A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep

Abstract Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

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Resilience of Small Ruminants to Climate Change and Increased Environmental Temperature: A Review

Animals ◽

10.3390/ani10050867 ◽

2020 ◽

Vol 10 (5) ◽

pp. 867 ◽

Cited By ~ 8

Author(s):

Aleena Joy ◽

Frank R. Dunshea ◽

Brian J. Leury ◽

Iain J. Clarke ◽

Kristy DiGiacomo ◽

...

Keyword(s):

Climate Change ◽

Heat Stress ◽

Ambient Temperature ◽

Environmental Conditions ◽

Environmental Temperature ◽

Small Ruminant ◽

Small Ruminants ◽

Continuous Exposure ◽

Hot Environments ◽

The Impact

Climate change is a major global threat to the sustainability of livestock systems. Climatic factors such as ambient temperature, relative humidity, direct and indirect solar radiation and wind speed influence feed and water availability, fodder quality and disease occurrence, with production being most efficient in optimal environmental conditions. Among these climatic variables, ambient temperature fluctuations have the most impact on livestock production and animal welfare. Continuous exposure of the animals to heat stress compromises growth, milk and meat production and reproduction. The capacity of an animal to mitigate effects of increased environmental temperature, without progressing into stress response, differs within and between species. Comparatively, small ruminants are better adapted to hot environments than large ruminants and have better ability to survive, produce and reproduce in harsh climatic regions. Nevertheless, the physiological and behavioral changes in response to hot environments affect small ruminant production. It has been found that tropical breeds are more adaptive to hot climates than high-producing temperate breeds. The growing body of knowledge on the negative impact of heat stress on small ruminant production and welfare will assist in the development of suitable strategies to mitigate heat stress. Selection of thermotolerant breeds, through identification of genetic traits for adaption to extreme environmental conditions (high temperature, feed scarcity, water scarcity), is a viable strategy to combat climate change and minimize the impact on small ruminant production and welfare. This review highlights such adaption within and among different breeds of small ruminants challenged by heat stress.

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The Impact of Anthropogenic Climate Change on Egyptian Livestock Production

Animals ◽

10.3390/ani11113127 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3127

Author(s):

Amira A. Goma ◽

Clive J. C. Phillips

Keyword(s):

Climate Change ◽

Heat Stress ◽

Milk Production ◽

Human Population ◽

Production Systems ◽

Livestock Production ◽

Mitigation Strategies ◽

Animal Products ◽

Alternative Scenarios ◽

The Impact

Egypt is one of the hottest countries in the world, and extreme climate events are becoming more frequent, which is consistent with the warming of the planet. The impact of this warming on ecosystems is severe, including on livestock production systems. Under Egyptian conditions, livestock already suffer heat stress periods in summer. The predicted increases in temperature as result of climate change will affect livestock production by reducing growth and milk production because of appetite suppression and conception rate reductions and will increase animal welfare concerns. In severe cases, these effects can result in death. We review the heat stress effects on livestock behaviour, reproduction, and production in the context of predicted climate change for Egypt over the course of this century and offer alternative scenarios to achieve food security for a growing human population. As an example, we combine predictions for reduced milk production during heat stress and human population trajectories to predict that milk availability per person will decline from 61 kg/year in 2011 to 26 kg/year in 2064. Mitigation strategies are discussed and include the substitution of animal-based foods for plant-based foods and laboratory-grown animal products.

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New loci and neuronal pathways for resilience to heat stress in animals

10.1101/2021.02.04.429719 ◽

2021 ◽

Author(s):

Evans K. Cheruiyot ◽

Mekonnen Haile-Mariam ◽

Benjamin G. Cocks ◽

Iona M. MacLeod ◽

Ruidong Xiang ◽

...

Keyword(s):

Heat Stress ◽

Milk Production ◽

Heat Tolerance ◽

Genome Wide Association ◽

Receptor Interaction ◽

Sequence Variants ◽

Neuronal System ◽

Vertebrate Species ◽

Genome Wide ◽

Management Approaches

AbstractClimate change and resilience to warming climates have implications for humans, livestock, and wildlife. The genetic mechanisms that confer thermotolerance to mammals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.Author summaryWhile understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. The ability to tolerate heat varies across individuals, with substantial genetic control of this complex trait. Dairy cattle are excellent model in which to find genes associated with individual variations in heat tolerance since they significantly suffer from heat stress due to the metabolic heat of lactation. By genome-wide association studies of more than 29,000 cows with 15 million sequence variants and controlled phenotype measurements, we identify many new loci associated with heat tolerance. The biological functions of these loci are linked to the neuronal system and neuroactive ligand-receptor interaction functions. Also, several putative causal mutations for heat tolerance are at genomic sites that are otherwise evolutionarily conserved across 100 vertebrate species. Overall, our findings provide new insight into the molecular and biological basis of heat tolerance that can help to develop genetic and management approaches to combat heat stress.

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Genomic Selection Improves Heat Tolerance in Dairy Cattle

Scientific Reports ◽

10.1038/srep34114 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 35

Author(s):

J. B. Garner ◽

M. L. Douglas ◽

S. R. O Williams ◽

W. J. Wales ◽

L. C. Marett ◽

...

