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

SimÃμes, K.S.; Silva, S.A.; Machado, Eduardo; Silva, M.S.

doi:10.4238/gmr16039776

Cited by 11 publications

(8 citation statements)

References 29 publications

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“…TRAP primers were efficient in the amplification of the genomic DNA of castor bean, corroborating the results obtained by Simões et al (2017).The high means and wide variation of SOC among the elite strains obtained in this study indicate genetic variability for the castor bean breeding program of NBIO-UFRB.…”

Section: Resultssupporting

confidence: 87%

“…The number of polymorphic fragments generated per combination varied from 2 (Trap17 x Arb2) to 10 (Trap28 x Arb4), with an average of 5.2 (Table 5). Simões et al (2017), when using a greater number of combinations of TRAP primers (330), including those used in this study, identified a variation from 2 (TRAP5 + ARB1; TRAP5 + ARB3; TRAP6 + ARB3; TRAP14 + ARB3; TRAP17 + ARB4; TRAP20 + ARB2; TRAP30 + ARB1; TRAP30 + ARB2; TRAP34 + ARB3) to 15 (TRAP22 + ARB6), with an average of 1.22 loci per combination.The mean of 5.2 polymorphic fragments per combination of primers found in the present study was close to the values of 4.8 derived from 70 combinations in castor bean (Simões et al, 2017), higher than 3.04 derived from 27 combinations of TRAP markers in sugarcane (Mirajkar et al, 2017) and lower than 13.30 derived from 12 TRAP combinations also in sugarcane (Creste et al, 2010).…”

Section: Resultsmentioning

confidence: 84%

“…The fixed primers were developed for the fatty acid synthesis metabolic pathway for castor bean crop. The fixed and direct primers were developed by Simões et al (2017). As reverse primer, six arbitrary primers were used according to Li and Quiros (2001) adapted by Hu and Vick (2003).…”

Section: Amplification Of Genomic Dna With Trap Primersmentioning

confidence: 99%

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Research Article Joint analysis for oil content and TRAP markers in elite castor bean strains

Simões¹,

Silva²,

Machado³

et al. 2020

Genet. Mol. Res.

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The demand for quality vegetable oil, such as castor oil, has been increasing significantly due to its great applicability in the cosmetic and industrial sector, especially with the advent of biodiesel. Castor bean produces a non-edible oil, with unique chemical properties, which makes it potentially useful for the production of cosmetics, aircraft lubricants and biodiesel. Breeding programs aimed at increasing the oil content in castor bean seeds are of paramount importance to meet the requirements of this market. In view of the above, we examined the genetic variability of elite castor bean strains through joint analysis of the oil content trait and TRAP (Target Region Amplification Polymorphism) molecular markers. This analysis was performed using the means for seed oil content of 40 elite castor bean strains, developed by the breeding program of the Genetic Improvement and Biotechnology Unit of the Federal University of Recôncavo da Bahia, together with genotyping of this population by means of 44 combinations of TRAP primers (fixed and arbitrary primers). Genetic dissimilarity between the strains was calculated through the Gower dissimilarity index, using the UPGMA clustering method. The means for oil content rangeed from 39.10 (UFRB 36) to 55.39% (UFRB 209), demonstrating that there is ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 19 (4): gmr18688 K.S. Simoes et al. 2 genetic variability among the strains. The 44 TRAP combinations enabled the identification of 380 fragments, 61% of which were polymorphic. The joint analysis formed three clusters, showing that there is genetic divergence among these elite strains. Therefore, joint analysis of the seed oil content trait and TRAP markers is efficient to evaluate the genetic dissimilarity in castor bean strains, demonstrating potential for the breeding program of the species.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 84%

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Research Article Joint analysis for oil content and TRAP markers in elite castor bean strains

Simões¹,

Silva²,

Machado³

et al. 2020

Genet. Mol. Res.

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“…Many molecular markers like SSR (Simple Sequence Repeats), SNP (Single Nucleotide Polymorphism), EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat), AFLP (Amplified Fragment Length Polymorphism), SCOT (Start Codon Targeted Polymorphism), RAPD (Random Amplified Polymorphic DNA), ISSR (Inter-Simple Sequence Repeat) and TRAP ((Target Region Amplification Polymorphism) have been used in assessing the genetic diversity of castor [17–26]. Nonetheless, irrespective of the marker systems used, the global analysis of the genetic diversity of castor germplasm shows the low levels of variability and a lack of geographically structured genetic population [17–19, 23].…”

Section: Introductionmentioning

confidence: 99%

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

et al. 2019

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Castor bean is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Currently, castor bean varieties suffer from low productivity and high risk of insect pests and diseases. It is in urgent need to mine elite genes from wild materials for castor breeding. 29 pairs of polymorphic SRAP primers out of 361 pairs were used to analyse the genetic diversity of 473 wild castor materials from South China. 203 bands were amplified by the 29 pairs of primers, of which 169 bands were polymorphic, with a polymorphic percentage of 83.25%. With an average number of alleles per locus (A p ) of 1.801, average number of effective alleles per locus ( A e ) of 1.713 and average percentage of polymorphic loci (P) of 90.04%, these primers were proven to be useful and effective. Nei’ genetic distance between the materials ranged from 1.04 to 25.02, with an average of 13.03. At the genetic distance of 25.02, the materials clustered into two major groups, consistent with the result of population structure analysis. However, more subgroups existed between 5.21 and 13.32. Although not all the materials from the same region were clustered in the same group, an obvious trend existed where the groups were related to regions to a great extent. Based on multiple indices, the genetic diversity of materials from Hainan was the lowest. However, there was not much difference between West Guangdong and Guangxi, although the former was slightly higher. Moderate genetic differentiation was observed in wild materials in South China. The genetic differentiation mainly occurred within population, with maximum differentiation in Guangxi, followed by West Guangdong and the minimum in Hainan. Nonetheless, there was an extensive geneflow between populations. The above results provided a direction for the conservation and breeding application of these materials.

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

Cited by 11 publications

References 29 publications

Research Article Joint analysis for oil content and TRAP markers in elite castor bean strains

Research Article Joint analysis for oil content and TRAP markers in elite castor bean strains

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China

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

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