title: Potential of SNP markers for the characterization of Brazilian cassava germplasm.
abstract: High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas. The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.
authors.affiliation: Embrapa Cassava and Fruits, Rua da Embrapa s/n, Cruz das Almas, BA, Brazil, eder.oliveira@embrapa.br.
authors.forename: Eder Jorge
authors.initials: EJ
authors.lastname: de Oliveira
authors.forename: Cláudia Fortes
authors.initials: CF
authors.lastname: Ferreira
authors.forename: Vanderlei
authors.initials: V
authors.lastname: da Silva Santos
authors.forename: Onildo Nunes
authors.initials: ON
authors.lastname: de Jesus
authors.forename: Gilmara Alvarenga Fachardo
authors.initials: GA
authors.lastname: Oliveira
authors.forename: Maiane Suzarte
authors.initials: MS
authors.lastname: da Silva
mesh_terms: D000704:Analysis of Variance; D001499:Bayes Theorem; D001938:Brazil; D005819:Genetic Markers; D005838:Genotype; D002365:Manihot / Q000235:genetics*; D015999:Multivariate Analysis; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis
chemical_list: D005819:Genetic Markers
references.citation: BMC Plant Biol. 2009 Sep 11;9:118
references.pmid: 19747391
references.citation: Theor Appl Genet. 2003 Oct;107(6):1083-93
references.pmid: 12856084
references.citation: Nat Rev Genet. 2004 Jan;5(1):63-9
references.pmid: 14666112
references.citation: Theor Appl Genet. 2012 Mar;124(4):685-95
references.pmid: 22069119
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Mol Ecol. 2001 Aug;10(8):1895-907
references.pmid: 11555234
references.citation: Evolution. 2007 Dec;61(12):2849-60
references.pmid: 17908247
references.citation: Curr Opin Plant Biol. 2002 Apr;5(2):94-100
references.pmid: 11856602
references.citation: Bioinformatics. 2012 Oct 1;28(19):2537-9
references.pmid: 22820204
references.citation: Bioinformatics. 2005 May 1;21(9):2128-9
references.pmid: 15705655
references.citation: Heredity (Edinb). 2009 Apr;102(4):330-41
references.pmid: 19156164
references.citation: Am J Hum Genet. 1980 May;32(3):314-31
references.pmid: 6247908
references.citation: Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321-3
references.pmid: 4519626
references.citation: Heredity (Edinb). 2000 Sep;85 Pt 3:219-30
references.pmid: 11012725
references.citation: Genetics. 2010 Nov;186(3):1033-44
references.pmid: 20805554
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: Plant Mol Biol. 2004 Nov;56(4):517-26
references.pmid: 15630616
references.citation: Heredity (Edinb). 2011 Oct;107(5):395-404
references.pmid: 21448229
references.citation: Genome. 2008 Nov;51(11):912-21
references.pmid: 18956024
references.citation: Ann Bot. 2013 Jan;111(1):1-19
references.pmid: 23104641
references.citation: PLoS Genet. 2006 Dec;2(12):e190
references.pmid: 17194218
references.citation: BMC Genet. 2010 Oct 15;11:94
references.pmid: 20950446
references.citation: Bioinformatics. 2008 Jun 1;24(11):1403-5
references.pmid: 18397895
references.citation: BMC Genomics. 2012 Mar 25;13:113
references.pmid: 22443094