Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs

Plateau-linear reaction norm model analysis of number born alive in purebred Landrace pigs using meteorological data in Japan

We performed a plateau-linear reaction norm model (RNM) analysis of number born alive (NBA) in purebred Landrace pigs, where breeding value changes according to maximum temperature at mating day, using public meteorological observation data in Japan. We analysed 52,668 NBA records obtained from 10,320 Landrace sows. Pedigree data contained 99,201 animals. Off-farm daily temperature data at the nearest weather station from each of the farms were downloaded from the Japan Meteorological Agency website. A plateau-linear RNM analysis based on daily maximum temperature on mating day (threshold temperature of 16.6°C) was performed. The percentage of the records with daily maximum temperatures at mating days of ≤16.6, ≥25.0, ≥30.0 and ≥35.0°C were 34.3%, 33.6%, 14.0% and 0.8%, respectively. The value of Akaike's information criterion for the plateau-linear RNM was lower than that for a simple repeatability model (RM). With the plateau-linear RNM, estimated value of heritability ranged from 0.14 to 0.15, while that from the RM analysis was 0.15. Additive genetic correlation between intercept and slope terms was estimated to be -0.52 from the plateau-linear RNM analysis. Estimated additive genetic correlations were >0.9 between NBA at different temperatures ranging from 16.6 to 37.6°C. For the 10,320 sows, average values of prediction reliability of the intercept and slope terms for breeding values in the plateau-linear RNM were 0.47 and 0.16, respectively. Increasing weight for slope term in linear selection index could bring positive genetic gain in the slope part, but prediction accuracy would decrease. Our results imply that genetically improving heat tolerance in sows reared in Japan focusing on NBA using RNM is possible, while RNM is more complex to implement and interpret. Therefore, further study should be encouraged to make genetic improvement for heat tolerance in sows more efficient.

Genomic regions, candidate genes, and pleiotropic variants associated with physiological and anatomical indicators of heat stress response in lactating sows

BACKGROUND

Heat stress (HS) poses significant threats to the sustainability of livestock production. Genetically improving heat tolerance could enhance animal welfare and minimize production losses during HS events. Measuring phenotypic indicators of HS response and understanding their genetic background are crucial steps to optimize breeding schemes for improved climatic resilience. The identification of genomic regions and candidate genes influencing the traits of interest, including variants with pleiotropic effects, enables the refinement of genotyping panels used to perform genomic prediction of breeding values and contributes to unraveling the biological mechanisms influencing heat stress response. Therefore, the main objectives of this study were to identify genomic regions, candidate genes, and potential pleiotropic variants significantly associated with indicators of HS response in lactating sows using imputed whole-genome sequence (WGS) data. Phenotypic records for 18 traits and genomic information from 1,645 lactating sows were available for the study. The genotypes from the PorcineSNP50K panel containing 50,703 single nucleotide polymorphisms (SNPs) were imputed to WGS and after quality control, 1,622 animals and 7,065,922 SNPs were included in the analyses.

RESULTS

A total of 1,388 unique SNPs located on sixteen chromosomes were found to be associated with 11 traits. Twenty gene ontology terms and 11 biological pathways were shown to be associated with variability in ear skin temperature, shoulder skin temperature, rump skin temperature, tail skin temperature, respiration rate, panting score, vaginal temperature automatically measured every 10 min, vaginal temperature measured at 0800 h, hair density score, body condition score, and ear area. Seven, five, six, two, seven, 15, and 14 genes with potential pleiotropic effects were identified for indicators of skin temperature, vaginal temperature, animal temperature, respiration rate, thermoregulatory traits, anatomical traits, and all traits, respectively.

CONCLUSIONS

Physiological and anatomical indicators of HS response in lactating sows are heritable but highly polygenic. The candidate genes found are associated with important gene ontology terms and biological pathways related to heat shock protein activities, immune response, and cellular oxidative stress. Many of the candidate genes with pleiotropic effects are involved in catalytic activities to reduce cell damage from oxidative stress and cellular mechanisms related to immune response.

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

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.

