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

Abstract

The Hongshan chicken is a Chinese indigenous breed that has two distinctly different tail types. Some chickens have stunted tails as compared to the normal phenotype, and they are termed rumpless. Rumplessness in other chicken breeds was caused by a reduction in the number of coccygeal vertebrae. However, X-ray examination showed that rumpless Hongshan chickens possess the normal number of coccygeal vertebrae. Our analyses of the main tail feathers and tissue sections led us to speculate that their stunted tail appearance may be the result of abnormal feather development. To investigate the genetic mechanism underlying rumplessness in Hongshan chickens, we analyzed the results of various crosses. The results indicated that rumplessness is a Z-linked dominant character. In addition, we chose some normal and rumpless individuals for pool-sequencing. Nucleotide diversity and Fst were calculated, and a selective sweep was detected on the Z chromosome. These analyses allowed us to reduce the search area to 71.8–72 Mb on the Z chromosome (galGal5.0). A pseudogene LOC431648 located in this region appeared a strong candidate involving in Wnt/β-catenin signaling pathway to regulate feather development in chickens.

Phenotypic Analysis of Growth and Morphological Traits in Miniature Breeds of Japanese Indigenous Chickens

“…Recently, population genomics has been used to identify candidate genes for several phenotypes ( Goto and Tsudzuki, 2017 ). Using indigenous Chinese chicken breeds, Wang et al (2017) identified candidate genes affecting rumplessness on the Z chromosome using population genomics. They conducted RNA-seq with feather follicles using wild-type and rumpless chickens to identify the causative variants ( Wang et al , 2017 ).…”

“…Using indigenous Chinese chicken breeds, Wang et al (2017) identified candidate genes affecting rumplessness on the Z chromosome using population genomics. They conducted RNA-seq with feather follicles using wild-type and rumpless chickens to identify the causative variants ( Wang et al , 2017 ). Recently, Li et al (2020) identified causal genes for feathered legs in chickens by combining classical linkage mapping using an experimental cross and high-resolution identical-by-descent mapping using whole-genome sequence data.…”

Genome‐wide association study confirms that the chromosome Z harbours a region responsible for rumplessness in Hongshan chickens

“…In Hongshan chickens, rumplessness is a distinct phenotype, because it is due to abnormal main tail feather development (Wang et al . ) rather than coccygeal vertebral abnormality as in other chicken breeds (Dunn ; Zwilling ; Landauer ). In our previous study, showing that rumplessness in Hongshan chickens is a sex‐linked dominant characteristic (Wang et al .…”

“…In our previous study, showing that rumplessness in Hongshan chickens is a sex‐linked dominant characteristic (Wang et al . ), we found a candidate gene (pseudogene LOC431648 on the Z chromosome) by population genetics analysis using genome re‐sequencing data (72.0 Mb, galGal 5.0) that may contribute to the trait. However, we failed to validate the gene by functional analysis to determine whether the gene is indeed responsible for the rumplessness in Hongshan chickens (data not shown).…”

Genome‐wide re‐sequencing and transcriptome analysis reveal candidate genes associated with the pendulous comb phenotype in domestic chickens

“…Several selective sweeps methods for detecting selection signals based on allele counts or allele frequencies are included in the aforementioned software. These selective sweep approaches have been shown to be efficient in uncovering genetic variation underlying phenotype diversity (Wang, Li, Ma, Zhang, & Zhang, 2017;Wang, Pi, Pan, Shen, & Qu, 2017). Moreover, NGS is also a powerful tool for high-throughput transcriptomics analysis (RNA-seq).…”