SNPchiMp: A database to disentangle the SNPchip jungle in bovine livestock

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Nicolazzi, Ezequiel L ^a   Picciolini, Matteo ^a   Strozzi, Francesco ^a   Schnabel, Robert D ^b   Lawley, Cindy ^c   Pirani, Ali ^d   Brew, Fiona ^d   Stella, Alessandra ^a,e  

^a PARCO TECNOLOGICO PADANO   (Italy)

^b UNIVERSITY OF MISSOURI   (United States)

^c ILLUMINA INC   (United States)

^d Thermo Fisher Scientific   (United States)

^e CNR   (Italy)

Author keywords

Assembly; Bovine livestock; GWAS; Imputation; Relational database; SNP chip; SNP data

Indexed keywords

ANIMALS; CATTLE; DATABASES, GENETIC; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; USER-COMPUTER INTERFACE;

EID: 84893709934     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-123     Document Type: Article

References (10)

1. Van Tassel CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008, 5:247-252. 10.1038/nmeth.1185, 18297082.
2. Bolormaa S, Pryce JE, Hayes BJ, Goddard ME. Multivariate analysis of a genome-wide association study in dairy cattle. J Dairy Sci 2010, 93:3818-3833. 10.3168/jds.2009-2980, 20655452.
3. Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, et al. Bayesian genome wide association analyses of growth and yearling ultrasound measures of carcass traits in Brangus heifers. J Anim Sci 2013, 90:3398-3409.
4. VanRaden PM, O'Connell JR, Wiggans GR, Weigel KA. Genomic evaluations with many more genotypes. Genet Sel Evol 2012, 43:10.
5. The Bovine HapMap Consortium Genome-wide survey of SNP variation uncovers the genetic structure of Cattle Breeds. Science 2009, 324:528-532. 2735092, 19390050, The Bovine HapMap Consortium.
6. Gautier M, Naves M. Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Mol Ecol 2009, 20:3128-3143.
7. Lund MS, de Roos APW, de Vries AG, Druet T, Ducrocq V, Fritz S, Guillaume F, Guldbrandtsen B, Liu Z, Reents R, Schrooten C, Seefried F, Su G. A common reference population from four European Holstein populations increases reliability of genomic predictions. Genet Sel Evol 2011, 43:43. 10.1186/1297-9686-43-43, 3292506, 22152008.
8. Hickey JM, Kinghorn BP, Tier B, van der Werf JHJ, Cleveland MA. A phasing and imputation method for pedigreed populations that result in a single-stage genomic evaluation. Gen Sel Evol 2012, 44:9.
9. Nicolazzi EL, Biffani S, Jansen G. Short communication: imputing genotypes using PedImpute fast algorithm combining pedigree and population information. J Dairy Sci 2013, 96:2649-2653. 10.3168/jds.2012-6062, 23462161.
10. Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q. Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. BMC Genet 2011, 12:85. 3224132, 21982513.