Genetic correlations between growth performance and carcass traits of purebred and crossbred pigs raised in tropical and temperate climates1

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.

Genetic evaluation of growth and reproductive performances of crossbred pigs reared under intensive system in tropical humid coastal climate

Pig farming is one of the most economically viable options for the rural backward and resource-poor farmers in Asian countries. Growth rate and litter size are the most important traits based on which the crossbreeding programs are typically planned in commercial pig farming. The modern system of farming with high yielding improved pig germplasm helps in economic growth in piggery enterprises. The present study was undertaken to evaluate the influence of various genetic and non-genetic factors on growth and reproductive performances of 75% crossbred progenies of Large White Yorkshire and indigenous Agonda Goan pigs. Body weights were recorded at birth, weaning, and at monthly intervals up to 10 months of age. Reproductive performances were also recorded for litter size and weights at birth and weaning stages, age at first farrowing, number of services per conception, farrowing interval, and pre-weaning mortality. The general linear model was used to estimate overall least square means of body weights at different ages considering the effects of different factors at certain levels viz., generation (i = first, second, third, fourth), sex (j = male, female), litter size at birth (k = 1-3, 4-6, 7-9, ≥10), parity (l = 1, 2, ≥3), season (m = summer, rainy, spring), and period of birth (n = 2012-2015, 2016-2019). The heritability and genetic correlations for different traits were estimated by restricted maximum likelihood (REML) method using WOMBAT software. The re(production) parameters were analyzed to assess the genetic improvement in successive generations. There was significant difference (p < 0.01) in body weights among different generations where animals belonging to latest generation showed maximum body weights indicating ideal selective breeding in the herd. Other fixed effects also had significant effects on growth performance which clearly signifies to the crucial influence of rearing environment and animal factors like parity of dams as well as litter size at birth. The overall birth weight, weaning weight, and weight at 10 months of age were 1.00 ± 0.01 kg, 7.57 ± 0.07 kg, and 81.58 ± 1.96 kg, respectively. Nevertheless, weaning weight and weight at marketing age (8 months) were 8.04 ± 0.27 kg and 75.48 ± 1.40 kg, respectively, in fourth generation, indicating higher post-weaning growth rate of 337.20 g/day. During this fourth generation, mean litter size at birth was 8.35 ± 0.43 and litter size at weaning was 7.79 ± 0.39 with lowest percentage of pre-weaning mortality (4.11 ± 1.51). The average age at first farrowing and farrowing interval was 293 ± 17.24 and 195 ± 4.78 days, respectively. There was apparently greater genetic gain in each generation except for the second generation which might be due to the environment and managemental issues that hindered reproductive performance traits and body growth. The heritability estimate for weaning weight was 0.45 and higher heritability values were observed for all the body weights except weight at third month. Genetic as well as phenotypic correlations were moderate to high among the growth traits. The heritability and genetic correlations at birth and weaning indicate the reliability of selection at an early age. The findings indicated that there is scope for improvement through genetic selection in later generations and the 75% crossbred pigs thrived well in the prevailing hot and humid tropical coastal climate. The improved germplasm could satisfy the farmers' need in a commercial venture with high economic return.

Genetic Parameters for Tolerance to Heat Stress in Crossbred Swine Carcass Traits

Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature-humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected. Its magnitude was more substantial for loin depth and carcass growth, but all the traits studied showed a different impact of heat stress and different magnitude of genotype by environment interaction. For backfat depth, heritability was larger under comfortable conditions (no heat stress), as compared to heat stress conditions. Genetic correlations between extreme values of environmental conditions were lower (∼0.5 to negative) for growth and loin depth. Based on the solutions obtained from the model, sires were ranked on their breeding value for general performance and tolerance to heat stress. Antagonism between overall performance and tolerance to heat stress was moderate. Still, the models tested can provide valuable information to identify genetic material that is resilient and can perform equally when environmental conditions change. Overall, the results obtained from this study suggest the existence of genotype by environment interaction for carcass traits, as a possible genetic contributor to heat tolerance in swine.

Genotype by environment interactions for performance and thermoregulation responses in growing pigs1,2

Heat stress affects pig health, welfare, and production, and thus the economic viability of the pig sector in many countries. Breeding for heat tolerance is a complex issue, increasingly important due to climate change and the development of pig production in tropical areas. Characterizing genetic determinism of heat tolerance would help building selection schemes dedicated to high performance in tropical areas. The main objective of our study was to estimate the genetic parameters for production and thermoregulation traits in two highly related growing pig populations reared in temperate (TEMP) or tropical humid (TROP) environment. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. Phenotypic data were obtained on a total of 1,297 pigs using the same procedures in both environments, for body weight (BW, at weeks 11 and 23), daily feed intake (ADFI), backfat thickness (BFT, at weeks 19 and 23), cutaneous temperature (CT, at weeks 19 and 23), and rectal temperature (RT, at weeks 19, 21, and 23). Feed conversion ratio (FCR) and residual feed intake (RFI) were computed for the whole test period (11 to 23 wk). Criteria comparing the fits to the data revealed genotype × environment (G × E) interactions for most traits but not for FCR. The variance components were obtained using two different methods, a restricted maximum likelihood method and a Bayesian Markov chain Monte Carlo method, considering that traits are either similar or different in each environment. Regardless of the method, heritability estimates for production traits were moderate to high, except for FCR (lower than 0.18). Heritability estimates for RT were low to moderate, ranging from 0.04 to 0.34. The genetic correlations of each trait between environments generally differed from 1, except for FCR and ADG. For most thermoregulation traits, they also did not differ significantly from zero, suggesting that the main genetic bases of heat tolerance may vary in different environment. Within environments, the unfavorable genetic correlations between production traits and RT suggest an antagonism between the ability to maintain inner temperature and the ability to increase ADFI and ADG. However, greater RT were also associated to leaner pigs and better feed efficiency. Nevertheless, due to large inaccuracies of these estimations, larger cohorts would be needed to decide about the best breeding schemes to choose for tropical pig production.