Table 1.
Genotypes of the causative mutation and their distribution in 26 chicken breeds.
Fig 1.
Variation in X-ray digital radiography with respect to Beijing-You foot polydactyly.
A-D show the different foot phenotypes of Beijing-You chicken, E-H show the X-ray digital radiography coordinately with A–D. A & E: non-polydactylous foot with four digits, identified from anterior to posterior (1, 2, 3, 4). B & F: Beijing-You foot with four digits, with a polyphalange in digit “1” making it digit “2” (2, 2, 3, 4). C & G: polydactylous Beijing-You foot with five digits (2, 1, 2, 3, 4). D & H: polydactylous Beijing-You foot with six digits (1, 2, 1, 2, 3, 4).
Fig 2.
Principal polydactyly subtypes in Beijing-You, Silkie, and Houdan chickens.
Two subtypes of polydactyly were found in the three chicken breeds, but with difference prevalence. Subtype I: principal subtype of Beijing-You (A) and Silkie (B), in which an extra toe was separated from the second phalanx in the most anterior toe; Subtype II: principal subtype of Houdan (C), with extra toe separation occurring from the first phalanx.
Fig 3.
Genotypes of causative SNP loci detected by sequencing and diagnostic PCR.
The genotypes shown on the left side are wild type (CC), mutation heterozygote (AC), and derived homozygote (AA), from top to bottom. The mutation genotypes were fully associated with polydactyly in Chinese chickens, regardless of whether the mutation was homozygotic or heterozygotic. PCR products digested by restriction enzyme BsrDI are presented on the right.
Fig 4.
Genome-wide scan for polydactyly in Houdan chickens.
Manhattan plot showing the association of all SNPs with the polydactyly trait of Houdan chickens. SNPs were plotted on the x-axis according to their position on each chromosome against their association with these traits on the y-axis (shown as -log10 P-value). The green line and black line indicate the genome-wide suggestive and significant association with P-values of 1.73 × 10−5 (1.00/57,657) and 8.67 × 10−7 (0.05/57,657), respectively.
Table 2.
Single nucleotide polymorphisms (SNPs) showing significant association with polydactyly in Houdans.