Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis).

Autor: Iamartino D; AIA-LGS Associazione Italiana Allevatori-Laboratorio Genetica e Servizi, Cremona, Italy.; Fondazione Parco Tecnologico Padano, Lodi, Italy., Nicolazzi EL; Bioinformatics core, Parco Tecnologico Padano, Lodi, Italy., Van Tassell CP; Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland, United States of America., Reecy JM; Department of Animal Science, Iowa State University, Ames, IA, United States of America., Fritz-Waters ER; Department of Animal Science, Iowa State University, Ames, IA, United States of America., Koltes JE; Department of Animal Science, Iowa State University, Ames, IA, United States of America., Biffani S; Fondazione Parco Tecnologico Padano, Lodi, Italy., Sonstegard TS; Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland, United States of America., Schroeder SG; Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland, United States of America., Ajmone-Marsan P; Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy., Negrini R; AIA-LGS Associazione Italiana Allevatori-Laboratorio Genetica e Servizi, Cremona, Italy.; Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy., Pasquariello R; Fondazione Parco Tecnologico Padano, Lodi, Italy., Ramelli P; Fondazione Parco Tecnologico Padano, Lodi, Italy., Coletta A; ANASB-Associazione Nazionale Allevatori Specie Bufalina, Centurano-Caserta, Italy., Garcia JF; Universidade Estadual Paulista (UNESP), Câmpus de Araçatuba, Sao Paulo, Brazil., Ali A; COMSATS Institute of Information Technology, Sahiwal, Pakistan., Ramunno L; Dipartimento di Scienze Zootecniche ed Ispezione degli Alimenti, Facoltà di Agraria, Università degli Studi di Napoli Federico II, Portici (NA), Italy., Cosenza G; Dipartimento di Scienze Zootecniche ed Ispezione degli Alimenti, Facoltà di Agraria, Università degli Studi di Napoli Federico II, Portici (NA), Italy., de Oliveira DAA; Universidade Federal De Minas Gerais (UFMG), Belo Horizonte, Brazil., Drummond MG; Universidade Federal De Minas Gerais (UFMG), Belo Horizonte, Brazil., Bastianetto E; Universidade Federal De Minas Gerais (UFMG), Belo Horizonte, Brazil., Davassi A; Affymetrix UK Ltd, High Wycombe, United Kingdom., Pirani A; Affymetrix UK Ltd, High Wycombe, United Kingdom., Brew F; Affymetrix UK Ltd, High Wycombe, United Kingdom., Williams JL; Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2017 Oct 05; Vol. 12 (10), pp. e0185220. Date of Electronic Publication: 2017 Oct 05 (Print Publication: 2017).
DOI: 10.1371/journal.pone.0185220
Abstrakt: Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.
Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K.
Results: This 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production.
Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.
Databáze: MEDLINE
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