title: GVCBLUP: a computer package for genomic prediction and variance component estimation of additive and dominance effects.
abstract: BACKGROUND
  Dominance effect may play an important role in genetic variation of complex traits. Full featured and easy-to-use computing tools for genomic prediction and variance component estimation of additive and dominance effects using genome-wide single nucleotide polymorphism (SNP) markers are necessary to understand dominance contribution to a complex trait and to utilize dominance for selecting individuals with favorable genetic potential.
  
  
  RESULTS
  The GVCBLUP package is a shared memory parallel computing tool for genomic prediction and variance component estimation of additive and dominance effects using genome-wide SNP markers. This package currently has three main programs (GREML_CE, GREML_QM, and GCORRMX) and a graphical user interface (GUI) that integrates the three main programs with an existing program for the graphical viewing of SNP additive and dominance effects (GVCeasy). The GREML_CE and GREML_QM programs offer complementary computing advantages with identical results for genomic prediction of breeding values, dominance deviations and genotypic values, and for genomic estimation of additive and dominance variances and heritabilities using a combination of expectation-maximization (EM) algorithm and average information restricted maximum likelihood (AI-REML) algorithm. GREML_CE is designed for large numbers of SNP markers and GREML_QM for large numbers of individuals. Test results showed that GREML_CE could analyze 50,000 individuals with 400 K SNP markers and GREML_QM could analyze 100,000 individuals with 50K SNP markers. GCORRMX calculates genomic additive and dominance relationship matrices using SNP markers. GVCeasy is the GUI for GVCBLUP integrated with an existing software tool for the graphical viewing of SNP effects and a function for editing the parameter files for the three main programs.
  
  
  CONCLUSIONS
  The GVCBLUP package is a powerful and versatile computing tool for assessing the type and magnitude of genetic effects affecting a phenotype by estimating whole-genome additive and dominance heritabilities, for genomic prediction of breeding values, dominance deviations and genotypic values, for calculating genomic relationships, and for research and education in genomic prediction and estimation.
authors.forename: Chunkao
authors.initials: C
authors.lastname: Wang
authors.forename: Dzianis
authors.initials: D
authors.lastname: Prakapenka
authors.forename: Shengwen
authors.initials: S
authors.lastname: Wang
authors.forename: Sujata
authors.initials: S
authors.lastname: Pulugurta
authors.forename: Hakizumwami Birali
authors.initials: HB
authors.lastname: Runesha
authors.affiliation: Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA. yda@umn.edu.
authors.forename: Yang
authors.initials: Y
authors.lastname: Da
mesh_terms: D000465:Algorithms; D000818:Animals; D001947:Breeding; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D005819:Genetic Markers
references.citation: PLoS One. 2014 Jan 08;9(1):e85792
references.pmid: 24416447
references.citation: BMC Bioinformatics. 2014 Aug 09;15:270
references.pmid: 25107495
references.citation: Genetics. 2013 Dec;195(4):1223-30
references.pmid: 24121775
references.citation: PLoS One. 2012;7(9):e45293
references.pmid: 23028912
references.citation: J Dairy Sci. 2010 Feb;93(2):743-52
references.pmid: 20105546
references.citation: Plant Genome. 2010;3(2):106-116
references.pmid: 21566722
references.citation: Am J Hum Genet. 2011 Jan 7;88(1):76-82
references.pmid: 21167468
references.citation: Genetics. 2001 Apr;157(4):1819-29
references.pmid: 11290733
references.citation: Ecol Evol. 2014 Apr;4(8):1381-8
references.pmid: 24834334
references.citation: BMC Bioinformatics. 2012 Nov 30;13:319
references.pmid: 23199373
references.citation: BMC Genomics. 2012 Oct 06;13:536
references.pmid: 23039970
references.citation: J Dairy Sci. 2013;96(12):8014-23
references.pmid: 24119810
references.citation: BMC Bioinformatics. 2008 Jul 21;9:315
references.pmid: 18644146
references.citation: J Dairy Sci. 2008 Nov;91(11):4414-23
references.pmid: 18946147
references.citation: G3 (Bethesda). 2012 Apr;2(4):429-35
references.pmid: 22540034
references.citation: Nat Genet. 2010 Jul;42(7):565-9
references.pmid: 20562875
references.citation: PLoS One. 2014 Jan 30;9(1):e87666
references.pmid: 24498162