Keyword(s):

Heat Stress ◽

Dairy Cattle ◽

Genomic Selection ◽

Milk Production ◽

Heat Tolerance ◽

Dairy Products ◽

Dairy Herds ◽

Physiological Indicators ◽

Genome Wide ◽

Heat Tolerant

Abstract Dairy products are a key source of valuable proteins and fats for many millions of people worldwide. Dairy cattle are highly susceptible to heat-stress induced decline in milk production, and as the frequency and duration of heat-stress events increases, the long term security of nutrition from dairy products is threatened. Identification of dairy cattle more tolerant of heat stress conditions would be an important progression towards breeding better adapted dairy herds to future climates. Breeding for heat tolerance could be accelerated with genomic selection, using genome wide DNA markers that predict tolerance to heat stress. Here we demonstrate the value of genomic predictions for heat tolerance in cohorts of Holstein cows predicted to be heat tolerant and heat susceptible using controlled-climate chambers simulating a moderate heatwave event. Not only was the heat challenge stimulated decline in milk production less in cows genomically predicted to be heat-tolerant, physiological indicators such as rectal and intra-vaginal temperatures had reduced increases over the 4 day heat challenge. This demonstrates that genomic selection for heat tolerance in dairy cattle is a step towards securing a valuable source of nutrition and improving animal welfare facing a future with predicted increases in heat stress events.

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Impact of climate change (heat stress) on livestock: adaptation and mitigation strategies for sustainable production

Agricultural Reviews ◽

10.18805/ag.r-1777 ◽

2018 ◽

Author(s):

S. K Das

Keyword(s):

Climate Change ◽

Heat Stress ◽

Milk Production ◽

Livestock Production ◽

Mitigation Measures ◽

Economic Losses ◽

Meat Production ◽

Impact Of Climate Change ◽

Formidable Challenge ◽

Adaptation And Mitigation

It is reported sporadically in different countries of the world including India that climate change has adverse effect on livestock productivity, particularly on milk production and growth which is reflected in meat production indirectly. Climate Change poses formidable challenge to the development of livestock sector in India. The rise in temperature between 2 to 3 °C over the entire country together with increased humidity resulting from climate change is likely to aggravate the heat stress in dairy animals resulting in reduced growth and milk production. Quantification of these potential impacts of climate on livestock production allows producers to gain a better understanding of the magnitude of the changes in production levels and potential indicators of livestock response, on which managemental actions depend. Economic losses resulting from temperature-induced reductions in production may justify adaptation and mitigation of adverse impact of climate change on animal. So in this paper impact of climate change on feed intake, production, reproduction, physiology, disease occurrence in livestock, poultry etc were discussed. Moreover different adaptive and mitigation measures were discussed to reduce adverse negative effect of climate change for sustainable livestock production

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Big dairy data to unravel effects of environmental, physiological and morphological factors on milk production of mountain-pastured Braunvieh cows

Royal Society Open Science ◽

10.1098/rsos.200638 ◽

2020 ◽

Vol 7 (7) ◽

pp. 200638

Author(s):

Solange Duruz ◽

Elia Vajana ◽

Alexander Burren ◽

Christine Flury ◽

Stéphane Joost

Keyword(s):

Climate Change ◽

Milk Production ◽

Environmental Conditions ◽

Natural Hazard ◽

Food Shortage ◽

High Mountain ◽

Physiological Factors ◽

Limited Impact ◽

New Model ◽

Lactation Cycle

The transhumance system, which consists in moving animals to high mountain pastures during summer, plays a considerable role in preserving both local biodiversity and traditions, as well as protecting against natural hazard. In cows, particularly, milk production is observed to decline as a response to food shortage and climatic stress, leading to atypical lactation curves that are barely described by current lactation models. Here, we relied on 5 million monthly milk records from over 200 000 Braunvieh and Original Braunvieh cows to devise a new model accounting for transhumance, and test the influence of environmental, physiological and morphological factors on cattle productivity. Counter to expectations, environmental conditions in the mountain showed a globally limited impact on milk production during transhumance, with cows in favourable conditions producing only 10% more compared with cows living in detrimental conditions, and with precipitation in spring and altitude revealing to be the most production-affecting variables. Conversely, physiological factors such as lactation number and pregnancy stage presented an important impact over the whole lactation cycle with 20% difference in milk production, and alter the way animals respond to transhumance. Finally, the considered morphological factors (cow height and foot angle) presented a smaller impact during the whole lactation cycle (10% difference in milk production). The present findings help to anticipate the effect of climate change and to identify problematic environmental conditions by comparing their impact with the effect of factors that are known to influence lactation.

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Spatially explicit estimation of heat stress-related impacts of climate change on the milk production of dairy cows in the United Kingdom

PLoS ONE ◽

10.1371/journal.pone.0197076 ◽

2018 ◽

Vol 13 (5) ◽

pp. e0197076 ◽

Cited By ~ 8

Author(s):

Nándor Fodor ◽

Andreas Foskolos ◽

Cairistiona F. E. Topp ◽

Jon M. Moorby ◽

László Pásztor ◽

...

