Plant Molecular Biology Reporter

, Volume 33, Issue 6, pp 1953–1966 | Cite as

Development of TRAP (Target Region Amplification Polymorphism) as New Tool for Molecular Genetic Analysis in Cassava

  • C. D. Carmo
  • D. B. Santos
  • L. B. Alves
  • G. A. F. Oliveira
  • E. J. Oliveira
Original Paper
First Online:

Abstract

Cassava (Manihot esculenta Crantz) lacks molecular studies for use in breeding and germplasm bank maintenance. This work aimed to develop and validate TRAP (target region amplification polymorphism) markers for cassava and evaluate their potential for structuring the genetic diversity of this species. Preliminary analyses with 396 combinations found 64 % of combinations with a good amplification pattern and polymorphism. The 69 most polymorphic TRAP combinations were used to characterize 46 cassava genotypes, from which 606 alleles (range 3 to 18 with a mean of 8.8 alleles per combination) were identified. The polymorphic information content (PIC) ranged from 0.03 to 0.38 (average 0.23), while 31 combinations showed a PIC >0.25. The resolving power (Rp) parameter ranged from 0.10 to 6.30 (average 3.21). The primers that were related to starch and carotenoid biosynthesis, cyanogenic compounds, post-harvest physiological deterioration, root formation, and defense responses were the most polymorphic (>70 % of polymorphic fragments, PIC > 0.25, and Rp > 3.21). A total of 37 private alleles were identified in 20 accessions. Bayesian clustering as implemented in STRUCTURE revealed the presence of two major clusters (K = 2) and four subclusters (K = 4). The group differentiation based on the molecular variance analysis (AMOVA) showed that most of the genetic variation is within groups but with significant differences between groups. Therefore, TRAP primers have a high polymorphism for use as a molecular tool in cassava, in addition to the association with genetic regions that may increase the chances of obtaining functional markers.

Keywords

Molecular marker Genetic diversity Cassava Expressed sequence 
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Notes

Acknowledgments

The authors thank Fundação de Amparo à Pesquisa do Estado da Bahia (Fapesb), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for the financial assistance and scholarship support.

Supplementary material

11105_2015_887_MOESM1_ESM.xlsx (16 kb)
ESM 1 (XLSX 16 kb)

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • C. D. Carmo
    • 1
  • D. B. Santos
    • 1
  • L. B. Alves
    • 1
  • G. A. F. Oliveira
    • 1
  • E. J. Oliveira
    • 2
  1. 1.Universidade Federal do Recôncavo da Bahia (UFRB)Cruz das AlmasBrazil
  2. 2.Embrapa Mandioca e Fruticultura (CNPMF)Cruz das AlmasBrazil

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