Effects of heterozygosity on performance of purebred and crossbred pigs

Abstract

Background In pigs, crossbreeding aims at exploiting heterosis, but heterosis is difficult to quantify. Heterozygosity at genetic markers is easier to measure and could potentially be used as an indicator of heterosis. The objective of this study was to investigate the effect of heterozygosity on various maternal and production traits in purebred and crossbred pigs. The proportion of heterozygosity at genetic markers across the genome for each individual was included in the prediction model as a fixed regression across or within breeds. Results Estimates of regression coefficients of heterozygosity showed large effects for some traits. For maternal traits, regression coefficient estimates were always in a favourable direction, while for production, meat and slaughter quality traits, they were both favourable and unfavourable. Traits with the largest estimated effects of heterozygosity were total number born, litter weight at 3 weeks, weight at 150 days, and age at 40 kg. Estimates of regression coefficients on heterozygosity differed between breeds. Traits with the largest effect of heterozygosity also showed a significant (P < 0.05) increase in prediction accuracy when heterozygosity was included in the model compared to the model without heterozygosity. Conclusions For traits with the largest estimates of regression coefficients on heterozygosity, the inclusion of heterozygosity in the model improved prediction accuracy. Using models that include heterozygosity would result in selecting different animals for breeding, which has the potential to improve genetic gain for these traits. This is most beneficial when crossbreds or several breeds are included in the estimation of breeding values and is relevant to all species, not only pigs. Thus, our results show that including heterozygosity in the model is beneficial for some traits, likely due to dominant gene action. Electronic supplementary material The online version of this article (10.1186/s12711-019-0450-1) contains supplementary material, which is available to authorized users.

Estimation of genetic parameters for weaning and yearling weights in a composite population used to form the Purunã breed

“…Although the genetic basis of heterosis is still a subject of investigation, its effect is difficult to quantify. Thus, heterozygosity, which represents the proportion of heterozygote genotypes in the population, may be a useful indicator and has been often used to evaluate the degree of heterosis (Akanno et al, 2018;Iversen et al, 2019;Prastowo et al, 2021). According to Queiroz et al (2013), heterozygosity has a significant effect on performance traits in Brangus animals and its inclusion in the model may improve prediction accuracy (Raidan et al, 2018).…”

Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations

“…The pooled indigenous animals had an average heterozygosity of 0.238 (SD = 0.023), consistent with the extra heterozygosity expected in admixtures between the African B. taurus and Bos indicus ancestral populations. Including heterozygosity proportion in the model for genetic evaluation increases the prediction accuracy of traits and it also has the potential to be used in mate selection in order to maximize heterozygosity in the offspring ( De Cara et al, 2011 ; Iversen et al, 2019 ). A previous study by Mbole-Kariuki et al (2014) using a medium-density (50k SNPs) dataset reported a lower average heterozygosity level for N’Dama 0.17 (SD = 0.08) than the pooled African B. taurus , and a higher average heterozygosity level for Sheko 0.26 (SD = 0.003) compared to the pooled indigenous animals in our study.…”

Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes

“…, piglet) per 10% increase in genomic inbreeding) in P1, P2 and CB , and were distributed across all QTL. As reference, estimates of inbreeding depression reported in the literature for litter size ranged from -2 to -9 piglets per 100% of observed homozygosity ( Xiang et al 2016 ; Iversen et al 2019 ).…”

“…Xiang et al's model also includes a regression on "genomic inbreeding" (observed homozygosity) in PB and CB animals to measure individual "inbreeding depression". This can be seen as the opposite of heterosis and therefore it is possible to correct by, and to predict, individual heterosis (Iversen et al 2019). In this manner, all essential aspects of the joint PB -CB prediction are considered in a single analysis.…”