Genetic diversity in Cola acuminata and Cola nitida using RAPD primers

Akinro, A Lawrence; Adesoye, I Adenubi; Fasola, R Taiye

doi:10.2298/gensr1901227a

Cited by 3 publications

(4 citation statements)

References 10 publications

(11 reference statements)

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“…Furthermore, percentage of polymorphic loci estimated at 99% confirms a high level of polymorphism of SNPs as stated by Ji et al (2012) and Forrest et al (2014). This percentage of polymorphic loci is higher than that obtained with RAPD markers in C. nitida (71.47%), and on five other Cola species (28.5%) in Nigeria (Akinro et al 2019;Wood and Ohimain 2020). These results illustrate the effectiveness of SNPs for genetic diversity analysis in kola tree compared to other molecular markers including RAPDs.…”

supporting

confidence: 72%

Genetic diversity and structure of kola tree (Cola nitida) clones germplasm in Côte d’Ivoire using Single Nucleotide Polymorphism markers

OUATTARA¹,

SÉRY²,

SARAKA³

et al. 2022

Biodiversitas

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Abstract. Ouattara Y, Koffi KG, Séry DJ-M, Saraka DM, Pokou ND, Gba KKM, Bonsson B, Akaffou DS, Sié RS. 2022. Genetic diversity and structure of kola tree (Cola nitida) clones germplasm in Côte d’Ivoire using Single Nucleotide Polymorphism markers. Biodiversitas 23: 4677-4685. The kola nut comes from the cola tree (Cola nitida [Vent.] Schott & Endl.), a product of economic interest to Côte d’Ivoire. The country is the leading producer and exporter. However, much of its collection has been destroyed due to urbanization and deforestation. This has resulted in the loss of much of its genetic diversity. This study aimed to determine genetic diversity and structure of C. nitida in Côte d’Ivoire using Single Nucleotide Polymorphism (SNPs) markers. Thirty clones from Côte d’Ivoire (14 clones) and Nigeria (16 clones) cultivated in CNRA (Centre National de Recherche Agronomique) were analyzed using 145 SNPs. GBS (Genotyping by Sequencing) technique was used for the genotyping. The results confirmed the existence of both origins (Côte d’Ivoire and Nigeria) by analyzing clones’ genetic structure and the principal coordinate analysis. The genetic diversity obtained was higher within origins than among origins. The two origins showed moderate differentiation (FST = 0.11) and the genetic distance was 0.46. The 30 clones were subdivided into six subgroups partially overlapping the geographical origins. Genetic differentiation among subgroups was moderate to very strong (FST ranging from 0.10 to 0.26). Four clones from Nigeria were close to those from Côte d’Ivoire. This genetic structuring highlights the possibilities for genetic improvement of kola trees in Côte d’Ivoire.

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confidence: 72%

Genetic diversity and structure of kola tree (Cola nitida) clones germplasm in Côte d’Ivoire using Single Nucleotide Polymorphism markers

OUATTARA¹,

SÉRY²,

SARAKA³

et al. 2022

Biodiversitas

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“…et al, 2013). In comparison with other genome regions, we found low nucleotide diversity for rps14 which shows rps14 the most promising gene as the land plant barcode according to the measures of universal application and high sequence divergence among the species (AKINRO et al, 2019;WANG H. T. et al, 2013;ZAHRA et al, 2016). (1993) model.…”

Section: Tajima's Neutrality Testmentioning

confidence: 79%

“…DNA barcoding is an advanced approach for the systematic and identification of taxon using a short genomic region (HEBERT et al, 2003). Information regarding DNA barcoding on Lamiaceae is very deficient in the literature (AKINRO et al, 2019). However, in the past few studies tested the utility of DNA barcoding in family Lamiaceae in terms of genetic variation (DE MATTIA et al (2011).…”

