title: Whole-genome resequencing of Xishuangbanna fighting chicken to identify signatures of selection.
abstract: Selective 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.
  
  
  
  We identified selection signals in 100-kb windows sliding in 10-kb steps by using two approaches: the pooled heterozygosity [Formula: see text] and the fixation index [Formula: see text] 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.
  
  
  
  This 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.
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
authors: Xing
authors: X
authors: Guo
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
authors: Qi
authors: Q
authors: Fang
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
authors: Chendong
authors: C
authors: Ma
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
authors: Bangyuan
authors: B
authors: Zhou
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
authors: Yi
authors: Y
authors: Wan
authors: College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People's Republic of China. jiangrunshen@ahau.edu.cn.
authors: Runshen
authors: R
authors: Jiang
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002645:Chickens / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic