Recurrent tandem duplication of a conserved enhancer underlies parallel genetic origins of rumplessness in chickens
Abstract
Congenital caudal body truncation in chickens—the rumpless phenotype—provides a powerful model for studying vertebrate axis elongation. This trait has been linked to misexpression of IRX1 and IRX2 in the embryonic tail bud, and breed-specific candidate mutations, including a deletion upstream of IRX1 proposed for the Piao breed, have been reported, yet whether the various breeds share a common causal basis has remained unresolved. By combining whole-genome resequencing, long-read sequencing, and population genomic analyses of four geographically isolated rumpless breeds (Chinese Piao, Japanese Uzurao, Belgian Barbu de Grubbe, and Chilean Araucana), we identify distinct tandem duplications of the IRX1/IRX2 intergenic region that converge on a single ∼700 bp conserved noncoding element, which we designate EnhRp. Haplotype and breakpoint analyses reveal that these duplications arose through at least two mutational events rather than a single shared origin. Functional assays in chicken embryos demonstrate that duplicating EnhRp acts as a hypermorphic gain-of-function mutation, elevating enhancer activity in the tail bud in a dose-dependent manner, consistent with the ectopic IRX1/IRX2 expression. Our findings support a model of parallel evolution in which distinct structural variants recurrently target a specific cis-regulatory element across at least two independent lineages, highlighting the critical role of noncoding variation in shaping morphological diversity.
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BibTeX
@article{wang2026recurrent,
title = {{Recurrent tandem duplication of a conserved enhancer underlies parallel genetic origins of rumplessness in chickens}},
author = {Sheng Wang and Kun Wang and Keiji Kinoshita and Kanta Takada and Takayuki Suzuki and Xuehai Ge and Wan-Dong Bao and Jin-Jin Zhang and Min-Min Yang and Tengfei Dou and Zhenhui Cao and Junjing Jia and Dong-Dong Wu and Nowlan H Freese and Susan C Chapman and Yun-Mei Wang and Ming-Shan Wang and Changrong Ge},
journal = {Molecular Biology and Evolution},
year = {2026},
month = oct,
doi = {10.1093/molbev/msag253},
url = {https://doi.org/10.1093/molbev/msag253},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Recurrent tandem duplication of a conserved enhancer underlies parallel genetic origins of rumplessness in chickens
AU - Sheng Wang
AU - Kun Wang
AU - Keiji Kinoshita
AU - Kanta Takada
AU - Takayuki Suzuki
AU - Xuehai Ge
AU - Wan-Dong Bao
AU - Jin-Jin Zhang
AU - Min-Min Yang
AU - Tengfei Dou
AU - Zhenhui Cao
AU - Junjing Jia
AU - Dong-Dong Wu
AU - Nowlan H Freese
AU - Susan C Chapman
AU - Yun-Mei Wang
AU - Ming-Shan Wang
AU - Changrong Ge
PY - 2026
DA - 2026/10/01
JO - Molecular Biology and Evolution
DO - 10.1093/molbev/msag253
UR - https://doi.org/10.1093/molbev/msag253
AB - Congenital caudal body truncation in chickens—the rumpless phenotype—provides a powerful model for studying vertebrate axis elongation. This trait has been linked to misexpression of IRX1 and IRX2 in the embryonic tail bud, and breed-specific candidate mutations, including a deletion upstream of IRX1 proposed for the Piao breed, have been reported, yet whether the various breeds share a common causal basis has remained unresolved. By combining whole-genome resequencing, long-read sequencing, and population genomic analyses of four geographically isolated rumpless breeds (Chinese Piao, Japanese Uzurao, Belgian Barbu de Grubbe, and Chilean Araucana), we identify distinct tandem duplications of the IRX1/IRX2 intergenic region that converge on a single ∼700 bp conserved noncoding element, which we designate EnhRp. Haplotype and breakpoint analyses reveal that these duplications arose through at least two mutational events rather than a single shared origin. Functional assays in chicken embryos demonstrate that duplicating EnhRp acts as a hypermorphic gain-of-function mutation, elevating enhancer activity in the tail bud in a dose-dependent manner, consistent with the ectopic IRX1/IRX2 expression. Our findings support a model of parallel evolution in which distinct structural variants recurrently target a specific cis-regulatory element across at least two independent lineages, highlighting the critical role of noncoding variation in shaping morphological diversity.
SN - 0737-4038
SN - 1537-1719
ER -