Overexpression of genes associated with hypoxia in cattle adapted to Trans Himalayan region of Ladakh

Hypoxia related genes modulate in similar fashion in skin fibroblast cells of yak (Bos grunniens) adapted to high altitude and native cows (Bos indicus) adapted to tropical climate during hypoxia stress

The present study was conducted to understand transcriptional response of skin fibroblast of yak (Bos grunniens) and cows of Bos indicus origin to hypoxia stress. Six primary fibroblast cell lines derived from three individuals each of Ladakhi yak (Bos grunniens) and Sahiwal cows (Bos indicus) were exposed to low oxygen concentration for a period of 24 h, 48 h and 72 h. The expression of 10 important genes known to regulate hypoxia response such as HIF1A, VEGFA, EPAS1, ATP1A1, GLUT1, HMOX1, ECE1, TNF-A, GPx and SOD were evaluated in fibroblast cells of Ladakhi yak (LAY-Fb) and Sahiwal cows (SAC-Fb) during pre- and post-hypoxia stress. A panel of 10 reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) were also evaluated for their expression stability to perform accurate normalization. The expression of HIF1A was significantly (p < 0.05) induced in both LAY-Fb (2.29-fold) and SAC-Fb (2.07-fold) after 24 h of hypoxia stress. The angiogenic (VEGFA), metabolic (GLUT1) and antioxidant genes (SOD and GPx) were also induced after 24 h of hypoxia stress. However, EPAS1 and ATP1A1 induced significantly (p < 0.05) after 48 h whereas, ECE1 expression induced significantly (p < 0.05) at 72 h after exposure to hypoxia. The TNF-alpha which is a pro-inflammatory gene induced significantly (p < 0.05) at 24 h in SAC-Fb and at 72 h in LAY-Fb. The induction of hypoxia associated genes indicated the utility of skin derived fibroblast as cellular model to evaluate transcriptome signatures post hypoxia stress in populations adapted to diverse altitudes.

Effect of short-term exposure to high-altitude hypoxic climate on feed-intake, blood glucose level and physiological responses of native and non-native goat

The exposure to high altitude and cold stress poses challenges in maintaining normal physiological standards and body homeostasis in non-native animals. To enhance our understanding of the physiology of native and non-native goats in high-altitude environments, we conducted a comparative study to examine the impact of natural hypoxic and cold stress conditions on their feed intake (FIT) and associated changes in physiological responses, including plasma glucose concentration (PGC). The study took place at an altitude of 3505.2 m above mean sea level and involved twenty-two healthy females from two different breeds of goats. This study was conducted over a period of 56 days after the arrival of non-native Black Bengal goats (BBN) and compared with native Changthangi (CHAN) goats. Both groups were extensively reared in a natural high-altitude and cold-stress environment in Leh, India, and were subjected to defined housing and management practices. The parameters evaluated included FIT, PGC, respiration rate, heart rate, pulse rate, and rectal temperature. High altitudes had a significant (p < 0.05) impact on FIT, PGC, respiration rate, heart rate, pulse rate, and rectal temperature in BBN, whereas these parameters remained stable in CHAN throughout the study period. Additionally, the detrimental effects of high-altitude stress were more pronounced in non-native goats compared to native goats. These findings suggest that physiological responses in non-native goats tend to stabilize after an initial period of adverse effects in high-altitude environments. Based on the physiological responses and glucose concentration, it is recommended to pay special attention to the nutrition of non-native goats for up to the third week (21 days) after their arrival in high-altitude areas.

Genomic adaptation of Ethiopian indigenous cattle to high altitude

The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.

"Not All Who Wander Are Lost": The Life Transitions and Associated Welfare of Pack Mules Walking the Trails in the Mountainous Gorkha Region, Nepal

Equids in general experience transient lives where ownership may change multiple times, for working equids this can be more extreme where ownership changes are not only numerous but abrupt, and situations encountered prove difficult, diverse and tough for equids to adapt. In this study, we investigate the life cycle of pack mules in Nepal, investigating the challenges they face during their lives through to end of life. To gain insight into the lives of mules, we conducted semi-structured interviews and livelihood surveys with 27 key informants, gathering the perspectives of the people working with mules. Welfare assessments of the mules were undertaken via the Equid Assessment Research and Scoping tool (EARS) by a trained assessor. Mules had to adapt swiftly to changes in industry type, enduring long distance transportation in overloaded vehicles and across country borders with no checks for biosecurity or welfare. Mules had to show swift adaptation to their new environment, to respond to and learn new tasks via inhumanely administered training, using inappropriate techniques, delivered by owners lacking in understanding of mule behaviour and learning. Environmental conditions were often hard; the negotiation of difficult terrain and challenging weather conditions during monsoon and subsequent high-altitude working without acclimatisation likely pushed mules to their biological limits. This study investigates the lives of a population of mules in the mountains of Nepal, developing a better understanding of their needs and their 'truth' or 'telos' informing what measures will help them to thrive.

Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh

The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.

