Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

Scarce Evidence of Heterosis for Growth Traits in Peruvian Guinea Pigs

This study aimed to estimate the heterosis for productive traits in a two-way crossbreeding scheme. Four guinea pig lines were originally selected for the following traits: line P1 for the growth rate, P2 for the partial feed conversion rate, M1 for the growth rate of the litter at 10 days of age, and M2 for the litter size at birth. The comparison included 176 purebreds (P1: 46, P2: 43, M1: 54 and M2: 33) and 150 crosses (P1P2: 42, P2P1: 38, M1M2: 11 and M2M1: 59); body weights at birth, 10 days, weaning and 60 days of age were analyzed. A linear fixed-effect model was used, and heterosis was estimated as the difference between the average performance of the crossbred and pure-line animals. The pure line comparisons showed that P2 was lower than P1 for weight at 10 days and weaning weight, while all other comparisons between the paternal and maternal pure lines were not significant. The results indicated significant positive heterosis effects for both types of crosses, but only for birth weight: 3.7% for paternal crosses and 12.7% for maternal crosses. The heterosis estimates were mostly positive but not significant for all other traits. A reason for the low levels of heterosis could be that the lines are not very genetically differentiated. These results suggest that applying a two-way crossbreeding scheme within paternal and maternal guinea pig lines for meat production is not recommended due to the absence of heterosis for growth traits.

Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs

Creating synthetic lines is the standard mating mode for commercial pig production. Traditional mating performance was evaluated through a strictly designed cross-combination test at the 'breed level' to maximize the benefits of production. The Duroc-Landrace-Yorkshire (DLY) three-way crossbred production system became the most widely used breeding scheme for pigs. Here, we proposed an 'individual level' genomic mating procedure that can be applied to commercial pig production with efficient algorithms for estimating marker effects and for allocating the appropriate boar-sow pairs, which can be freely accessed to public in our developed HIBLUP software at https://www.hiblup.com/tutorials#genomic-mating. A total of 875 Duroc boars, 350 Landrace-Yorkshire sows and 3573 DLY pigs were used to carry out the genomic mating to assess the production benefits theoretically. The results showed that genomic mating significantly improved the performances of progeny across different traits compared with random mating, such as the feed conversion rate, days from 30 to 120 kg and eye muscle area could be improved by -0.12, -4.64 d and 2.65 cm2, respectively, which were consistent with the real experimental validations. Overall, our findings indicated that genomic mating is an effective strategy to improve the performances of progeny by maximizing their total genetic merit with consideration of both additive and dominant effects. Also, a herd of boars from a richer genetic source will increase the effectiveness of genomic mating further.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations

Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.