TY - JOUR
T1 - Genomic insight into the influence of selection, crossbreeding, and geography on population structure in poultry
AU - Wu, Zhou
AU - Bosse, Mirte
AU - Rochus, Christina M
AU - Groenen, Martien A M
AU - Crooijmans, Richard P M A
N1 - Funding Information:
We would like to thank the Centre for Genetic Resources, the Netherlands (CGN) of WUR for providing the samples used in this study. We also thank networks of fancy poultry breeders in the Netherlands, who provided phenotypic information of the breeds.
Funding Information:
The sequencing data generated in this work were supported by the IMAGE Project from the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 677353). We would like to thank the China Scholarship Council for the financial support to ZW (Grant No. 201606350175).
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - BACKGROUND: In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic impact using whole-genome sequence data.RESULTS: Looking at the genetic differences between breeds, the Dutch chicken breeds demonstrated a complex and admixed subdivided structure. The dissection of this complexity highlighted the influence of selection adhering to management purposes, as well as the role of geographic distance within subdivided breed clusters. Identification of signatures of genetic differentiation revealed genomic regions that are associated with diversifying phenotypic selection between breeds, including dwarf size (bantam) and feather color. In addition, with a case study of a recently developed bantam breed developed by crossbreeding, we provide a genomic perspective on the effect of crossbreeding.CONCLUSIONS: This study demonstrates the complex population structure of local traditional Dutch chicken, and provides insight into the genomic basis and the factors involved in the formation of this complexity.
AB - BACKGROUND: In poultry, the population structure of local breeds is usually complex mainly due to unrecorded breeding. Local chicken breeds offer an interesting proxy to understand the complexity of population structure in the context of human-mediated development of diverse morphologies and varieties. We studied 37 traditional Dutch chicken breeds to investigate population structure and the corresponding genomic impact using whole-genome sequence data.RESULTS: Looking at the genetic differences between breeds, the Dutch chicken breeds demonstrated a complex and admixed subdivided structure. The dissection of this complexity highlighted the influence of selection adhering to management purposes, as well as the role of geographic distance within subdivided breed clusters. Identification of signatures of genetic differentiation revealed genomic regions that are associated with diversifying phenotypic selection between breeds, including dwarf size (bantam) and feather color. In addition, with a case study of a recently developed bantam breed developed by crossbreeding, we provide a genomic perspective on the effect of crossbreeding.CONCLUSIONS: This study demonstrates the complex population structure of local traditional Dutch chicken, and provides insight into the genomic basis and the factors involved in the formation of this complexity.
U2 - 10.1186/s12711-022-00775-x
DO - 10.1186/s12711-022-00775-x
M3 - Article
C2 - 36670351
SN - 0999-193X
VL - 55
SP - 1
EP - 12
JO - Genetics Selection Evolution
JF - Genetics Selection Evolution
IS - 1
M1 - 5
ER -