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High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing.

Fábio Pértille1, Carlos Guerrero-Bosagna2, Vinicius Henrique da Silva1

  • 1Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.

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Summary
This summary is machine-generated.

CornellGBS, a cost-effective genotyping by sequence method, was optimized for chickens. This approach successfully identified numerous single nucleotide polymorphisms (SNPs) for improved chicken breeding and genetic studies.

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Area of Science:

  • Animal Genetics
  • Genomics
  • Agricultural Science

Background:

  • High-throughput genotyping is crucial for animal breeding but often limited by high costs.
  • Efficient and cost-effective genotyping methods are needed for large-scale application in chicken production.

Purpose of the Study:

  • To optimize and validate the CornellGBS (Genotyping by Sequence) approach for chicken genotyping.
  • To assess the cost-effectiveness and performance of CornellGBS in identifying single nucleotide polymorphisms (SNPs) in chickens.

Main Methods:

  • Optimized the CornellGBS method for chicken DNA using PstI enzyme digestion and Illumina sequencing.
  • Genotyped 462 chickens, ligating adapters with barcodes for individual animal identification.
  • Applied filtering parameters to identify and analyze SNPs.

Main Results:

  • Identified 134,528 SNPs, with 67,096 'unique tags' meeting a 90% call rate.
  • Discovered that 20.7% of unique tags were novel, not previously reported in dbSNP.
  • Achieved 92.6% concordance with a Whole Chicken-genome re-sequencing dataset, demonstrating high accuracy.

Conclusions:

  • CornellGBS is a high-performing and cost-effective (~$50/sample) genotyping method for chickens.
  • This approach shows particular efficacy in identifying SNPs in exonic regions and microchromosomes.
  • CornellGBS has the potential to significantly advance whole-genome selection (WGS) and genome-wide association studies (GWAS) in chicken breeding programs.