Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection.

Xing Guo,Qi Fang,Runshen Jiang,Yi Wan,Chendong Ma,Bangyuan Zhou

doi:10.1186/s12711-016-0239-4

Abstract

BackgroundSelective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes. The identification of selection signatures can help to elucidate the mechanisms of selection and accelerate genetic improvement. Fighting chickens have undergone extensive artificial selection, resulting in modifications to their morphology, physiology and behavior compared to wild species. Comparing the genomes of fighting chickens and wild species offers a unique opportunity for identifying signatures of artificial selection.ResultsWe identified selection signals in 100-kb windows sliding in 10-kb steps by using two approaches: the pooled heterozygosity ({text{H}}_{text{p}} ) and the fixation index (F_{text{ST}} ) between Xishuangbanna fighting chicken (YNLC) and Red Jungle Fowl. A total of 413 candidate genes were found to be putatively under selection in YNLC. These genes were related to traits such as growth, disease resistance, aggressive behavior and energy metabolism, as well as the morphogenesis and homeostasis of many tissues and organs.ConclusionsThis study reveals mechanisms and targets of artificial selection, which will contribute to improve our knowledge about the evolution of fighting chickens and facilitate future quantitative trait loci mapping.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0239-4) contains supplementary material, which is available to authorized users.

Highlights

Selective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes
Detection of single nucleotide polymorphism (SNP) A total of 16.40 × 106 SNPs were identified from the genomes of 14 individuals, i.e. eight YNLC (13.15 × 106 SNPs) and six Red Jungle Fowl (RJF) individuals (13.87 × 106 SNPs)
Most SNPs identified for the YNLC individuals were located in intergenic and intron regions (57.16 and 38.77 %, respectively); 1.36 % of these 13.15 × 106 SNPs were predicted to be within protein-coding regions and 0.40 % as amino acid altering mutations; 1.30 % of the 13.15 × 106 SNPs were within 1-kb regions upstream or downstream of the transcription start or end sites, and may have a possible role in transcriptional regulation, with 510 SNPs of these residing within splice sites (Table 1; see Additional file 2: Table S2)

Summary

Introduction

Selective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes. Fighting chickens have undergone extensive artificial selection, resulting in modifications to their morphology, physiology and behavior compared to wild species. Comparing the genomes of fighting chickens and wild species offers a unique opportunity for identifying signatures of artificial selection. The Xishuangbanna fighting chicken (YNLC) is a typical fighting chicken breed that has been subjected to strong artificial selection, which has led to remarkable phenotypic characteristics in morphology, physiology, and behavior. Selection leads to specific changes in the patterns of variation among selected loci and in neutral loci linked to them.

Methods

Results

Conclusion