Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds

Zhi, Yihao; Wang, Dandan; Zhang, Ke; Wang, Yangyang; Geng, Wanzhuo; Chen, Botong; Li, Hong; Li, Zhuanjian; Tian, Yadong; Kang, Xiangtao; Liu, Xiaojun

doi:10.3390/ani13040753

Cited by 11 publications

(2 citation statements)

References 79 publications

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“…Chen et al [ 33 ] found that the increase in copy number of CRADD by one in Luxi game chickens (a typical cockfighting breed) may be responsible for the fast muscle growth trait. Zhi et al [ 34 ] identified that CRADD may be related to body size in Henan gamecock. Although, CRADD is not directly involved in growth-related pathways, it is involved in cell apoptosis, which is equally important in controlling cell number as cell proliferation is.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Li,

Jin,

Wang

et al. 2024

Animals

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Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.

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Section: Discussionmentioning

confidence: 99%

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Li,

Jin,

Wang

et al. 2024

Animals

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“…Gushi chicken is one of the widely farmed backyard chicken breeds in China, known for its high‐quality meat and eggs. These chickens are mainly reared in Gushi County, with a breed history of more than 2000 years (Zhi et al., 2023). It has excellent characteristics, including rough feeding resistance, strong disease resistance, and delicious meat quality.…”

Section: Introductionmentioning

confidence: 99%

Depletion of tilmicosin residue in Gushi chickens following oral administration via drinking water

Zhang,

Qian,

et al. 2023

Vet Pharm & Therapeutics

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This study aimed to examine the depletion of tilmicosin residues in Gushi chickens following the administration at a concentration of 75 mg/L in their drinking water for three consecutive days. Plasma, liver, kidney, lung, muscle, and skin + fat samples were collected from 6 chickens at 6 h, 1, 3, 5, and 7 days after the treatment. Tilmicosin concentrations in the samples were determined using a high‐performance liquid chromatography (HPLC) method. The findings revealed that the highest tilmicosin residues were detected in the liver, followed by the kidney, lung, skin + fat, muscle, and plasma. Notably, at 7 days post‐treatment, no drug residue was detected in all samples except for the liver and kidney. The non‐compartmental model was employed to calculate relevant pharmacokinetic parameters. The elimination half‐lives (t1/2λz) of tilmicosin were as follows, ranked from long to short: skin + fat (45.42 h), liver (44.17 h), kidney (40.06 h), plasma (37.64 h), lung (31.39 h), and muscle (30.05 h). Considering the current residue depletion and the maximum residue limits (MRLs) set by Chinese regulatory authorities, the withdrawal times for tilmicosin were estimated as 18.91, 10.81, and 8.58 days in the kidney, liver, and skin + fat, respectively. A rounded‐up value of 19 days was selected as the conclusive withdrawal time. Furthermore, based on the observed tilmicosin concentrations in plasma and lung, combined with previously reported minimum inhibitory concentration (MIC) values against Mycoplasma gallisepticum, the current dosing regimen was deemed adequate for treating Mycoplasma gallisepticum infections in Gushi chickens.

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Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits

Rostamzadeh Mahdabi,

Esmailizadeh,

Han

et al. 2024

Veterinary Medicine & Sci

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Runs of homozygosity (ROH) are contiguous stretches of identical genomic regions inherited from both parents. Assessment of ROH in livestock species contributes significantly to our understanding of genetic health, population genetic structure, selective pressure and conservation efforts. In this study, whole genome re‐sequencing data from 140 birds of 10 Iranian indigenous chicken ecotypes, 3 commercial chicken breeds and 1 red junglefowl (RJF) population were used to investigate their population genetic structure, ROH characteristics (length and frequency) and genomic inbreeding coefficients (FROH). Additionally, we examined ROH islands for selection footprints in the indigenous chicken populations. Our results revealed distinct genetic backgrounds, among which the White Leghorn breed exhibited the greatest genetic distance from other populations, while the gamecock populations formed a separate cluster. We observed significant differences in ROH characteristics, in which the commercial breeds showed a higher number of ROH compared to indigenous chickens and red junglefowls. Short ROH ranging from 0.1 to 1 Mb were dominant among the populations. The Arian line had the highest mean length of ROH, while the White Leghorn breed showed the highest number of ROH. Among indigenous chickens, the Lari‐Afghani ecotype exhibited the highest FROH, but the Sari inherited the richest genetic diversity. Interestingly, GGA16 carried no ROH in the red junglefowls, whereas GGA22 had the highest FROH across all populations, except in the Isfahan ecotype. We also identified ROH islands associated with genetic adaptations in indigenous ecotypes. These islands harboured immune‐related genes contributing to disease resistance (TLR2, TICAM1, IL22RA1, NOS2, CCL20 and IFNLR1), heat tolerance and oxidative stress response (NFKB1, HSF4, OSGIN1 and BDNF), and muscle development, lipid metabolism and reproduction (MEOX2, CEBPB, CDS2 and GnRH‐I). Overall, this study highlights the genetic potential of indigenous chickens to survive and adapt to their respective environments.

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Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds

Cited by 11 publications

References 79 publications

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Depletion of tilmicosin residue in Gushi chickens following oral administration via drinking water

Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits

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