Next Article in Journal

CCN2 Activates Cellular Senescence Leading to Kidney Fibrosis in Folic Acid-Induced Experimental Nephropathy

Next Article in Special Issue

Evidence for Pituitary Repression of the Human Growth Hormone-Related Placental Lactogen Genes and a Role for P Sequences

Previous Article in Journal

Potential Pathogenetic Role of the D313Y Mutation in the GLA Gene in Anderson Fabry Disease: Two Case Reports

Previous Article in Special Issue

Potential Association of the CSMD1 Gene with Moderate Intellectual Disability, Anxiety Disorder, and Obsessive–Compulsive Personality Traits

You seem to have javascript disabled. Please note that many of the page functionalities won't work as expected without javascript enabled.

Search for Articles:

Title / Keyword

Author / Affiliation / Email

Journal

Article Type

Advanced Search

Section

Special Issue

Volume

Issue

Number

Page

Logical OperatorOperator

Search Text

Search Type

Submit to this Journal Review for this Journal Propose a Special Issue

Article Menu

Share Help Cite Discuss in SciProfiles

Order Article Reprints

Font Type:

Font Size:

Line Spacing:

Column Width:

Background:

Open AccessArticle

Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed

by

Ronglang Cai

^1,2,

Shuang Gu

^1,2,

Boxuan Zhang

^1,2,

Xuemei Deng

^1,2,

Mostafa Galal Abdelfattah

³

,

Ning Yang

^1,2,

Hesham Y. A. Darwish

^4,*

and

Congjiao Sun

^1,2,*

¹

Frontier Science Center for Molecular Design Breeding, State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing 100193, China

²

National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing 100193, China

³

Department of Poultry Production, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt

⁴

Department of Applied Biotechnology, Molecular Biology Researches & Studies Institute, Assiut University, Assiut 71526, Egypt

^*

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2025, 26(9), 4399; https://doi.org/10.3390/ijms26094399

Submission received: 1 April 2025 / Revised: 30 April 2025 / Accepted: 2 May 2025 / Published: 6 May 2025

(This article belongs to the Collection Feature Papers in Molecular Genetics and Genomics)

Download

Browse Figures

Review Reports Versions Notes

Abstract

Heat-stress resilience is vital for poultry in tropical/subtropical regions where high temperatures impair productivity. Ake chickens, as the only naked-neck chicken breed in China, exhibit robust resistance to heat stress, but this breed lacks clarity in its genetic origins. This study utilized the next-generation sequencing data from 22 chicken breeds to conduct phylogenetic and population analyses. Gene flow analysis revealed a gene migration event from Iranian naked-neck chickens and Indian local breeds to Ake chickens, and population separation estimates suggested that the naked-neck gene was introduced to China around 500–600 years ago. NJ-tree, PCA, and population structure analyses showed that Ake chickens cluster with Yunnan native breeds, which diverged only 100–200 years ago. A selective sweep in the candidate region on chromosome 3 (97.0–97.37 Mb) showed elevated genetic differentiation (F_ST) and reduced nucleotide diversity (π) compared to the genome-wide average, indicating rapid fixation of the trait under natural/artificial selection. Demographic reconstruction indicated that the current effective size of Ake chickens is stable at 2000–3000 individuals. These findings deepen our understanding of Ake chicken evolution and provide valuable insights for conservation and the development of heat-stress-resistant poultry breeds.

Keywords: Ake chicken; population phylogenetic and structure analysis; gene flow; effective population size; population separation history

Share and Cite

MDPI and ACS Style

Cai, R.; Gu, S.; Zhang, B.; Deng, X.; Abdelfattah, M.G.; Yang, N.; Darwish, H.Y.A.; Sun, C. Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed. Int. J. Mol. Sci. 2025, 26, 4399. https://doi.org/10.3390/ijms26094399

AMA Style

Cai R, Gu S, Zhang B, Deng X, Abdelfattah MG, Yang N, Darwish HYA, Sun C. Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed. International Journal of Molecular Sciences. 2025; 26(9):4399. https://doi.org/10.3390/ijms26094399

Chicago/Turabian Style

Cai, Ronglang, Shuang Gu, Boxuan Zhang, Xuemei Deng, Mostafa Galal Abdelfattah, Ning Yang, Hesham Y. A. Darwish, and Congjiao Sun. 2025. "Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed" International Journal of Molecular Sciences 26, no. 9: 4399. https://doi.org/10.3390/ijms26094399

APA Style

Cai, R., Gu, S., Zhang, B., Deng, X., Abdelfattah, M. G., Yang, N., Darwish, H. Y. A., & Sun, C. (2025). Genetic and Evolutionary Analysis of Ake Chicken: New Insights into China’s Sole Indigenous Naked-Neck Chicken Breed. International Journal of Molecular Sciences, 26(9), 4399. https://doi.org/10.3390/ijms26094399

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop