Definition of Environmental Variables and Critical Periods to Evaluate Heat Tolerance in Large White Pigs Based on Single-Step Genomic Reaction Norms

Freitas, P.H.F.; Johnson, Jay S; Chen, S.; Oliveira, Hinayah Rojas de; Tiezzi, Francesco; Lázaro, Sirlene Fernandes; Huang, Yijian; Gu, Youping; Schinckel, A. P.; Brito, Luiz F.

doi:10.3389/fgene.2021.717409

Cited by 18 publications

(15 citation statements)

References 58 publications

(132 reference statements)

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“…At present, there are many studies on the mechanisms by which oxidative stress affects reproductive performance in sows, but there are few studies on the differentiation of sows in response to oxidative stress and the underlying mechanisms [ 58 ]. In addition, the growing practice suggests that differences between the rearing environment of breeding pigs (friendly environment) and that of commercial pigs (a more challenging environment) result in some individuals often failing to exhibit their due genetic potential, and, therefore, genotype-by-environment interactions (GEI) are increasingly being considered in pig breeding programs in order to improve the environmental adaptation, productivity, and economic benefits for the pig industry [ 59 , 60 , 61 ]. Therefore, GEI is becoming an important focus for the pig industry.…”

Section: Discussionmentioning

confidence: 99%

A Mutation in Endogenous saRNA miR-23a Influences Granulosa Cells Response to Oxidative Stress

Wang

Zeng

et al. 2022

Antioxidants

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Phenotypes are the result of the interaction between the gene and the environment, so the response of individuals with different genotypes to an environment is variable. Here, we reported that a mutation in miR-23a influences granulosa cells (GCs) response to oxidative stress, a common mechanism of environmental factors affecting female reproduction. We showed that nuclear miR-23a is a pro-apoptotic miRNA in porcine GCs through the activation of the transcription and function of NORHA, a long non-coding RNA (lncRNA) induces GC apoptosis and responses to oxidative stress. Mechanistically, miR-23a acts as an endogenous small activating RNA (saRNA) to alter histone modifications of the NORHA promoter through the direct binding to its core promoter. A C > T mutation was identified at −398 nt of the miR-23a core promoter, which created a novel binding site for the transcription factor SMAD4 and recruited the transcription repressor SMAD4 to inhibit miR-23a transcription and function in GCs. Notably, g.−398C > T mutation in the miR-23a promoter reduced GCs response to oxidative stress. In addition, g.−398C > T mutation was significantly associated with sow fertility traits. In short, our findings preliminarily revealed the genetic basis of individual differences in the response to oxidative stress from the perspective of a single mutation and identified miR-23a as a candidate gene for the environmental adaptation to oxidative stress.

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Section: Discussionmentioning

confidence: 99%

A Mutation in Endogenous saRNA miR-23a Influences Granulosa Cells Response to Oxidative Stress

Wang

Zeng

et al. 2022

Antioxidants

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“…Public weather station records for all farms were obtained from the Local Climatological Data at the National Oceanic and Atmosphere Administration, NOAA (http://www.ncdc.noaa.gov/cdo-web/datatools/lcd?prior%20=%20N) as described by Freitas et al. (2021). The average distance between the public weather station and the farms was 30 km (ranging from 7 to 64 km).…”

Section: Methodsmentioning

confidence: 99%

“…gov/ cdo-web/ datat ools/ lcd? prior% 2520=% 2520N ) as described by Freitas et al (2021). The average distance between the public weather station and the farms was 30 km (ranging from 7 to 64 km).…”

Section: Environmental Variablesmentioning

confidence: 99%

“…Several studies have investigated the genetic background of HS response in swine and defined the best critical periods and climatic variables to be used when predicting animal performance in adverse climatic conditions (Carabaño et al., 2017; Chen et al., 2021; Freitas et al., 2021; Misztal, 2017; Shi et al., 2021; Tiezzi et al., 2020; Zhang et al., 2019). These studies have shown that there is genetic variability for heat tolerance and that genetic progress can be achieved through direct genetic and genomic selection for improved climatic adaptation.…”

Section: Introductionmentioning

confidence: 99%

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Genomic predictions and GWAS for heat tolerance in pigs based on reaction norm models with performance records and data from public weather stations considering alternative temperature thresholds

