Journal
DNA RESEARCH
Volume 22, Issue 3, Pages 205-217Publisher
OXFORD UNIV PRESS
DOI: 10.1093/dnares/dsv005
Keywords
SNP; next-generation sequencing; chicken; selection signature; functional variants
Categories
Funding
- BBSRC/DEFRA LINK grant
- National Council for Scientific and Technological Development - Brazil (CNPq) [201306/2010-7]
- Research Council UK (RCUK)
- BBSRC [BB/I025328/1, BB/I011005/1, BBS/E/D/20211550, BBS/E/D/20310000, BBS/E/D/20211551] Funding Source: UKRI
- MRC [G0900740, MR/K001744/1] Funding Source: UKRI
- NERC [NBAF010003] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BBS/B/13500, BBS/E/D/20211551, BB/I011005/1, BB/I025328/1, BBS/E/D/20310000, G18647, BBS/E/D/20211550] Funding Source: researchfish
- Medical Research Council [G0900740, MR/K001744/1] Funding Source: researchfish
- Natural Environment Research Council [NBAF010003] Funding Source: researchfish
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Next-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonymous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding.
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