Identification of Internal Reference Genes in Peripheral Blood Mononuclear Cells of Cattle Populations Adapted to Hot Arid Normoxia and Cold Arid Hypoxia Environments

To estimate gene expression in a reliable manner, quantitative real-time polymerase chain reaction data require normalisation using a panel of stably expressed reference genes (RGs). To date, information on an appropriate panel of RGs in cattle populations reared at cold arid high-altitude hypoxia and hot arid tropical normoxia environments is not available. Therefore, the present study was carried out to identify a panel of stably expressed RGs from 10 candidate genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, HMBS, B2M, RPS15, and ACTB) in peripheral blood mononuclear cells (PBMCs) of cattle populations reared at cold arid high-altitude hypoxia and hot arid normoxia environments. Four different statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder were used to assess the stability of these genes. A total of 30 blood samples were collected: six adult heifers each of Ladakhi (LAC) and Holstein Frisian crosses (HFX) and 4 Jersey (JYC) cows from cold arid high-altitude hypoxia environments (group I) and five adult heifers each of Sahiwal (SAC), Karan Fries (KFC), and Holstein Friesian (HFC) cows from hot arid normoxia environments (group II). Combined analysis of group I and group II resulted in identification of a panel of RGs like RPS9, RPS15, and GAPDH that could act as a useful resource to unravel the accurate transcriptional profile of PBMCs from diverse cattle populations adapted to distinct altitudes.

Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.

Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions

The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions. Blood samples were collected after the exposure to the TN and HS conditions and the relative expression of genes was measured by qPCR. The bulls exhibited lower expression of ATP1A1 in the HS condition than in the TN condition (1.98 ± 0.27 and 2.86 ± 0.26, P = 0.02), while the relative expression of NR3C1, POMC, and LEP did not differ (P > 0.05) between climatic conditions. The breed and feed intake influenced NPY and LEP expression levels (P < 0.05). Different climate conditions associated with residual feed intake can modify the gene expression patterns of ATP1A1 and NPY. The association observed among all genes studied shows that they are involved in appetite control. Bos taurus and Bos indicus bulls exhibited similar adaptability to tropical climate conditions.

Haematological and biochemical profiling of Ladakhi cow: A native cattle of high altitude Leh-Ladakh, India

Ladakhi cattle is a native breed of cattle which is well adapted to hypobaric-hypoxia and cold-stress conditions prevalent at high altitude. These cattle are the main source of A2 quality milk. However, their utility, health and dairy production managements were not standardised for optimum dairy farm economics. Moreover, the haematological and biochemical parameters have not been investigated in details in adult Ladakhi cows, which is the primary requirement of farm health managements. Thus, the objective of this study was to examine the haematology and biochemical parameters in adult Ladakhi cow to establish baseline reference values. Clinically healthy female Ladakhi cattle (10) were selected from the Ladakhi cattle research section, DIHAR, Leh. The resulted haematological and biochemical parameters were compared with already reported reference values for low lander cattle and high lander native and crossbred cattle. Haematological findings revealed that RBC, Hb, heamatocrit, MCV and WBC were within the reference range, rather MCH and MCHC values were more than the reference range. Biochemical findings revealed that albumin, glucose, creatinine, uric acid, alkaline phosphatase, and aspartate aminotransferase were within the reference range limits of low lander. However, urea, triglycerides, total protein values were higher than the reference range and calcium was less than the reference range. These findings indicated that the native Ladakhi cattle are in healthy condition and metabolically adapted to high altitude stress. Hence, these hemato-biochemical profile could be the good biomarkers to evaluate their health status in high altitude stress condition.

Chemometric Analysis of Antioxidant and Mineral Elements in Colostrum of Native and Non-native Goat Breeds to Hypoxic Conditions at High Altitude

Colostrum of goat is a well-known nutritional source of animal product, which is attributed to innumerable nutritional properties. To enrich nutritional resources for understanding various nutritional values of animal product at high altitude, chemometric analysis of antioxidant and mineral element study was carried out by comparing antioxidants capacity, free radical scavenging activity, and certain mineral elements in colostrums of native and non-native goat breeds. Colostrum samples were collected from native Changthangi (CNG) and non-native Sirohi (SIRO) goat breeds, situated at naturally exposed high altitude of 3505.2 m above mean sea level. The antioxidant of samples was measured by ferric reducing ability of plasma (FRAP) and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) activity assay, and mineral elemental quantification of Fe, Mg, Mn, Zn, Co, Cu, K, Ca, B, Ni, and Cr was performed using ICP-OES. The values of FRAP, DPPH, and Fe, Mg, Mn, Zn, Co, Cu, K, and Ca in colostrums of native goat breed was significantly (p ≤ 0.05) higher than the non-native goat. These data conclude that high altitude native goat has more antioxidant and mineral elements in colostrum than non-native colostrum. This study could provide a basis for establishing the role of colostrum supplements as a natural source to strengthen the endurance to modalities for the survival of newborn kids of goat within the native high altitude environment. This is the first report of a comparative chemometric analysis of colostrums of goat species and can be utilized to characterize the nutritional aspect of animal product with unique antioxidant and mineral nutrients composition in colostrum of goat.

Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan

The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.