title: High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing.
abstract: Chicken genotyping is becoming common practice in conventional animal breeding improvement. Despite the power of high-throughput methods for genotyping, their high cost limits large scale use in animal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and cost-effective genotyping by sequence approach developed in plants, for its application in chickens. Here we describe the successful genotyping of a large number of chickens (462) using CornellGBS approach. Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifying individual animals, and then sequenced on Illumina platform. After filtering parameters were applied, 134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 had a minimum taxon call rate of 90% and were considered 'unique tags'. Interestingly, 20.7% of these unique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs were concordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes. The application of CornellGBS in chickens showed high performance to infer SNPs, particularly in exonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample) and powerful alternative to current genotyping methods, which has the potential to improve whole-genome selection (WGS), and genome-wide association studies (GWAS) in chicken production.
authors.affiliation: Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Fábio
authors.initials: F
authors.lastname: Pértille
authors.affiliation: IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
authors.forename: Carlos
authors.initials: C
authors.lastname: Guerrero-Bosagna
authors.affiliation: Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Vinicius Henrique da
authors.initials: VH
authors.lastname: Silva
authors.affiliation: Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Boschiero
authors.affiliation: Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: José de Ribamar da Silva
authors.initials: Jde R
authors.lastname: Nunes
authors.affiliation: Brazilian Agricultural Research Corporation (EMBRAPA) Swine &Poultry, Concórdia, Santa Catarina, Brazil.
authors.forename: Mônica Corrêa
authors.initials: MC
authors.lastname: Ledur
authors.affiliation: IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Jensen
authors.affiliation: Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
authors.forename: Luiz Lehmann
authors.initials: LL
authors.lastname: Coutinho
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D003362:Cost-Benefit Analysis; D005260:Female; D016678:Genome; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques / Q000191:economics*; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics*; D008297:Male; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000191:economics