Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
Sungbong Jang1, Roger Ros-Freixedes2, John M Hickey3
1Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA. jsbng8615@gmail.com.
Genetics, Selection, Evolution : GSE
|July 26, 2023
Summary
Whole-genome sequence data can improve genomic predictions in pigs, especially for maternal lines and fertility traits. However, benefits vary by pig line and variant selection method, showing limited overall advantage in pigs.
Area of Science:
- Animal Genomics
- Quantitative Genetics
- Livestock Breeding
Background:
- Whole-genome sequence (WGS) data offer causative variants beyond standard single nucleotide polymorphism (SNP) chip data.
- Investigating the utility of preselected WGS variants for genomic predictions in pig breeding is crucial.
Purpose of the Study:
- To evaluate the impact of using preselected variants from WGS on single-step genomic predictions in maternal and terminal pig lines.
- To compare prediction accuracy using WGS-derived SNP sets versus standard SNP chips.
Main Methods:
- Studied two maternal and four terminal pig lines, analyzing eight and seven traits, respectively.
- Generated two preselected SNP sets (Top40k and ChipPlusSign) from WGS data based on genome-wide association studies (GWAS).
- Compared single-step genomic prediction accuracies using preselected SNP sets against the standard porcine SNP chip.
Main Results:
- Maternal lines showed accuracy increases of 0.6% (ChipPlusSign) and 4.9% (Top40k) over the standard chip, with Top40k excelling for fertility traits.
- Terminal lines experienced an average accuracy loss of 1% with Top40k, while ChipPlusSign yielded a small gain of 0.9%.
- Adjusting SNP variances slightly improved accuracies but results were inconsistent across lines and traits.
Conclusions:
- The advantage of using WGS variants for genomic predictions in pigs is contingent on the specific line, population size, and variant preselection strategy.
- While WGS data offer benefits with large populations, their overall advantage in pigs remains limited.
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