Identifying Genetic Differences Between Dongxiang Blue-Shelled and White Leghorn Chickens Using Sequencing Data

Area of Science:

• Comparative genomics
• Poultry genetics
• Animal breeding

Background:

• Dongxiang Blue-shelled chicken: a valuable Chinese indigenous poultry breed.
• White Leghorn: Italian native breed with superior growth and fertility.
• Need to understand genetic differences for breed improvement.

Purpose of the Study:

• Identify potential selected regions (PSRs) in Dongxiang Blue-shelled chicken and White Leghorn genomes.
• Analyze genetic variations and functional annotations.
• Compare genomic signatures related to growth, fertility, and egg quality.

Main Methods:

• Genome reduction sequencing to detect single nucleotide polymorphisms (SNPs).
• Cross-population extended haplotype homozygosity, EigenGWAS, and mixed-model association methods.
• Gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses.

Main Results:

• Identified 2424 outlier loci, with 2144 in White Leghorn and 280 in Dongxiang Blue-shelled chicken.
• Discovered 327 PSRs (297 genes) in White Leghorn and 94 PSRs (54 genes) in Dongxiang Blue-shelled chicken.
• Highlighted key genes (e.g., TMEM141, CLIC3, SLCO1B3) and enriched pathways (metabolism, signal transduction) in each breed.

Conclusions:

• Significant genetic differences exist between the two breeds, reflecting distinct selection pressures.
• White Leghorn shows selection related to immunity, reproduction, and growth.
• Dongxiang Blue-shelled chicken exhibits selection related to metabolism and traits like bone mineral content.