Fig 1.
Photographs of the four traits known to be associated with North American Araucanas (NAAs).
(A) NAA with ear-tufts, a pea comb, and rumplessness and (B) NAA laid blue shelled eggs.
Fig 2.
The relationship between groups of birds.
(A) Principal Components Analysis and (B) Dendrogram. Colors of dots in PCA and labels in dendrogram correspond to different groups of birds. Violet dots and text represent North American Araucana, green dots and text represent Korean Domestics, gold dots and text represent White Leghorns, and red dots and text represent Korean Araucana.
Table 1.
Phenotypes for NAA selected for whole-genome resequencing.
Fig 3.
Visualization of multidimensional scaling plot.
Discriminant model from random forest analysis on North American Araucanas (NAAs) compared to all other groups. The ellipses represent three standard errors around the centroid for each group. Violet dots represent NAA. Yellow dots represent the combined group of birds from Korean Domestics, White Leghorns and Korean Araucana.
Table 2.
Candidate genes selected based on annotation of the top 22 markers found to be within genes and fitting the pattern of the alternate allele being present at a higher frequency in the NAA samples.
Fig 4.
The negative tail of the ZHp distribution presented along chromosomes 1–28, 30, 32, 33, and LGE64. The Z and W chromosomes were not included because the sex of many birds in the study was not reported. Each dot represents a creeping window of up to 40 kb. The horizontal red line stands for the suggestive sweep significance level at ZHp = -4. The horizontal blue line stands for the strong sweep significance level at ZHp = -6. (A) Results from six North American Araucana, (B) results from three Korean Araucana, (C) results from three White Leghorns, and (D) results from three Korean Domestics.
Table 3.
Descriptive statistics of the negative ZHp values for all conducted selective sweeps.
Table 4.
Regions defined as strong selective sweeps in six NAAs.
Table 5.
Break end structural variants present in study population on chromosome 15 (NC 006102.4).
All tufted birds are characterized by an 8.3kb heterozygous deletion on chromosome 15.
Table 6.
Detecting the mutation for pea comb by identifying copy-number variations in SOX5.
This table contains the median value of Log2 ratios comparing WL to NAA, KA and KD in the first intron of SOX5.
Table 7.
Results from genotyping of wildtype, tailed, partial and rumpless NAA chicken breeds for SNP variants SV1 and SV2 from wing vein blood.