indicated better scope of AFC for indirect selection of life-time traits at an early age. This also indicated that the present Tharparkar cattle herd had sufficient genetic diversity through the selection of AFC for the improvement of first lactation production and lifetime traits.

Systems biology under heat stress in Indian cattle

Transcriptome profiling of Vrindavani and Tharparkar cattle (n = 5 each) revealed that more numbers of genes were dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.9 % of upregulated genes in Vrindavani downregulated in Tharparkar and 17.8% upregulated genes in Tharparkar downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study, we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.

Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle

The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.

Quantification and comparison of TLR2 activity in monocyte-derived macrophages of zebu and crossbred cattle

The present study was conducted to quantify and compare TLR2 (toll-like receptor 2) activity in monocyte-derived macrophages of zebu (Tharparkar) and crossbred (Holstein-Friesian × Jersey × Brown Swiss × Hariana) cattle. The cells were either induced with Pam3CSK4 or kept as control. The TLR2 activity was quantified in terms of IκB-α inhibitory subunit (NFKBIA) messenger RNA (mRNA) copies using real-time, one-step reverse transcription-polymerase chain reaction (RT-PCR). Toll-like receptor 2 activity of induced cells was in the range of 1060421 ± 477937 (n=3) to 3514715 ± 290222 (n=3) copies for Tharparkar cattle (n=7) and in the range of 1365532 ± 47243 (n=3) to 3016510 ± 172340 (n=3) copies for the crossbred cattle (n=7). For uninduced cells, this activity was within the range of 117 ± 51 (n=3) to 293 ± 103 (n=3) copies for the Thraparkar cattle (n=7), and in the range of 182 ± 122 (n=3) to 296 ± 88 (n=3) copies for the crossbred cattle (n=7). The TLR2 activity of induced cells in both groups was found to be significantly higher than that of the respective uninduced cells (P<0.0001). Furthermore, upon comparison, TLR2 activities of induced and uninduced cells of the Tharparkar were not found to be significantly different from those of the crossbred cattle (P=0.8154 and P=0.6670). In the present study, we have quantified and compared, for the first time, TLR2 activity in terms of NFKBIA mRNA copies in monocyte-derived macrophages of Tharparkar and crossbred cattle and found that both have equivalent TLR2 activity.

Impact of heat stress and hypercapnia on physiological, hematological, and behavioral profile of Tharparkar and Karan Fries heifers

Aim:

The present investigation was undertaken to study the impact of heat stress and hypercapnia on physiological, hematological, and behavioral profile of Tharparkar and Karan Fries (KF) heifers.

Materials and Methods:

The animals of both the breeds of Tharparkar and KF were exposed at different temperatures and CO₂ levels. Exposure conditions of 25°C, 400 ppm CO₂ level, and 60% relative humidity (RH) were taken as a control condition. The exposure conditions 40°C with two levels of CO₂ 500 ppm and 600 ppm with RH 55±5% and exposure conditions 42°C with two levels of CO₂ 500 ppm and 600 ppm with RH 55±5% were taken as treatments. The exposure period in each condition was 4 h daily for 5 consecutive days.

Results:

Physiological responses (respiration rate [RR], pulse rate [PR], and rectal temperature [RT]) were significantly (p<0.01) higher and different during all exposure conditions compared to control condition in both the breeds of cattle. KF heifers had higher RR, PR, and RT than Tharparkar heifers. Hematological parameters, namely, red blood cell, hemoglobin, and packed cell volume were significantly higher and different during all exposure condition than control in both the breeds, whereas no significant changes were observed in total leukocyte count and differential leukocyte count. Blood pH increased with increase in temperature and CO₂ levels and was significantly higher than control conditions. PCO₂ and base excess were significantly (p<0.05) lower, and PO₂ was higher during different exposure conditions than control in both breeds. Restlessness and excitement signs were observed in all the exposure conditions as compared to control condition in both the breeds.

Conclusion:

Changes in physiological responses, behavioral pattern, and hematological parameters reflect the current functional status of the body system, and it can be used as an index for assessing the adaptation capacity of cattle to predict changes occurring in climate variables due to increasing CO₂ levels and environmental temperature.

