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| The Analysis on Genetic Evolution of Bian Chicken (Gallus gallus) Population Based on RAD-seq Technology |
| LI Guo-Hui1, Wei Qing-Yu2, ZHANG Hui-Yong1, YIN Jian-Mei1, XUE Qian1, ZHU Yun-Fen1, SU Yi-Jun1, WANG Ke-Hua1, ZOU Jian-Min1, HAN Wei1,* |
1 National Chickens Genetic Resources, Jiangsu Institute of Poultry Science, Yangzhou 225125, China;
2 Sciences of Shanxi Agricultural Academy Institute of Animal Husbandry & Veterinary, Taiyuan 030032, China |
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Abstract Bian chicken (Gallus gallus) is a valuable genetic resource as a Chinese native chicken. It is of great significance to explore the genetic diversity and molecular genetic evolution of the population at the molecular level. In this study, RAD-seq simplified genome sequencing technology was employed to identify SNP markers in Bian chickens and compare the genetic differences between the Bian chicken population and the other breeds population by calculating the genetic statistics. Functional annotation was conducted for the selected genes during evolution. The results showed that 319 727 SNP markers were identified in Bian chickens. The average observed heterozygosity (0.193) and nucleotide diversity (0.231) were in the medium levels, but inbreeding coefficient(0.167) was relatively high.The linkage disequilibrium analysis showed that there was no strong linkage disequilibrium between the alleles of Bian chickens population. The clustering results of the structure model showed that Bian chicken and Dagu chicken, Anyi gray chicken, Langshan chicken had a close relationship and belonged to the same type. 200 selected genes were identified through the Fst and θπ testing. Gene Ontology (GO) and KEGG analysis showed that these selected genes were mainly enriched in metabolism, neuroactive ligand-receptor interaction, mitogen-activated protein kinase (MAPK), vascular smooth muscle contraction signal pathways. The function analysis of the genes including nitric oxide synthase (NOS2), heterochromatin protein 1 binding protein 3 (HP1BP3), aprataxin (APTX), prostaglandin endoperoxide synthase 2 (PTGS2) and phospholipase A2 group 4 type alpha (PLA2G4A) was helpful to understand the molecular mechanism of special traits such as cold resistance, hypoxia, fertility, nervous system development and stress resistance in Bian chicken. The results of the study provide molecular basis for the genetic evolution and evaluation and conservation of local chicken breeds.
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Received: 06 July 2019
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Corresponding Authors:
* hanwei830@163.com
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