Potential of SNP markers for the characterization of Brazilian cassava germplasm

• Published in: Theoretical and applied genetics 2014-06, Vol.127 (6), p.1423-1440
• Main Authors: de Oliveira, Eder Jorge, Ferreira, Cláudia Fortes, da Silva Santos, Vanderlei, de Jesus, Onildo Nunes, Oliveira, Gilmara Alvarenga Fachardo, da Silva, Maiane Suzarte
• Format: Article
• Language: English
• Subjects: Agricultural production; Agricultural research; Agriculture; Analysis of Variance; Bayes Theorem; Bayesian analysis; Bayesian theory; Biochemistry; Biomedical and Life Sciences; Biotechnology; Brazil; Cassava; conservation programs; Crops; Discriminant analysis; Genetic aspects; Genetic diversity; Genetic Markers; Genetic research; genetic variation; Genotype; Germplasm; germplasm conservation; Germplasm resources; Life Sciences; Manihot - genetics; Manihot esculenta; Morphology; Multivariate Analysis; Original Paper; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; Principal Component Analysis; probability; provenance; single nucleotide polymorphism; Single nucleotide polymorphisms
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-014-2309-8

KEY MESSAGE : 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.