TRAP and SRAP markers to find genetic variability in complex polyploid Paullinia cupana var. sorbilis

Guarana [Paullinia cupana var. sorbilis (Mart.) Ducke] is a typical South American plant, native to the Amazon, with subspontaneous occurrence in Maués, Amazonas, Brazil, where it was domesticated and cultivated by the Sateré‐Mawé indigenous community. Guarana is an original Brazilian product with great economic and industrial potential owing to the energetic, antioxidant, and medicinal properties of its seeds. In spite of its importance, there is still a gap in knowledge about genetic diversity and adaptations that might improve agro‐industrial uses of guarana seeds. This study was aimed at estimating phytochemical diversity, classification, and typology of guarana genotypes. Agro‐industrial potential among eight genotypes was estimated based on phytochemical characters (theobromine, caffeine, catechin, and epicatechin content, quantified by high performance liquid chromatography) and yield in three locations from harvests between 2015 and 2016. Phytochemical divergence was assessed by the mean Euclidean distance. Grouping was performed by the unweighted pair‐group method using arithmetic averages. Metabolite content varied considerably between genotypes (e.g., among caffeine [3.23–7.35%], catechin [0.20–3.57%], and epicatechin [0.09–4.22%]), and dry seed yield was the character with the greatest variation (0.048–5.13 kg plant−1). The metabolic profile variations of the genotypes were clustered into three chemotypes: energetic and antioxidant guarana (genotypes CIR815, CIR904, and CMA498); antioxidant guarana (genotypes BRS‐Maués and CMU874); and energetic guarana (genotypes CMA831, CMU952, and BRS‐CG372). Genotypes CIR815, CIR904, and CMU874 have the potential to be future commercial cultivars, providing quality raw material for soft drinks, energy drinks, and pharmaceutical products.

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“…This fact was confirmed by Silva et al. (2016), who also found similarity between genotypes from different origins. Nascimento Filho et al.…”

Section: Discussionsupporting

confidence: 72%

Phytochemistry divergence among guarana genotypes as a function of agro‐industrial characters

et al. 2020

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“…The PIC values found in the present study were ranged from 0.18 to 0.42 with lignin-related genes and from 0.22 to 0.45 with sucrose-related genes. These values were wider than those obtained in the guarana plant which ranged from 0.29 to 0.37 [ 28 ] while it was comparable to the result found in sugarcane that ranged from 0.2 to 0.4 with an average of 0.3 [ 32 ]. The PIC measures the discriminatory power of a marker system where the theoretical maximum PIC value for a dominant marker is 0.5 [ 34 ].…”

Section: Discussionsupporting

confidence: 59%

“…These markers are characterized by their simplicity, high yield, reproducibility, and can be sequenced [ 26 ]. TRAP marker systems are used to study genetic diversity in different crop species such as castor bean [ 27 ], guarana [ 28 ], lettuce [ 29 ], mango [ 30 ], salvia [ 31 ], sugarcane [ 32 , 33 ], sunflower [ 34 ], and wheat [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

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

Khidr

Mekuriaw

Hegazy

et al. 2020

Journal of Genetic Engineering and Biotechnology

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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.

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“…For other crops, higher PIC values were found: guaraná, PIC ranged from 0.29 to 0.36, average of 0.33, for 5 TRAP combinations (Da Silva et al, 2016), and sunflower, PIC ranged from 0.02 to 0.50, average of 0.39, for 12 TRAP combinations (Yue et al, 2009).…”

Section: Resultsmentioning

confidence: 93%

“…Figure 1 shows the DNA amplification of the elite lineages of castor bean using TRAP markers. Studies using TRAP markers have been conducted with other crops: guaraná (total number of polymorphic bands ranged from 12 to 33, with 79% polymorphism, and fragment size between 100 and 800 bp) (Da Silva et al, 2016); Dendrobium (genotyped with 13 TRAP markers, obtaining 510 fragments, including 500 polymorphic fragments, and 97.8% polymorphism) (Feng et al, 2015); Diospyros kaki (genotyped with 36 combinations of TRAP primers with an amplification of 2184 fragments, of which 2072 were polymorphic fragments and 94.87% polymorphism) (Luo et al, 2013); and sugarcane (21 TRAP combinations, for sucrose synthesis, with an amplification of 340 polymorphic fragments, with an average of 16.2 fragments, and 9 TRAP combinations for drought tolerance, resulting in 155 polymorphic fragments, with an average of 17.2 fragments per primer combination) (Creste et al, 2010). These studies corroborate the results obtained for castor bean, because they show that TRAP markers are highly polymorphic and appropriate for studying genetic divergence and other applications, for example, mapping associations and QTLs.…”

Section: Resultsmentioning

confidence: 99%

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

et al. 2017

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ABSTRACT. Castor bean (Ricinus communis L.) is a tropical plant of great commercial interest and a potential source of biodiesel. The development of genetically improved cultivars with high amounts of oil in the seeds and low ricin toxicity is crucial to increase the productivity of this crop. The use of TRAP (target region amplification polymorphism) markers to develop elite lineages and study genetic divergence is fundamental to advance the genetic improvement of this species. The goal of this study was to evaluate the genetic divergence among 40 elite lineages of R. communis, which belong to the NBIO-UFRB Genetic Improvement Program, using TRAP markers involved in the biosynthesis of oil and ricin. Total DNA was extracted and quantified from the leaf tissue of the castor bean plants, and 70 TRAP combinations (fixed and arbitrary primers) were used to genotype the 40 lineages. Of the 580 fragments amplified, 335 were polymorphic (58%). The genetic dissimilarity among the lineages was calculated by the Jaccard dissimilarity index using the UPGMA grouping method. A dendrogram was generated, and four groups formed, showing divergence among the elite lineages that favors selection. The TRAP 2 K.S. Simões et al. Genetics and Molecular Research 16 (3): gmr16039776 molecular markers were efficient at characterizing the genetic variability among the lineages and, because TRAP markers are functional markers involved in the biosynthesis of oil and ricin, they are important when studying the association between a marker and a candidate gene.

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TRAP and SRAP markers to find genetic variability in complex polyploid Paullinia cupana var. sorbilis

Cited by 15 publications

References 22 publications

Phytochemistry divergence among guarana genotypes as a function of agro‐industrial characters

Phytochemistry divergence among guarana genotypes as a function of agro‐industrial characters

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

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

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