Journal
JOURNAL OF ANIMAL SCIENCE
Volume 93, Issue 7, Pages 3292-3302Publisher
OXFORD UNIV PRESS INC
DOI: 10.2527/jas.2015-8879
Keywords
Duroc; genes; genome-wide associations; intramuscular fat; selection signatures
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Funding
- College of Agriculture and Life Sciences
- Ensminger program, State of Iowa
- Hatch
- MINECO [AGL2009-09779, AGL2012-33529]
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Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations, one under positive selection for IMF and the other selected for decreased backfat but under stabilizing selection for IMF, were used to identify signatures of selection associated with IMF using 60,000 single-nucleotide polymorphism data. The effects of selection were analyzed between 2 lines or groups representing selected and control animals within each population using a discriminant analysis of principal components and Wright's fixation index (F-ST). Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. Each statistical method identified 10-20 selection signatures. A few haplotype-based signatures of selection agreed with results from a genome-wide association study (GWAS), while F-ST measures showed a better agreement with GWAS results. Agreement of marker-trait associations and signatures of selection was limited, and further examination will be necessary to understand the effect of selection on IMF and why some regions identified by GWAS did not appear to respond to the selection practiced. The genes in 21 consensus selection signatures were examined. Several genes with an effect on overall fatness were identified, but further research is needed to assess whether or not some of them could have a specific effect on IMF.
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