Title:	High-throughput and cost-effective chicken genotyping using next-generation sequencing.
Authors:	PÉRTILLE, F. BOSAGNA, C. G. SILVA, V. H. da BOSCHIERO, C. NUNES, J. de R. da S. LEDUR, M. C. JENSEN, P. COUTINHO, L. L.
Affiliation:	FÁBIO PÉRTILLE, ESALQ; CARLOS GUERRERO BOSAGNA, Linköping University; VINICIUS HENRIQUE DA SILVA, ESALQ; CLARISSA BOSCHIERO, ESALQ; JOSÉ DE RIBAMAR DA SILVA NUNES, ESALQ; MONICA CORREA LEDUR, CNPSA; PER JENSEN, Linköping University; LUIZ LEHMANN COUTINHO, ESALQ.
Date Issued:	2016
Citation:	Scientific Reports, v. 6, n. 26929, 2016.
Description:	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 costeffective 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 wholegenome selection (WGS), and genome-wide association studies (GWAS) in chicken production.
Thesagro:	Melhoramento genético animal Produção animal Avicultura
NAL Thesaurus:	Animal breeding Poultry production
DOI:	10.1038/srep26929
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CNPSA)