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. 2025 May 30;104(9):105377.
doi: 10.1016/j.psj.2025.105377. Online ahead of print.

Whole-genome sequencing revealed genetic structure, patterns of selection and molecular identity card in "Yufen 1″ D line chickens

Cong Liu  1 , Jianing Liu  2 , Haishan Guo  2 , Shuangxing Liu  2 , Pingquan Liu  2 , Tingqi Zhu  2 , Wenting Li  3 , Kejun Wang  1 , Xiangtao Kang  1 , Zhunan Li  4 , Guirong Sun  5
Affiliations

Whole-genome sequencing revealed genetic structure, patterns of selection and molecular identity card in "Yufen 1″ D line chickens

Cong Liu et al. Poult Sci. .

Abstract

The "Yufen 1" D line (D) chicken is characterized by strong disease resistance and a high feed conversion rate as a newly bred line. There are few reports on D chicken. In order to investigate the genetic diversity, population structure and selection signals of the D chicken, this study analyzed the genome-wide data of 15 D line chickens and 11 publicly available Chinese indigenous chicken breeds, the red jungle fowls. The genetic diversity of the D chicken was significantly lower than that of the Chinese indigenous chicken breeds and the red jungle fowl, but the inbreeding coefficient (FROH) was lower. On the one hand, this may be due to the small size of the conserved population, and on the other hand, it suggests that the D line may have received artificial selection during the selection process. Population structure analysis revealed that the D chicken was separated from Chinese indigenous chicken breeds and red jungle fowl, and had a high degree of genetic differentiation from other non-D chicken populations, suggesting that the D chicken is a unique poultry genetic resource worthy of our subsequent enhanced protection and utilization. The selective sweep analysis revealed that the genes selected in the D chicken were mainly enriched in the Toll and Imd signaling pathway and the Gastric acid secretion signaling pathway, including REL, UBE2V1, KCNJ16, and SLC26A7, which might be related to the excellent traits of high disease resistance and high feed conversion ratio in D chicken. In addition, the constructed molecular identity card of D chickens can be used to identify the authenticity of D chickens. These results lay the foundation for further research, conservation, and breeding of "Yufen 1" D line chickens.

Keywords: Genetic diversity; Population structure; Selective sweep analysis; Whole genome resequencing; “Yufen 1” D line chickens.

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Figures

Fig 1
Fig 1
Runs of homozygosity of different chicken breeds. Statistical for the number of runs of homozygosity (A), total length of runs (B) and inbreeding coefficient (C).
Fig 2
Fig 2
(A) Neighbor-joining (NJ) phylogenetic tree of 13 breeds, (B) PCA analysis, and (C) population structure of the 13 breeds.
Fig 3
Fig 3
(A) Manhattan plot of Fst analyses with DC population against NDC, (B) Manhattan plot of Pi analyses with DC, (C) Manhattan plot of Pi analyses with NDC, (D) Signals intersection by Fst and pi about DC vs NDC.
Fig 4
Fig 4
(A) GO and (B) enrichment analysis.
Fig 5
Fig 5
PCA results (A) and NJ-tree (B) results for 1000 sites.
See this image and copyright information in PMC

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