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

Autor(es)

Pertille, Fabio ^[1] ; Guerrero-Bosagna, Carlos ^[2] ; da Silva, Vinicius Henrique ^[1] ; Boschiero, Clarissa ^[1] ; da Silva Nunes, Jose de Ribamar ^[1] ; Ledur, Monica Correa ^[3] ; Jensen, Per ; Coutinho, Luiz Lehmann ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Anim Sci & Pastures Dept, Anim Biotechnol Lab, Luiz de Queiroz Coll Agr ESALQ, Sao Paulo - Brazil

^[2] Linkoping Univ, AVIAN Behav Genom & Physiol Grp, IFM Biol, Linkoping - Sweden

^[3] Brazilian Agr Res Corp EMBRAPA Swine & Poultry, Concordia, SC - Brazil

• Tipo de documento: Artigo Científico
• Fonte: SCIENTIFIC REPORTS; v. 6, MAY 25 2016.
• Citações Web of Science: 12

Resumo

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 (similar to 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. (AU)

• Processo FAPESP: 14/08704-0 - Identificação de locos de interesse zootécnico na galinha doméstica
• Beneficiário: Luiz Lehmann Coutinho
• Modalidade de apoio: Auxílio à Pesquisa - Temático