Selection signatures for high altitude adaptation in livestock: A review.

High altitude adapted livestock species (cattle, yak, goat, sheep, and horse) has critical role in the human socioeconomic sphere and acts as good source of animal source products including milk, meat, and leather, among other things. These species sustain production and reproduction even in harsh environments on account of adaptation resulting from continued evolution of beneficial traits. Selection pressure leads to various adaptive strategies in livestock whose footprints are evident at the different genomic sites as the "Selection Signature". Scrutiny of these signatures provides us crucial insight into the evolutionary process and domestication of livestock adapted to diverse climatic conditions. These signatures have the potential to change the sphere of animal breeding and further usher the selection programmes in right direction. Technological revolution and recent strides made in genomic studies has opened the routes for the identification of selection signatures. Numerous statistical approaches and bioinformatics tools have been developed to detect the selection signature. Consequently, studies across years have identified candidate genes under selection region found associated with numerous traits which have a say in adaptation to high-altitude environment. This makes it pertinent to have a better understanding about the selection signature, the ways to identify and how to utilize them for betterment of livestock populations as well as farmers. This review takes a closer look into the general concept, various methodologies, and bioinformatics tools commonly employed in selection signature studies and summarize the results of recent selection signature studies related to high-altitude adaptation in various livestock species. This review will serve as an informative and useful insight for researchers and students in the field of animal breeding and evolutionary biology.

Heat stress adaptation in cows - Physiological responses and underlying molecular mechanisms.

Heat stress is a key abiotic stressor for dairy production in the tropics which is further compounded by the ongoing climate change. Heat stress not only adversely impacts the production and welfare of dairy cows but severely impacts the economics of dairying due to production losses and increased cost of rearing. Over the years, selection has ensured development of high producing breeds, however, the thermotolerance ability of animals has been largely overlooked. In the past decade, the ill effects of climate change have made it pertinent to rethink the selection strategies to opt for climate resilient breeds, to ensure optimum production and reproduction. This has led to renewed interest in evaluation of the impacts of heat stress on cows and the underlying mechanisms that results in their acclimatization and adaptation to varied thermal ambience. The understanding of heat stress and associated responses at various level of animal is crucial to device amelioration strategies to secure optimum production and welfare of cows. With this review, an effort has been made to provide an overview on temperature humidity index as an important indicator of heat stress, general effect of heat stress in dairy cows, and impact of heat stress and subsequent response at physiological, haematological, molecular and genetic level of dairy cows.

Bayesian estimates for genetic and phenotypic parameters of growth traits in Sahiwal cattle.

Analyses were carried out for the estimation of (co)variance components and genetic parameters for birth weight (BWT), 6-month weight (6WT), 12-month weight (12WT), 18-month weight (18WT), 24-month weight (24WT), 30-month weight (30WT), 36-month weight (36WT), weight at first service (WFS), and weight at first calving(WFC) in Sahiwal cattle. Data for 802 lifetime records (raw data) were collected over a period of 30 years (1990-2019) for various growth traits in the herd for Sahiwal cows maintained at the livestock farm unit of ICAR-NDRI Karnal, Haryana, India. Bayesian estimates using the multi-trait Gibbs sampling animal model approach were calculated in the present study. Total heritability for BWT, 6WT, 12WT, 18WT, 24WT, 30WT, 36WT, WFS, and WFC by Bayesian modeling was estimated as 0.22 ± 0.0052, 0.47 ± 0.0037, 0.30 ± 0.0025, 0.65 ± 0.0021, 0.32 ± 0.0039, 0.33 ± 0.0027, 0.39 ± 0.0031, 0.49 ± 0.0020, and 0.57 ± 0.0023, respectively, along with its Monte Carlo error in Sahiwal cattle. Direct genetic covariances between body weight traits were ranging from - 2762.5 for 18WT and WFC to 4739.6 between WFS and WFC. Environmental covariances were ranging from - 169.98 for 30WT and 36WT to 4539.4 between WFS and WFC. Family relationships as well as the existing interaction effects between two or more traits in opposite direction effect lead to negative estimates for genetic covariances between some of the combinations with various growth traits. Although most of the estimates for posteriori were somewhat skewed, the marginalization effect enabled them to fit into the Gaussian distribution, by comparing the mean, mode, and median with each other. Results suggest that genetic progress through growth traits can be achieved if the selection is carried out for highly heritable 18-month weight as well as for the selection of pubertal and fertility traits, viz., 24WT, 30WT, 36WT, WFS, and WFC with a balanced feeding and optimum management.

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.

Characterization of thermo-physiological, hematological, and molecular changes in response to seasonal variations in two tropically adapted native cattle breeds of Bos indicus lineage in hot arid ambience of Thar Desert.

The selection of climate resilient animal is necessary to secure the future of sustainable animal production. The present investigation therefore was an effort to unravel answers to the adaptation at physiological, hematological, and molecular levels in cows of hot arid region that helps them to survive harsh environment, to continue production and reproduction. This investigation was carried out in indicine cows over a period of one year, encompassing four seasons, wherein physiological data of 50 animals, hematological data of 15 animals, and gene expression profile of 5 animals from each of Sahiwal and Kankrej breeds per season was generated. In total, 5600 physiological observations, 1344 hematological observations, and 480 molecular samples were processed. The meteorological data revealed a high diurnal variation of temperature across seasons, with THI exceeding 80 during the months of summer and hot-humid seasons, indicating significant heat stress (HS). The physiological parameters showed an increasing trend with the incremental THI, with significantly (p < 0.05) higher values of rectal temperature (RT), respiration rate (RR), pulse rate (PR), and body surface temperature (BST) at ventral (VT), lateral (LT), dorsal (DT), and frontal (FT), in both breeds recorded during HS. The hematological pictures also revealed significant (p < 0.05) seasonal perturbations in erythrocytic and leucocytic parameters. Moreover, the molecular response was driven by a significant (p < 0.05) upregulation of all the key HSPs, HSP70, HSP90, HSP60, and HSP40, except HSP27 during the hotter months of summer and hot-humid seasons. The expression of HSF1, an important transcriptional regulator of  HSP70 was also significantly (p < 0.05) upregulated during summer season in both breeds. All the molecular chaperones revealed a significant upregulation during the summer season, followed by a decreasing trend by hot-humid season. The study indicated a well-developed thermotolerance mechanism in animals of both breeds, with Kankrej cows exhibiting better thermotolerance compared to Sahiwal cows.