A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens

Abstract

Shank color of domestic chickens varies from black to blue, green, yellow, or white, which is controlled by the combination of melanin and xanthophylls in dermis and epidermis. Dermal shank pigmentation of chickens is determined by sex-linked inhibitor of dermal melanin (Id), which is located on the distal end of the long arm of Z chromosome, through controlling dermal melanin pigmentation. Although previous studies have focused on the identification of Id and the linear relationship with barring and recessive white skin, no causal mutations have yet been identified in relation to the mutant dermal pigment inhibiting allele at the Id locus. In this study, we first used the 600K Affymetrix Axiom HD genotyping array, which includes ~580,961 SNP of which 26,642 SNP were on the Z chromosome to perform a genome-wide association study on pure lines of 19 Tibetan hens with dermal pigmentation shank and 21 Tibetan hens with yellow shank to refine the Id location. Association analysis was conducted by the PLINK software using the standard chi-squared test, and then Bonferroni correction was used to adjust multiple testing. The genome-wide study revealed that 3 SNP located at 78.5 to 79.2 Mb on the Z chromosome in the current assembly of chicken genome (galGal4) were significantly associated with dermal shank pigmentation of chickens, but none of them were located in known genes. The interval we refined was partly converged with previous results, suggesting that the Id gene is in or near our refined genome region. However, the genomic context of this region was complex. There were only 15 SNP markers developed by the genotyping array within the interval region, in which only 1 SNP marker passed quality control. Additionally, there were about 5.8-Mb gaps on both sides of the refined interval. The follow-up replication studies may be needed to further confirm the functional significance for these newly identified SNP.

The Genetics of Skin Color Variation in Farm Animals

“…The genome-wide study revealed that 3 SNP located at 78.5 to 79.2 Mb on the Z chromosome in the current assembly of chicken genome (galGal4) were significantly associated with dermal shank pigmentation of chickens, but none of them were located in known genes. The interval we refined was partly converged with previous results, suggesting that the Id gene is in or near our refined genome region [11]. Zhang, et al [12] investigated the genetic basis of the gray dilution phenotype in the Anti tile-like gray chicken.…”

“…This indicates ASIP participates in the regulation of skin color, which is supported by the recent study in zebrafish and avain [9,10]. Li, et al [11] used the 600K Affymetrix Axiom HD genotyping array to perform a genome-wide association study on pure lines of 19 Tibetan hens with dermal pigmentation shank and 21 Tibetan hens with yellow shank to refine the Id location. The genome-wide study revealed that 3 SNP located at 78.5 to 79.2 Mb on the Z chromosome in the current assembly of chicken genome (galGal4) were significantly associated with dermal shank pigmentation of chickens, but none of them were located in known genes.…”

A novel sex-linked mutant affecting tail formation in Hongshan chicken

“…We obtained 40 offspring, 22 of which were dwarf females with normal tails, 16 rumpless males with normal body size, and the two others were males with normal tail and normal body size. The second breed was a Jianghan chicken that had green shanks, which is a recessive trait determined by an unknown gene on the Z chromosome 14 , 42 . We obtained 39 offspring, 17 of which were rumpless and yellow-shanked males, 19 were normal tailed and green-shanked females, two were rumpless and green-shanked males, and one was a normal tailed and yellow-shanked male.…”

Developing a 670k genotyping array to tag ∼2M SNPs across 24 horse breeds

“…High-density ~670k genotyping arrays were used in domestic cattle to identify structural variation [39,40]. Other studies have leveraged this technology to discover and refine loci associated with production traits [41][42][43]. Based on reports from other domestic animals, coupled with preliminary analyses performed here, we anticipate similar performance and increased power for map-based studies to soon follow in the horse.…”