Inheritance of feed intake-based resilience traits and their correlation with production traits in Finnish pig breeds

High resilience against diseases, changing environmental conditions, and other stress factors and the ability to efficiently recover to normal status, is becoming increasingly important in pig production. Finding new phenotypes that relate to resilience is a crucial step for improving the resilience of pigs through selection. The objective of this study was to extract resilience-related phenotypes based on fluctuations in daily feed intake (DFI, g) and time spent in feeding per day (TPD, min) and to estimate the heritability of these traits and genetic correlations with production traits (PT). Resilience-related traits with high enough heritability and with either favorable or neutral genetic correlation with PT could be used in the selection program to improve the productivity and welfare of pigs. In this study, we used data from 7,347 Finnish Yorkshire, Landrace, and crossbred pigs raised at the test station. Six pig-specific resilience-related phenotypes were extracted from the individual DFI and TPD: root mean square error (RMSE), quantile regression (QR), and coefficient of variation (CV). RMSE was calculated from the differences between the actual DFI (or TPD) and the pig-specific predicted values. QR was based on the number of days that a pig belonged to the group with the lowest 5% of pigs based on DFI (or TPD), and CV was calculated over the daily observations of DFI (or TPD). PT included average daily gain (ADG, g), backfat thickness (BF, mm), and feed conversion rate (FCR, g/g). The heritability estimates for resilience-related traits varied between 0.07 ± 0.02 (QRDFI) and 0.20 ± 0.03 (RMSETPD). The genetic correlations between resilience-related traits and PT were mostly neutral, but for example, RMSEDFI had a favorable genetic correlation with FCR and BF but an unfavorable correlation with ADG. Lastly, we observed that pigs belonging to the lowest 10% group based on their breeding value (BV) for QRTPD had a lower proportion (10% incidence) of sick days compared to the highest 10% BV group (30% incidence). Therefore, pigs exhibiting small TPD variation (related to high resilience) tend to be less susceptible to sickness than pigs with large TPD variation (related to low resilience). Given its moderate heritability, neutral genetic correlation with PT, and positive effect on health, QRTPD can be considered the most promising resilience-related trait in the Finnish production system.

Reaction-norm animal model analysis of average daily gain heat tolerance in purebred Duroc pigs

The present study aimed to genetically improve growth performance under high-heat environments by specifically designing a reaction-norm animal model (RNAM) for purebred Duroc pigs in Japan. A total of 54,750 records of average daily gain (ADG) measured for pigs reared at four farms in different prefectures were analyzed. Estimated maximum daily temperatures at the respective farm locations were used to calculate the average cumulative thermal load (TL). The TL values served as an indicator of high-heat environments for pigs. The plausible cumulative period length and threshold temperature for calculating TL were determined to be 8 weeks until just before shipping and 25°C, respectively. Variance components were estimated via RNAM analysis using TL as a linear covariate. The estimated additive genetic variances under both responsive and non-responsive to TL were found to be significant. Moreover, the estimated heritability of ADG ranged from 0.38 to 0.73 for TL values of 0-8. These results suggest that the RNAM developed holds the potential for improving the genetic ability of growth under high-heat environments in pigs.

Genetic parameters for automatically-measured vaginal temperature, respiration efficiency, and other thermotolerance indicators measured on lactating sows under heat stress conditions

BACKGROUND

Genetic selection based on direct indicators of heat stress could capture additional mechanisms that are involved in heat stress response and enable more accurate selection for more heat-tolerant individuals. Therefore, the main objectives of this study were to estimate genetic parameters for various heat stress indicators in a commercial population of Landrace × Large White lactating sows measured under heat stress conditions. The main indicators evaluated were: skin surface temperatures (SST), automatically-recorded vaginal temperature (TV), respiration rate (RR), panting score (PS), body condition score (BCS), hair density (HD), body size (BS), ear size, and respiration efficiency (Reff).

RESULTS

Traits based on TV presented moderate heritability estimates, ranging from 0.15 ± 0.02 to 0.29 ± 0.05. Low heritability estimates were found for SST traits (from 0.04 ± 0.01 to 0.06 ± 0.01), RR (0.06 ± 0.01), PS (0.05 0.01), and Reff (0.03 ± 0.01). Moderate to high heritability values were estimated for BCS (0.29 ± 0.04 for caliper measurements and 0.25 ± 0.04 for visual assessments), HD (0.25 ± 0.05), BS (0.33 ± 0.05), ear area (EA; 0.40 ± 0.09), and ear length (EL; 0.32 ± 0.07). High genetic correlations were estimated among SST traits (> 0.78) and among TV traits (> 0.75). Similarly, high genetic correlations were also estimated for RR with PS (0.87 ± 0.02), with BCS measures (0.92 ± 0.04), and with ear measures (0.95 ± 0.03). Low to moderate positive genetic correlations were estimated between SST and TV (from 0.25 ± 0.04 to 0.76 ± 0.07). Low genetic correlations were estimated between TV and BCS (from - 0.01 ± 0.08 to 0.06 ± 0.07). Respiration efficiency was estimated to be positively and moderately correlated with RR (0.36 ± 0.04), PS (0.56 ± 0.03), and BCS (0.56 ± 0.05 for caliper measurements and 0.50 ± 0.05 for the visual assessments). All other trait combinations were lowly genetically correlated.

