Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity in Sugarcane Germplasm Collections

Abstract

Target region amplification polymorphism (TRAP) is a fairly new PCR-based molecular marker technique which uses gene-based information for primer design. The objective of this study was to evaluate the utility of TRAP markers for assessing genetic diversity and interrelationships in sugarcane germplasm collections. Thirty genotypes from the genera Saccharum, Miscanthus, and Erianthus were used in the study. Among the genus Saccharum were the species, S. officinarum L., S. barberi Jesw., S. sinense Roxb., S. spontaneum L., S. robustum Brandes and Jeswiet ex Grassl, cultivars, cultivar-derived mutants and interspecific hybrids between S. officinarum and S. spontaneum. Six fixed primers, designed from sucrose-and cold tolerance-related EST (expressed sequence tags) sequences, paired with three arbitrary primers, were used to characterize the germplasm. Both the cluster and principal coordinate (PCoA) analyses placed the Erianthus spp. and Miscanthus spp. genotypes distinctly from each other and from the Saccharum species, thus, supporting their taxonomic classification as separate genera. Genotypes of the low sucrose and cold tolerant species, S. spontaneum, formed one distinct group, while the rest of the Saccharum species formed one interrelated cluster with no distinct subgroups. Sequence analysis of TRAP bands derived from a S. spontaneum genotype revealed homology with known gene sequences from other grass species including Sorghum. A BLASTn search using the homologous sequences from Sorghum matched with the S. officinarum GenBank accession from which the fixed TRAP primer was designed. These results ratify TRAP as a potentially useful marker technique for genetic diversity studies in sugarcane.

Molecular Breeding of Grasses by Transgenic Approaches for Biofuel Production

“…Based on species richness and the geographic distributions of endemic species, India was considered the center of maximum variation of the Saccharum complex (Mukherjee, 1957). Eventually, the genus Miscanthus was added to the Saccharum complex, because it was thought to be involved in the origin of Saccharum (Daniels et al, 1975, as cited in Alwala et al, 2006;and Amalraj & Balasundaram, 2006).…”

Molecular Markers: Assisted Selection in Soybeans

“…The polymorphism is generated from a combination of a fixed primer designed from an EST sequence of interest, and an arbitrary primer. Recent studies have reported the use of TRAP markers to access genetic diversity in sugarcane and identification of possible candidate genes for cold tolerance and metabolic pathway involved in sucrose (Alwala et al, 2006). The technique is extremely simply practice involving the extraction of genomic DNA and a PCR reaction.…”

Genetic diversity in sugarcane varieties in Brazil based on the Ward-Modified Location Model clustering strategy

“…Since the success of the development of new varieties of sugarcane is associated with the ability to correctly choose the best individuals to be the progenitors of the new varieties, a better understanding of the genetic diversity between the clones used as progenitors is essential in defining the new crosses (Alwala et al, 2006;Santos et al, 2012). To achieve this objective, it is necessary to characterize the germplasm collection of the breeding program.…”