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

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.