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Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data
Sunghyun Cho1, Prabuddha Manjula1, Minjun Kim1,2
1Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
Genes
|June 2, 2021
Summary
This study analyzed genetic selection signals in Korean native chickens (KNCs) to improve the breed. Key genes influencing traits like egg production and meat quality were identified, guiding future breeding strategies for KNCs.
Area of Science:
- Animal Genetics and Breeding
- Genomics and Bioinformatics
Background:
- Korean native chickens (KNCs) are an indigenous breed of South Korea, restored in the 1990s but with underdeveloped populations.
- Previous efforts focused on maintaining purebred KNC populations, necessitating genetic investigation for efficient breed improvement.
Purpose of the Study:
- To investigate the genetic features of KNC populations using selection signal analysis.
- To identify genetic regions associated with important economic traits for efficient KNC improvement.
Main Methods:
- Utilized 600K single nucleotide polymorphism (SNP) data from 191 KNCs across five lines (NG, NL, NR, NW, NY) and 54 commercial chickens.
- Employed haplotype phasing with EAGLE software and selection signal detection using the 'rehh' package in R software.
- Analyzed quantitative trait locus (QTL) regions and linkage disequilibrium (LD) patterns for candidate genes.
Main Results:
- Identified common signatures of selection in KNCs, with candidate regions linked to reproductive organs, eggshell traits, immunity, and organ development.
- Observed high LD block patterns in genes such as LPP, IGF11, LMNB2, ERBB4, GABRB2, NTM, APOO, PLOA1, CNTN1, NTSR1, DEF3, CELF1, and MEF2D.
- Found specific selective sweep regions in NL (broiler traits) and NW (layer traits) lines, indicating potential for targeted improvement.
Conclusions:
- Genetic analysis revealed key regions and genes associated with economically important traits in KNCs.
- Recommended focused improvement of egg traits in the NL line and meat traits in the NW line.
- Advised a multi-trait improvement strategy for other KNC lines based on identified genetic signatures.
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