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High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
1Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
1Animal Biotechnology Laboratory, Animal Science and Pastures Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.
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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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 26929Article in journal (Refereed) Published
Abstract [en]

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 inanimal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and costeffectivegenotyping by sequence approach developed in plants, for its application in chickens. Herewe 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 identifyingindividual 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 hada minimum taxon call rate of 90% and were considered ‘unique tags’. Interestingly, 20.7% of theseunique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs wereconcordant 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 inexonic 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 wholegenomeselection (WGS), and genome-wide association studies (GWAS) in chicken production.

Place, publisher, year, edition, pages
Nature Publishing Group, 2016. Vol. 6, 26929
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:liu:diva-128866DOI: 10.1038/srep26929ISI: 000376503900001PubMedID: 27220827OAI: oai:DiVA.org:liu-128866DiVA: diva2:932980
Note

Funding agencies: University of Sao Paulo from Sao Paulo Research Foundation (FAPESP) [2014/08704-0]; Embrapa Swine and Poultry National Research Center; ERC GeneWell project; PRODETAB project [038-01/01]; CAPES; CNPq; program Science Without Borders - National Council for

Available from: 2016-06-02 Created: 2016-06-02 Last updated: 2017-11-30

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