Whole-genome resequencing reveals genetic indels of feathered-leg traits in domestic chickens

Whole-genome resequencing provides the opportunity to explore the genomic variations and pave way for further functional assays to map the economical trait loci. In this study, we sequenced the genomes of mixed chicken samples from a full-sib family, with feathered and unfeathered legs at an average effective depth of 4.43×\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$4.43\times $$\end{document}, using Illumina Hiseq 2000 instruments. Over 2.1 million nonredundant short indels (1–71 bp) were obtained. Among them, 16,375 common indels that were polymorphic between the comparison groups were revealed for further analysis. The majority of the common differential indels (76.52%) were novel. Follow-up validation assays confirmed that 80% randomly selected indels represented true variations. The indels were annotated based on the chicken genome sequence assembly. As a result, 16,375 indels were found to be located within 2756 annotated genes, with only 33 (0.202%) located in exons. By integrated analysis of the 2756 genes with gene function and known quantitative trait loci, we identified a total of 24 promising candidate genes potentially affecting feathered-leg trait, i.e. FGF1, FGF4, FGF10, FGFR1, FRZB, WNT1, WNT3A, WNT11, PCDH1, PCDH10, PCDH19, SOX3, BMP2, NOTCH2, TGF-β\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta $$\end{document}2, DLX5, REPS2, SCN3B, TCF20, FGF3, FSTL1, WNT7B, ELOVL2 and FGF8. Our findings provide a basis for further study and reveal key genes for feathered-leg trait in chickens.