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

被引：66

作者：

Iamartino, Daniela ^{[1
,2
]}

Nicolazzi, Ezequiel L. ^{[3
,16
]}

Van Tassell, Curtis P. ^{[4
]}

Reecy, James M. ^{[5
]}

Fritz-Waters, Eric R. ^{[5
]}

Koltes, James E. ^{[5
,14
]}

Biffani, Stefano ^{[2
]}

Sonstegard, Tad S. ^{[4
,15
]}

Schroeder, Steven G. ^{[4
]}

Ajmone-Marsan, Paolo

Negrini, Riccardo ^{[1
,6
]}

Pasquariello, Rolando ^{[2
]}

Ramelli, Paola ^{[2
]}

Coletta, Angelo ^{[7
]}

Garcia, Jose F. ^{[8
]}

Ali, Ahmad ^{[9
]}

Ramunno, Luigi ^{[10
]}

Cosenza, Gianfranco ^{[10
]}

de Oliveira, Denise A. A. ^{[11
]}

Drummond, Marcela G. ^{[11
]}

Bastianetto, Eduardo ^{[11
]}

Davassi, Alessandro ^{[12
]}

Pirani, Ali ^{[12
]}

Brew, Fiona ^{[12
]}

Williams, John L. ^{[13
]}

机构：

[1] AIA LGS, Cremona, Italy

[2] Fdn Parco Tecnol Padano, Lodi, Italy

[3] Parco Tecnol Padano, Bioinformat Core, Lodi, Italy

[4] USDA ARS, Anim Genom & Improvement Lab, BARC, Beltsville, MD USA

[5] Iowa State Univ, Dept Anim Sci, Ames, IA USA

[6] Univ Cattolica S Cuore, Inst Zootech, Piacenza, Italy

[7] ANASB, Centurano Caserta, Italy

[8] Univ Estadual Paulista, UNESP, Campus Aracatuba, Sao Paulo, Brazil

[9] COMSATS Inst Informat Technol, Sahiwal, Pakistan

[10] Univ Napoli Federico II, Fac Agr, Dipartimento Sci Zootecn & Ispez Alimenti, Portici, NA, Italy

[11] Univ Fed Minas Gerais, Belo Horizonte, MG, Brazil

[12] Affymetrix UK Ltd, High Wycombe, Bucks, England

[13] Univ Adelaide, Sch Anim & Vet Sci, Davies Res Ctr, Roseworthy, SA, Australia

[14] Univ Arkansas, Dept Anim Sci, Fayetteville, AR 72701 USA

[15] Recombinetics Inc, St Paul, MN USA

[16] Council Dairy Cattle Breeding, 4201 Northview Dr One Town Ctr, Bowie, MD USA

来源：

PLOS ONE | 2017年 / 12卷 / 10期

关键词：

PREDICTION;

D O I：

10.1371/journal.pone.0185220

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 (R) Buffalo Genotyping Array 90K. Results This 90K "SNP-Chip" was tested in several river buffalo populations and found to have similar to 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.

引用

页数：18

共 36 条

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