CONCLUSIONS

A comprehensive landscape of heritabilities and genetic correlations for various thermotolerance indicators in lactating sows were estimated. All traits evaluated are under genetic control and heritable, with different magnitudes, indicating that genetic progress is possible for all of them. The genetic correlation estimates provide evidence for the complex relationships between these traits and confirm the importance of a sub-index of thermotolerance traits to improve heat tolerance in pigs.

Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance

Heat stress is a major problem that constrains pig productivity. Understanding and identifying adaptation to heat stress has been the focus of recent studies, and the identification of genome-wide selection signatures can provide insights into the mechanisms of environmental adaptation. Here, we generated whole-genome re-sequencing data from six Chinese indigenous pig populations to identify genomic regions with selection signatures related to heat tolerance using multiple methods: three methods for intra-population analyses (Integrated Haplotype Score, Runs of Homozygosity and Nucleotide diversity Analysis) and three methods for inter-population analyses (Fixation index (F_ST), Cross-population Composite Likelihood Ratio and Cross-population Extended Haplotype Homozygosity). In total, 1 966 796 single nucleotide polymorphisms were identified in this study. Genetic structure analyses and F_ST indicated differentiation among these breeds. Based on information on the location environment, the six breeds were divided into heat and cold groups. By combining two or more approaches for selection signatures, outlier signals in overlapping regions were identified as candidate selection regions. A total of 163 candidate genes were identified, of which, 29 were associated with heat stress injury and anti-inflammatory effects. These candidate genes were further associated with 78 Gene Ontology functional terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways in enrichment analysis (P < 0.05). Some of these have clear relevance to heat resistance, such as the AMPK signalling pathway and the mTOR signalling pathway. The results improve our understanding of the selection mechanisms responsible for heat resistance in pigs and provide new insights of introgression in heat adaptation.

Effect of ambient temperature on average daily gain of pigs evaluated using public weather data and a plateau-linear regression model

We performed a plateau-linear regression model analysis of the average daily gain (ADG) of pigs on daily average temperature at the end of performance testing (T). Records for performance testing between 30 kg and 105 kg of 2268 purebred Duroc pigs raised at the National Livestock Breeding Center Miyazaki Station were used. Off-farm ambient temperatures were measured at the nearest Automated Meteorological Data Acquisition System station at Kobayashi, Miyazaki (Kobayashi station). A plateau-linear regression equation was obtained in which ADG decreased by 12.6 g for every 1°C when T > 21.1°C. We calculated the expected age in day at the end of testing (D105) using the regression equation obtained and T observed at the Kobayashi station in 2020. The number of days that D105 was prolonged due to higher T was 125 days, corresponding to approximately one third of the year. These results could contribute to planning and management of stable pork production in response to heat in Japan.

The Genetics of Thermoregulation in Pigs: A Review

Heat stress (HS) affects pig performance, health and welfare, resulting in a financial burden to the pig industry. Pigs have a limited number of functional sweat glands and their thermoregulatory mechanisms used to maintain body temperature, are challenged by HS to maintain body temperature. The genetic selection of genotypes tolerant to HS is a promising long-term (adaptation) option that could be combined with other measures at the production system level. This review summarizes the current knowledge on the genetics of thermoregulation in pigs. It also discusses the different phenotypes that can be used in genetic studies, as well as the variability in thermoregulation between pig breeds and the inheritance of traits related to thermoregulation. This review also considers on-going challenges to face for improving heat tolerance in pigs.

