An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing

Area of Science:

• Genomics
• Animal Genetics
• Molecular Biology

Background:

• Single nucleotide polymorphisms (SNPs) are crucial for understanding complex traits in livestock.
• Efficient SNP discovery and genotyping are vital for advancing chicken genetics research.
• Existing SNP chip technology has limitations in SNP density and cost-effectiveness.

Purpose of the Study:

• To develop and validate a highly multiplexed genotyping by genome reducing and sequencing (GGRS) method for SNP discovery in chicken.
• To compare the efficiency and SNP yield of GGRS with existing SNP chip technology.
• To assess the potential of GGRS for large-scale genomic applications in chicken.

Main Methods:

• Construction of a 252-plex sequencing library using the GGRS method.
• Sequencing of the library on an Illumina HiSeq 2500 platform with paired-end sequencing.
• Bioinformatic analysis for SNP identification and filtering, followed by comparison with Illumina 60K chicken SNP chip data.

Main Results:

• Successful sequencing generated approximately 400 million raw reads, yielding an average of 1.4 million good reads per sample.
• A total of 91,767 SNPs were identified with excellent representation across samples and chromosomes.
• GGRS identified 34,131 more SNPs than the Illumina 60K SNP chip, offering higher SNP density at a reduced cost of $18 per sample for over 3528 samples.

Conclusions:

• The GGRS method provides a highly efficient and cost-effective approach for SNP discovery and genotyping in chicken.
• This method significantly increases SNP density compared to current SNP chip technology.
• GGRS holds substantial promise for advancing genome-wide association studies and genomic selection in chicken populations.