Section: Amplification Of Genomic Dnamentioning

confidence: 99%

“…Thus, researchers have examined the idea that an easy and rapid way of species identification and defining species boundaries is possible with the use of short DNA sequence (ERIĆ et al, 2019;SEVINDIK, 2019), which possess a standardized position in the genome, called as DNA barcode (HEBERT et al, 2004;FRÉZAL and LEBLOIS, 2008). DNA barcoding is a new approach designed to provide rapid, accurate and automatable species identification by using short standardized gene regions as internal species tags (AKINRO et al, 2019;GRITSENKO et al, 2019;PATI et al, 2019). Molecular identification methods have been used in forensics, food and taxonomy-based identification (TELETCHEA et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Phylogeny and diversity of lamiaceae based on rps14 gene in Pakistan

Ayaz¹,

Zaman²,

Saqib³

et al. 2020

Genetika

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The present research work was carried out to conduct concordance between the molecular data and the phylogenetic relationship between the selected species of Lamiaceae. We studied 34 species collected from various phytogeographical areas of Pakistan. Molecular DNA was isolated from fresh leaf specimens of the selected taxa. The rps14 gene was amplified for the isolation of DNA sequencing and the amplified products were sequenced and analyzed for phylogenetic analysis. The sequenced products were analyzed using bioinformatics tools such as MEGA7, I-TASSER (Iterative Threading Assembly Refinement) and SAVES (The Structure Analysis and Verification Server). ExPASY translate tool was used for the translation of nucleotide sequences to amino acid sequences. Phlomis cashmeriana with Origanum vulgare, and Lamium album with Lamium amplexicaul showed a close relationship in both phylogenetic trees with well-represented bootstrap (BS) values. The pairwise distance ranged from 0.013 to 0.19 with an overall mean distance of 0.068 was also observed. I-TASSER software was utilized to predict the 3D protein structures followed by stereochemical analysis. Based on the present finding it is determined that the rps14 gene would be used as a DNA barcode for the identification of plant taxa. Additionally, it is needed for the development of additional reliable molecular markers to resolve the systematics issues in the family Lamiaceae.

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Molecular and Morphological Diversity Studies of Five Cola (Schott and Endl.) Species in Ibadan, Nigeria

Wood

Ohimain

2020

ARRB

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Intra- and inter-species genetic diversity study was carried out comparing the molecular and morphological characters of five Cola species namely Cola acuminata, Cola nitida, Cola millenii, Cola lepidota and Cola gigantea collected from five locations in Ibadan, Nigeria. Sixteen Cola accessions were analysed based on 7 quantitative characters, 12 qualitative characters and 8 Random Amplified Polymorphic DNA primers. From the quantitative characters studied, high significant difference across the location and species was recorded as leaf length had the strongest variability while the species obtained from Botany Nursery showed strongest locational effect on the vegetative leaf characters. All quantitative characters analysed were good determinants for delimiting Cola species. Cola lepidota recorded the highest variability compared to the other Cola species. Qualitative characters studied revealed that leaf surface, seed colour, and floral colour are strong characters for delimiting Cola species. Molecular analysis showed that 309 fragments were recorded, of which 28.5% were polymorphic while 8.4% were monomorphic. Genetic similarities ranged from 0.44 to 0.93 for the 16 Cola accessions with a mean value of 0.67. Deductions from the combined effect of molecular and morphological characters showed high variability for the characters analysed and a likely monophyletic relationship for the 16 Cola accessions. Molecular and morphological determinants observed in this study can help Cola breeders identify species of interest. We recommend further research on the variability of Cola species.

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Genetic diversity in Cola acuminata and Cola nitida using RAPD primers

Cited by 3 publications

References 10 publications

Genetic diversity and structure of kola tree (Cola nitida) clones germplasm in Côte d’Ivoire using Single Nucleotide Polymorphism markers

Genetic diversity and structure of kola tree (Cola nitida) clones germplasm in Côte d’Ivoire using Single Nucleotide Polymorphism markers

Phylogeny and diversity of lamiaceae based on rps14 gene in Pakistan

Molecular and Morphological Diversity Studies of Five Cola (Schott and Endl.) Species in Ibadan, Nigeria

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