Estimation of genetic parameters and accuracy of genomic prediction for production traits in Duroc pigs

Abstract

Genetic parameters and accuracy of genomic prediction for production traits in a Duroc population were estimated. Data were on 24 828 purebred Duroc pigs born in 2000–2016. After quality control procedures, 30 263 single nucleotide polymorphism markers and 560 animals remained that were used to predict the genomic breeding values of individuals. Accuracies of predicted breeding values for average daily gain (ADG), backfat thickness (BF), loin muscle area (LMA), lean percentage (LP) and age at 90 kg (D90) between pedigree-based and single-step methods were compared. Analyses were carried out with a multivariate animal model to estimate genetic parameters for production traits while univariate analyses were performed to predict the genomic breeding values of individuals. Heritability estimates from pedigree analysis were moderate to high. Heritability estimates and standard error for ADG, BF, LMA, LP and D90 were 0.35 ± 0.01, 0.35 ± 0.11, 0.24 ± 0.04, 0.42 ± 0.11 and 0.37 ± 0.03, respectively. Genetic correlations of ADG with BF and LP were low and negative. Genetic correlations of LMA with ADG, BF, LP and D90 were –0.37, –0.27, 0.48 and 0.31, respectively. High correlations were observed between ADG and D90 (–0.98), and also between BF and LP (–0.93). Accuracies of genomic breeding values for ADG, BF, LMA, LP and D90 were 0.30, 0.33, 0.38, 0.40 and 0.28, respectively. Corresponding accuracies using pedigree-based method were 0.29, 0.32, 0.38, 0.39 and 0.27, respectively. The results showed that the single-step method did not show significant advantage compared to the pedigree-based method.

Genetic Analysis of Major Production and Reproduction Traits of Korean Duroc, Landrace and Yorkshire Pigs

“…According to Clutter [ 21 ], several studies reported an average h 2 of 0.49, which was in line with our findings. Lopez et al also had an h 2 of 0.35, further supporting our values [ 15 ]. In other studies, consistent h 2 estimates were published in Duroc pigs (0.53 ± 0.15) [ 33 ], as well as in Landrace (0.54 ± 0.01) and Yorkshire pigs (0.45 ± 0.01) [ 14 ].…”

“…Our study suggested that ADG and DAYS105 were firmly and oppositely (−0.96 to −0.97) genetically linked. In Duroc pigs, a similar high, opposite correlation (−0.98) was reported previously [ 15 ]. Such high r g values essentially indicate that selection for either ADG or DAYS105 could result in favorable changes in both of these traits.…”

“…Another work considering DAYS90 in Korean pigs found more similar values, such as 0.36–0.37 in Duroc, 0.37–0.38 in Landrace and 0.41–0.42 in Yorkshire pigs [ 13 ]. Other comparable h 2 values of DAYS90 include an h 2 of 0.37 in Duroc and 0.37 to 0.42 in Landrace pigs [ 15 , 31 ]. Furthermore, Hoque et al, who studied DAYS105 in Japanese Duroc pigs, also showed some agreements with our findings [ 5 ].…”

“…Similarly, some studies were also available that presented slightly lower h 2 values, such as 0.28 in US Duroc pigs and 0.30 in crossbred pigs [ 27 , 28 ]. It was evident that the differences that existed between reports on similar Korean pigs [ 14 , 15 ] could be explained by various factors, such as the differences in data structures (multi-parity records), adopted models and sampling errors [ 29 ].…”

“…According to current practices, Korean pig selection is based mainly on DAYS105, BFT, TNB and NBA. Therefore, many of these traits have been studied previously in Korean pigs [ 13 , 14 , 15 ]. However, DAYS105 was not assessed extensively due to its recent adoption in the breeding program.…”