Expression of HSP70 genes in skin of zebu (Tharparkar) and crossbred (Karan Fries) cattle during different seasons under tropical climatic conditions

Skin is most important environmental interface providing a protective envelope to animals. It's always under the influence of both internal and external stressors. Heat shock proteins (HSP) are highly conserved stress proteins which play crucial roles in environmental stress tolerance and thermal adaptation. Present study was planned to observe the relative mRNA expression of inducible (HSP70.1 and HSP70.2) and constitutive (HSP70.8) HSP in skin of zebu (Tharparkar) and crossbred (Karan Fries) cattle during different seasons. Skin biopsies were collected from rump region of each animal, aseptically during winter, spring and summer season. Quantitative real time polymerase chain reaction was performed to examine the gene expression of constitutive (HSP70.8) and inducible (HSP70.1 and HSP70.2) HSP in skin of both the breeds during different seasons. Present study observed higher expression of both constitutive and inducible HSP genes in both the breeds during summer and winter than spring season, but magnitude of increase was higher during summer than winter. During summer season, expression pattern of HSPs in skin showed breed differences, where constitutive HSP expression was higher in Tharparkar than Karan Fries and that of inducible HSP was higher in Karan Fries than Tharparkar. Hence, present study suggested that HSP may be conveniently used as biomarkers for assessing protective response of skin against heat stress in zebu and crossbred cattle. Variation in expression between breeds is associated with their heat tolerance and thermal adaptability. In summary, skin of zebu cattle (Tharparkar) is more resistant to summer stress than crossbred (Karan Fries), providing greater protection against heat stress during summer season. Superior skin protective mechanism of zebu (Tharparkar) than crossbred (Karan-Fries) cattle against heat stress may contribute to superior adaptability of zebu cattle to tropical climatic conditions than crossbreed.

Association of ATP1A1 gene polymorphism with thermotolerance in Tharparkar and Vrindavani cattle

Aim:

One of the major biochemical aspects of thermoregulation is equilibrium of ion gradient across biological membranes. Na⁺/K⁺-ATPase, a member of P type-ATPase family, is a major contributor to the mechanism that actively controls cross-membrane ion gradient. Thus, we examined ATP1A1 gene that encodes alpha-1 chain of Na⁺/K⁺-ATPase, for genetic polymorphisms.

Materials and Methods:

A total of 100 Vrindavani (composite cross strain of Hariana x Holstein-Friesian/Brown Swiss/Jersey) and 64 Tharparkar (indigenous) cattle were screened for genetic polymorphism in ATP1A1 gene, using polymerase chain reaction single-strand conformation polymorphism and DNA sequencing. For association studies, rectal temperature (RT) and respiration rate (RR) of all animals were recorded twice daily for 3 seasons.

Results:

A SNP (C2789A) was identified in exon 17 of ATP1A1 gene. Three genotypes namely CC, CA, and AA were observed in both, Vrindavani and Tharparkar cattle. The gene frequencies in Tharparkar and Vrindavani for allele A were 0.51 and 0.48, and for allele C were 0.49 and 0.52, respectively, which remained at intermediate range. Association study of genotypes with RT and RR in both cattle population revealed that the animals with genotype CC exhibited significantly lower RT and higher heat tolerance coefficient than CA and AA genotypes.

Conclusion:

Differential thermoregulation between different genotypes of ATP1A1 gene indicate that the ATP1A1 gene could be potentially contributing to thermotolerance in both, Tharparkar, an indigenous breed and Vrindavani, a composite crossbred cattle.

Peripheral blood leukocytes transcriptomic signature highlights the altered metabolic pathways by heat stress in zebu cattle

High temperature during summer greatly affects animal production due to altered reproductive and metabolic functions. However, information regarding high throughput analysis of change in gene expression in diary animals are relatively nil. In present study, gene expression profiling by microarray was done in peripheral blood leukocytes of heat exposed (42 °C, 4h) cattle (n=3), Tharparkar (Bos indicus). A total 460 transcripts were differentially expressed with a fold change of ⩾ 2. Randomly selected real-time validation showed that 73.08% correlation with microarray data. Functional annotation and pathway study of the DEGs reveals that, up-regulated genes significantly (P<0.05) affect the protein processing and NOD like receptor pathways, while down regulated genes were significantly (P<0.05) found to associated with Glycolytic pathways. In conclusion, the present study showed that heat stress affects expression of significant number of genes in peripheral blood leukocytes and further analysis is required to understand their functional role in livestock.