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

Simple Summary Selection of pigs in Russia is carried out within the framework of separate large holdings. Such a system does not allow for the use of sufficiently large amounts of data (on all individuals of the breed) to obtain the most reliable breeding value estimates. This problem is especially relevant for low-inherited reproduction traits (for example, prolificacy), which are the main ones for maternal pig breeds. In this regard, our study considered the possibility of improving the accuracy of the breeding value assessment of Large White pigs (replacement pigs, sows and boars) through the use of genomic data obtained on a high-density hybridization chip. 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.

Automated summary

Pig selection in Russia is hindered by the structure of large-scale breeding enterprises, limiting data usage for accurate breeding value estimation. This study evaluated the use of genomic data to improve breeding value assessment of Large White pigs, confirming the effectiveness of ssGBLUP methodology. Genomic prediction showed significant reliability increase for low heritable reproduction traits, equivalent to adding information about additional descendants in the evaluation dataset.