Parallel Evolution of Polydactyly Traits in Chinese and European Chickens

Abstract

Polydactyly is one of the most common hereditary congenital limb malformations in chickens and other vertebrates. The zone of polarizing activity regulatory sequence (ZRS) is critical for the development of polydactyly. The causative mutation of polydactyly in the Silkie chicken has been mapped to the ZRS; however, the causative mutations of other chicken breeds are yet to be established. To understand whether the same mutation decides the polydactyly phenotype in other chicken breeds, we detected the single-nucleotide polymorphism in 26 different chicken breeds, specifically, 24 Chinese indigenous breeds and 2 European breeds. The mutation was found to have fully penetrated chickens with polydactyly in China, indicating that it is causative for polydactyly in Chinese indigenous chickens. In comparison, the mutation showed no association with polydactyly in Houdan chickens, which originate from France, Europe. Based on the different morphology of polydactyly in Chinese and European breeds, we assumed that the trait might be attributable to different genetic foundations. Therefore, we subsequently performed genome-wide association analysis (GWAS) to locate the region associated with polydactyly. As a result, a ~0.39 Mb genomic region on GGA2p was identified. The region contains six candidate genes, with the causative mutation found in Chinese indigenous breeds also being located in this region. Our results demonstrate that polydactyly in chickens from China and Europe is caused by two independent mutation events that are closely located in the chicken genome.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication

“…A total of 7,908,722 SNPs were validated in the duck dbSNP database, which covered 96.2% of the database ( Supplemental Table S2 ). For the 28,199,227 SNPs not confirmed by dbSNPs, 390 randomly selected nucleotide sites were further validated using diagnostic PCR combined with Sanger sequence method described in previous researchM [ 8 , 72 , 73 ]. The result showed 100% accuracy, indicating the high reliability of the called SNP variation identified in this study.…”

Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis

“…Similarly, for poultry, and particularly chickens, the genetic factors underlying many phenotypic traits have been studied in detail. For example, at the DNA level, phenotype traits of chicken, such as earlobe colour 2 and polydactyly 3 , have been investigated using different approaches such as genome-wide association studies and re-sequencing analysis. Genes and their allelic relationships that affect eggshell 4,5 and feather colour 6 have also been characterised at the RNA level.…”

Detection and Utility of Genetic Variation in Chinese Local Chicken Breeds

“…Using this F 2 population, that crest phenotype of Silkie is located on the E22C19W28 linkage group, and that it shows complete association to the HOXC-cluster on this chromosome by linkage analysis and genome-wide association [60]. Other several different appearance traits have been identified and located such as pigmentation [61], rose comb [62], silky [63], Polydactyly [64], muffs, and beards [65] in Chinese Silkie chicken and other breeds.…”