Suitability of target region amplified polymorphism (TRAP) markers to discern genetic variability in sweet sorghum

Background Sweet sorghum is an emerging biofuel candidate crop with multiple benefits as a source of biomass energy. Increase of biomass and sugar productivity and quality is a central goal in its improvement. Target region amplified polymorphism (TRAP) is a polymerase chain reaction (PCR) based functional marker system that can detect genetic diversity in the functional region of target genes. Thirty sweet sorghum genotypes were used to study the potential of 24 pairs of TRAP marker system in assessing genetic diversity with regard to three lignin and three sucrose biosynthesis genes. Results A total of 1638 bands were produced out of which 1161 (70.88%) were polymorphic at least at one locus. The average polymorphic information content (PIC), resolving power (RP), marker index (MI), Shannon’s diversity index (H), and gene diversity values were 0.32, 8.86, 1.74, 3.25, and 0.329, respectively. Analysis of molecular variance (AMOVA) revealed a highly significant genetic variation both within and among accessions studied (P = 0.01). However, the variation within the population was higher than among the populations (accessions). Bootstrap analysis showed that the number of loci amplified using this marker system is sufficient to estimate the available genetic diversity. The thirty genotypes were categorized into five clusters using a similarity matrix at 0.72 coefficient of similarity. The genotypes were also grouped mostly according to their geographic origin where the Ethiopian and Egyptian genotypes tend to fall in specific clusters. Moreover, the genotypes reflected the same pattern of distribution when ordinated using principal coordinate analysis. Conclusions In conclusion, TRAP marker can be used as a powerful tool to study genetic diversity in sweet sorghum.

Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.