Characterization of the acute heat stress response in gilts: III. Genome-wide association studies of thermotolerance traits in pigs

Kim, Kwan‐Suk; Seibert, J. T.; Edea, Zewde; Graves, K. L.; Kim, Eui-Soo; Keating, Aileen F.; Baumgard, Lance H.; Ross, Jason W.; Rothschild, Max F.

doi:10.1093/jas/sky131

Cited by 27 publications

(18 citation statements)

References 71 publications

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“…This further supports a possible second QTL that is independent of the level of milk production and shows pleiotropy for the heat tolerance traits. Other published GWAS have also reported an association of the GHR gene with milk production in heat-stressed cows [15] and respiratory rates in pigs during heat stress [17]. Several studies have also implicated the GHR polymorphisms to milk production in bovines, e.g., Chr20:31888449 phenylalanine-to-tyrosine missense mutation [26].…”

Section: Discussionmentioning

confidence: 99%

“…Several genome-wide association studies ( GWAS ) using Single nucleotide polymorphisms ( SNPs ) have been conducted over the last decade to identify candidate causal genes for various heat tolerance traits (rectal temperature, heart rate, sweating rate, rate of milk yield decline, etc.) in dairy cattle [13–16] and pigs [17]. However, these GWAS were underpowered, with the largest sample size to date of around 5,000 animals [13, 14].…”

Section: Introductionmentioning

confidence: 99%

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

Cheruiyot

Haile‐Mariam

Cocks

et al. 2021

Preprint

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Climate 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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Cheruiyot

Haile‐Mariam

Cocks

et al. 2021

Preprint

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“…The use of whole-genome data, allowed us to also pinpoint genetic variants within these genes that may have a functional impact and thus may explain some of the phenotypic differences that exist between CHCU and CHFR animals. For example, 1253 SNPs were detected within the ATP9A gene, which is associated with heat tolerance in pigs [32]. Among these SNPs, one (rs207874965) is located within the 3′UTR, five SNPs have the potential to alter splicing, and 22 SNPs are in the upstream region, including 20 that modify TFBS.…”

Section: Putative Selective Sweeps Between Cuban and French Charolaismentioning

confidence: 99%

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

et al. 2021

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Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. Results In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Conclusions Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.

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“…The studies show that the base of changes in feeding behaviour are primarily genes involved in immune response and function. The same approach (GWAS) was also lately used in the study of Kim et al [ 43 ] to evaluate the genomic base of the physiological indicators of heat stress such as respiration rate, rectal temperature and skin temperature.…”

Section: Thermoregulation Behavioural and Physiological Changes Imentioning

confidence: 99%

Use of Different Cooling Methods in Pig Facilities to Alleviate the Effects of Heat Stress—A Review

Godyń

Herbut

Angrecka

et al. 2020

Animals

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An increase in the frequency of hot periods, which has been observed over the past decades, determines the novel approach to livestock facilities improvement. The effects of heat stress are revealed in disorders in physiological processes, impaired immunity, changes in behaviour and decreases in animal production, thus implementation of cooling technologies is a key factor for alleviating these negative consequences. In pig facilities, various cooling methods have been implemented. Air temperature may be decreased by using adiabatic cooling technology such as a high-pressure fogging system or evaporative pads. In modern-type buildings large-surface evaporative pads may support a tunnel ventilation system. Currently a lot of attention has also been paid to developing energy- and water-saving cooling methods, using for example an earth-air or earth-to-water heat exchanger. The pigs’ skin surface may be cooled by using sprinkling nozzles, high-velocity air stream or conductive cooling pads. The effectiveness of these technologies is discussed in this article, taking into consideration the indicators of animal welfare such as respiratory rate, skin surface and body core temperature, performance parameters and behavioural changes.

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Characterization of the acute heat stress response in gilts: III. Genome-wide association studies of thermotolerance traits in pigs

Cited by 27 publications

References 71 publications

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

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

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

Use of Different Cooling Methods in Pig Facilities to Alleviate the Effects of Heat Stress—A Review

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