Keyword(s):

Climate Change ◽

United Kingdom ◽

Heat Stress ◽

Dairy Cows ◽

Milk Production ◽

Spatially Explicit ◽

The United Kingdom ◽

Impacts Of Climate Change

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Calcium : magnesium ratio affects environmental stress sensitivity in the serpentine-endemic Alyssum inflatum (Brassicaceae)

Australian Journal of Botany ◽

10.1071/bt14235 ◽

2015 ◽

Vol 63 (2) ◽

pp. 39 ◽

Cited By ~ 7

Author(s):

Rasoul Ghasemi ◽

Zohreh Zare Chavoshi ◽

Robert S. Boyd ◽

Nishanta Rajakaruna

Keyword(s):

Climate Change ◽

Heat Stress ◽

Environmental Stress ◽

Environmental Conditions ◽

Environmental Stresses ◽

Stress Sensitivity ◽

Ammonium Concentration ◽

Serpentine Soils ◽

Stress Control ◽

Calcium Magnesium

Plants endemic to serpentine soils are adapted to harsh environmental conditions typical of those soils, particularly, low (<1) calcium (Ca) : magnesium (Mg) ratios. We compared survival of two perennial Alyssum species native to Iran under experimental manipulations of Ca : Mg ratio, including when Ca : Mg ratio was varied under conditions of high ammonium concentration and heat stress. Alyssum inflatum is a serpentine endemic capable of nickel (Ni) hyperaccumulation, whereas A. lanceolatum is found on non-serpentine soils and is not known to hyperaccumulate Ni. We grew plants of both species under four Ca : Mg ratios (0.4, 2, 20, 40) and tested survival when plants were exposed to elevated ammonium levels (0, 1 and 4 mM) and heat stress (control conditions vs a 5-h 36°C treatment daily for 5 days). Alyssum lanceolatum was more tolerant of Ca : Mg ratio variation (100% survival in all treatments), whereas A. inflatum survival was maximum at Ca : Mg = 2, reduced at Ca : Mg = 0.4, and very low for Ca : Mg ratios of 20 and 40. Alyssum lanceolatum also tolerated ammonium and heat stress, whereas survival of A. inflatum declined at higher Ca : Mg ratios when subjected to both stresses. We conclude that at higher Ca : Mg ratios, the serpentine endemic has reduced tolerance for these environmental stresses and may be more susceptible to human-driven climate change-associated stressors than the non-serpentine species.

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Population Specific Adaptations in Venom Production to Abiotic Stressors in a Widely Distributed Cnidarian

10.1101/2020.02.28.969204 ◽

2020 ◽

Cited By ~ 1

Author(s):

Maria Y. Sachkova ◽

Jason Macrander ◽

Joachim M. Surm ◽

Reuven Aharoni ◽

Shelcie S. Menard-Harvey ◽

...

Keyword(s):

Heat Stress ◽

Local Adaptation ◽

Environmental Conditions ◽

Uv Light ◽

Geographic Range ◽

Nematostella Vectensis ◽

Latitudinal Cline ◽

Downregulated Gene ◽

Abiotic Stressors ◽

Antagonistic Interactions

AbstractNematostella vectensis is a sea anemone (Actiniaria, Cnidaria) inhabiting estuaries over a broad geographic range where environmental conditions such as temperatures and salinity vary widely. In cnidarians, antagonistic interactions with predators and prey are mediated by their venom, which may be metabolically expensive. In this study, we challenged Nematostella polyps with heat, salinity, UV light stressors and a combination of all three to determine how abiotic stressors impact toxin expression for individuals collected across this species’ range. Transcriptomics and proteomics revealed that the highly abundant toxin Nv1 was the most downregulated gene under heat stress conditions in multiple populations. Physiological measurements demonstrated that venom is metabolically costly to produce suggesting that downregulating venom expression under stressful conditions may be advantageous. Strikingly, under a range of abiotic stressors, individuals from different geographic locations along this latitudinal cline modulate venom production levels differently in a pattern reflecting local adaptation.

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A map of climate change-driven natural selection in Arabidopsis thaliana

10.1101/321133 ◽

2018 ◽

Cited By ~ 3

Author(s):

Moises Exposito-Alonso ◽

Hernán A. Burbano ◽

Oliver Bossdorf ◽

Rasmus Nielsen ◽

Detlef Weigel ◽

...

Keyword(s):

Climate Change ◽

Arabidopsis Thaliana ◽

Natural Selection ◽

Local Adaptation ◽

Genetic Variants ◽

Species Range ◽

Genome Wide ◽

Genetic Makeup ◽

Environmental Limits ◽

Genome Information

Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risk of biodiversity associated with climate change1, however, do not typically take into account the genetic makeup of populations and how natural selection impacts it2. We made use of the extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection along the genome3. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant portion of this climate-driven natural selection over variants was predictable from signatures of local adaptation (R2=29-52%), as genetic variants found in geographic areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and Western Siberian populations — at the edges of the species’ environmental limits — currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe4, we forecast an increase in directional natural selection moving northwards from the southern end, and putting many native A. thaliana populations at evolutionary risk.

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