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

Properly quantifying environmental heat stress (HS) is still a major challenge in livestock breeding programs, especially as adverse climatic events become more common. The definition of critical periods and climatic variables to be used as the environmental gradient is a key step for genetically evaluating heat tolerance (HTol). Therefore, the main objectives of this study were to define the best critical periods and environmental variables (ENV) to evaluate HT and estimate variance components for HT in Large White pigs. The traits included in this study were 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). Seven climatic variables based on public weather station data were compared based on three criteria, including the following: (1) strongest G×E estimate as measured by the slope term, (2) ENV yielding the highest theoretical accuracy of the genomic estimated breeding values (GEBV), and (3) variable yielding the highest distribution of GEBV per ENV. Relative humidity (for BFT, MDP, NBD, WN, and WW) and maximum temperature (for OTW, TNB, NBA, IBF, and IWE) are the recommended ENV based on the analyzed criteria. The acute HS (average of 30 days before the measurement date) is the critical period recommended for OTW, BFT, and MDP in the studied population. For WN, WW, IBF, and IWE, a period ranging from 34 days prior to farrowing up to weaning is recommended. For TNB, NBA, and NBD, the critical period from 20 days prior to breeding up to 30 days into gestation is recommended. The genetic correlation values indicate that the traits were largely (WN, WW, IBF, and IWE), moderately (OTW, TNB, and NBA), or weakly (MDP, BFT, and NBD) affected by G×E interactions. This study provides relevant recommendations of critical periods and climatic gradients for several traits in order to evaluate HS in Large White pigs. These observations demonstrate that HT in Large White pigs is heritable, and genetic progress can be achieved through genetic and genomic selection.

Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

BACKGROUND

There is an increasing need to account for genotype-by-environment (G × E) interactions in livestock breeding programs to improve productivity and animal welfare across environmental and management conditions. This is even more relevant for pigs because selection occurs in high-health nucleus farms, while commercial pigs are raised in more challenging environments. In this study, we used single-step homoscedastic and heteroscedastic genomic reaction norm models (RNM) to evaluate G × E interactions in Large White pigs, including 8686 genotyped animals, for reproduction (total number of piglets born, TNB; total number of piglets born alive, NBA; total number of piglets weaned, NW), growth (weaning weight, WW; off-test weight, OW), and body composition (ultrasound muscle depth, MD; ultrasound backfat thickness, BF) traits. Genetic parameter estimation and single-step genome-wide association studies (ssGWAS) were performed for each trait.

RESULTS

The average performance of contemporary groups (CG) was estimated and used as environmental gradient in the reaction norm analyses. We found that the need to consider heterogeneous residual variance in RNM models was trait dependent. Based on estimates of variance components of the RNM slope and of genetic correlations across environmental gradients, G × E interactions clearly existed for TNB and NBA, existed for WW but were of smaller magnitude, and were not detected for NW, OW, MD, and BF. Based on estimates of the genetic variance explained by the markers in sliding genomic windows in ssGWAS, several genomic regions were associated with the RNM slope for TNB, NBA, and WW, indicating specific biological mechanisms underlying environmental sensitivity, and dozens of novel candidate genes were identified. Our results also provided strong evidence that the X chromosome contributed to the intercept and slope of RNM for litter size traits in pigs.

CONCLUSIONS

We provide a comprehensive description of G × E interactions in Large White pigs for economically-relevant traits and identified important genomic regions and candidate genes associated with GxE interactions on several autosomes and the X chromosome. Implementation of these findings will contribute to more accurate genomic estimates of breeding values by considering G × E interactions, in order to genetically improve the environmental robustness of maternal-line pigs.

Evidence for recombination variability in purebred swine populations

This study aimed to investigate interpopulation variation due to sex, breed and age, and the intrapopulation variation in the form of genetic variance for recombination in swine. Genome-wide recombination rate and recombination occurrences (RO) were traits studied in Landrace (LR) and Large White (LW) male and female populations. Differences were found for sex, breed, sex-breed interaction, and age effects for genome-wide recombination rate and RO at one or more chromosomes. Dams were found to have a higher genome-wide recombination rate and RO at all chromosomes than sires. LW animals had higher genome-wide recombination rate and RO at seven chromosomes but lower at two chromosomes than LR individuals. The sex-breed interaction effect did not show any pattern not already observable by sex. Recombination increased with increasing parity in females, while in males no effect of age was observed. We estimated heritabilities and repeatabilities for both investigated traits and obtained the genetic correlation between male and female genome-wide recombination rate within each of the two breeds studied. Estimates of heritability and repeatability were low (h²  = 0.01-0.26; r = 0.18-0.42) for both traits in all populations. Genetic correlations were high and positive, with estimates of 0.98 and 0.94 for the LR and LW breeds, respectively. We performed a GWAS for genome-wide recombination rate independently in the four sex/breed populations. The results of the GWAS were inconsistent across the four populations with different significant genomic regions identified. The results of this study provide evidence of variability for recombination in purebred swine populations.