Application of Genomic Data for Reliability Improvement of Pig Breeding Value Estimates

Abstract

Replacement pigs’ genomic prediction for reproduction (total number and born alive piglets in the first parity), meat, fatness and growth traits (muscle depth, days to 100 kg and backfat thickness over 6–7 rib) was tested using single-step genomic best linear unbiased prediction ssGBLUP methodology. These traits were selected as the most economically significant and different in terms of heritability. The heritability for meat, fatness and growth traits varied from 0.17 to 0.39 and for reproduction traits from 0.12 to 0.14. We confirm from our data that ssGBLUP is the most appropriate method of genomic evaluation. The validation of genomic predictions was performed by calculating the correlation between preliminary GEBV (based on pedigree and genomic data only) with high reliable conventional estimates (EBV) (based on pedigree, own phenotype and offspring records) of validating animals. Validation datasets include 151 and 110 individuals for reproduction, meat and fattening traits, respectively. The level of correlation (r) between EBV and GEBV scores varied from +0.44 to +0.55 for meat and fatness traits, and from +0.75 to +0.77 for reproduction traits. Average breeding value (EBV) of group selected on genomic evaluation basis exceeded the group selected on parental average estimates by 22, 24 and 66% for muscle depth, days to 100 kg and backfat thickness over 6–7 rib, respectively. Prediction based on SNP markers data and parental estimates showed a significant increase in the reliability of low heritable reproduction traits (about 40%), which is equivalent to including information about 10 additional descendants for sows and 20 additional descendants for boars in the evaluation dataset.

Case Study on Increasing Breeding Value Estimation Reliability of Reproductive Traits in Serbian Highly Prolific Large White and Landrace Sows

“…The increase in the average reliability of EBVs is probably a consequence of the increased volume of information included in the joint evaluation, as reported in the research of many authors [ 18 , 36 , 37 , 38 ]. The reliability of the EBVs for the NBA was much higher than in [ 39 ]. These authors reported much lower values for the reliability of EBVs in highly prolific sows, i.e., 0.33 for the NBA compared to 0.74 recorded in our study.…”

“…These authors reported much lower values for the reliability of EBVs in highly prolific sows, i.e., 0.33 for the NBA compared to 0.74 recorded in our study. Even though the data on pedigree and own phenotype were used in both studies, the sample was much smaller in the estimation of BV in the mentioned study [ 39 ], which can be related to the amount of information in the pedigree file and the smaller volume of data on phenotype.…”

Weighted Single-Step Genomic Best Linear Unbiased Prediction Method Application for Assessing Pigs on Meat Productivity and Reproduction Traits

“…In the previous article, we discussed the increase in the accuracy of breeding value estimates by including genomic data on the characteristics of meat and fattening productivity and reproduction traits in pigs [39]. However, in this study, we decided to evaluate the validity of the procedure application for individual SNP marker effect weighting and compared the obtained estimates' reliability with traditional BLUP AM (Scenario 4) and ssGBLUP (Table 4).…”

Advanced median-based genetic similarity analysis in Kazakh Tazy dogs: A novel approach for breed conformity assessment

“…This problem can be overcome by using genetic data to improve the reliability of breeding value estimates for dogs in the bonitation process. Information at the DNA level may lead to faster genetic improvement than relying on phenotypic data and pedigrees alone [1–5]…”