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. 2020 Oct 6;18(1):59.
doi: 10.1186/s43141-020-00071-5.

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

Yehia A Khidr  1 , Sileshi A Mekuriaw  2   3 , Adel E Hegazy  2 , Enass Amer  2
Affiliations

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

Yehia A Khidr et al. J Genet Eng Biotechnol. .

Abstract

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.

Keywords: Lignin; Molecular markers; Sucrose.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
TRAP profiling of thirty sweet sorghum genotypes amplified with COMT/Em2 primer combination in a 1.5% Agarose gel compared with a 50 bp lane
Fig. 2
Fig. 2
UPGMA cluster analysis based on 24 TRAP marker combinations showing similarity among 30 sweet sorghum based on similarity index
Fig. 3
Fig. 3
Principal coordinate analysis of 30 sweet sorghum genotypes using 24 TRAP marker combinations using the dissimilarity distance matrix
Fig. 4
Fig. 4
Gene diversity and polymorphic information content in 30 sweet sorghum genotypes
Fig. 5
Fig. 5
Bootstrap analysis of 24 TRAP marker combinations based on Nei’s genetic distance
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