Freitas,

Johnson,

Tiezzi

et al. 2023

J Animal Breeding Genetics

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Genetic improvement of livestock productivity has resulted in greater production of metabolic heat and potentially greater susceptibility to heat stress. Various studies have demonstrated that there is genetic variability for heat tolerance and genetic selection for more heat tolerant individuals is possible. The rate of genetic progress tends to be greater when genomic information is incorporated into the analyses as more accurate breeding values can be obtained for young individuals. Therefore, this study aimed (1) to evaluate the predictive ability of genomic breeding values for heat tolerance based on routinely recorded traits, and (2) to investigate the genetic background of heat tolerance based on single‐step genome‐wide association studies for economically important traits related to body composition, growth and reproduction in Large White pigs. Pedigree information was available for 265,943 animals and genotypes for 8686 animals. The studied traits included ultrasound backfat thickness (BFT), ultrasound muscle depth (MDP), piglet weaning weight (WW), off‐test weight (OTW), interval between farrowing (IBF), total number of piglets born (TNB), number of piglets born alive (NBA), number of piglets born dead (NBD), number of piglets weaned (WN) and weaning‐to‐estrus interval (IWE). The number of phenotypic records ranged from 6059 (WN) to 172,984 (TNB). Single‐step genomic reaction norm predictions were used to calculate the genomic estimated breeding values for each individual. Predictions of breeding values for the validation population individuals were compared between datasets containing phenotypic records measured in the whole range of temperatures (WR) and datasets containing only phenotypic records measured when the weather station temperature was above 10°C (10C) or 15°C (15C), to evaluate the usefulness of these datasets that may better reflect the within‐barn temperature. The use of homogeneous or heterogeneous residual variance was found to be trait‐dependent, where homogeneous variance presented the best fit for MDP, BFT, OTW, TNB, NBA, WN and IBF, while the other traits (WW and IWE) had better fit with heterogeneous variance. The average prediction accuracy, dispersion and bias values considering all traits for WR were 0.36 ± 0.05, −0.07 ± 0.13 and 0.76 ± 0.10, respectively; for 10C were 0.39 ± 0.02, −0.05 ± 0.07 and 0.81 ± 0.05, respectively; and for 15C were 0.32 ± 0.05, −0.05 ± 0.11 and 0.84 ± 0.10, respectively. Based on the studied traits, using phenotypic records collected when the outside temperature (from public weather stations) was above 10°C provided better predictions for most of the traits. Forty‐three and 62 candidate genomic regions were associated with the intercept (overall performance level) and slope term (specific biological mechanisms related to environmental sensitivity), respectively. Our results contribute to improve genomic predictions using existing datasets and better understand the genetic background of heat tolerance in pigs. Furthermore, the genomic regions and candidate genes identified will contribute to future genomic studies and breeding applications.

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“…Severe environmental consequences of the climate change, particularly extreme temperatures and the resulting physiological challenges to cope with them ( Koch et al, 2019 ), sparked increased interest in recent years in research on G×E in farm animals to increase their resilience ( Passamonti et al, 2021 ). Currently, investigation of G×E in farm animals relies largely on quantitative genetic and QTL mapping approaches to measure G×E and to identify the underlying loci (e.g., Freitas et al, 2021 ). Such studies generally require large cohorts with phenotypes recorded in different environments.…”

Section: Introductionmentioning

confidence: 99%

Exploration of genotype-by-environment interactions affecting gene expression responses in porcine immune cells

Muráni

Hadlich

2023

Front. Genet.

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As one of the keys to healthy performance, robustness of farm animals is gaining importance, and with this comes increasing interest in genetic dissection of genotype-by-environment interactions (G×E). Changes in gene expression are among the most sensitive responses conveying adaptation to environmental stimuli. Environmentally responsive regulatory variation thus likely plays a central role in G×E. In the present study, we set out to detect action of environmentally responsive cis-regulatory variation by the analysis of condition-dependent allele specific expression (cd-ASE) in porcine immune cells. For this, we harnessed mRNA-sequencing data of peripheral blood mononuclear cells (PBMCs) stimulated in vitro with lipopolysaccharide, dexamethasone, or their combination. These treatments mimic common challenges such as bacterial infection or stress, and induce vast transcriptome changes. About two thirds of the examined loci showed significant ASE in at least one treatment, and out of those about ten percent exhibited cd-ASE. Most of the ASE variants were not yet reported in the PigGTEx Atlas. Genes showing cd-ASE were enriched in cytokine signaling in immune system and include several key candidates for animal health. In contrast, genes showing no ASE featured cell-cycle related functions. We confirmed LPS-dependent ASE for one of the top candidates, SOD2, which ranks among the major response genes in LPS-stimulated monocytes. The results of the present study demonstrate the potential of in vitro cell models coupled with cd-ASE analysis for the investigation of G×E in farm animals. The identified loci may benefit efforts to unravel the genetic basis of robustness and improvement of health and welfare in pigs.

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Definition of Environmental Variables and Critical Periods to Evaluate Heat Tolerance in Large White Pigs Based on Single-Step Genomic Reaction Norms

Cited by 18 publications

References 58 publications

A Mutation in Endogenous saRNA miR-23a Influences Granulosa Cells Response to Oxidative Stress

A Mutation in Endogenous saRNA miR-23a Influences Granulosa Cells Response to Oxidative Stress

Genomic predictions and GWAS for heat tolerance in pigs based on reaction norm models with performance records and data from public weather stations considering alternative temperature thresholds

Exploration of genotype-by-environment interactions affecting gene expression responses in porcine immune cells

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