DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Khan, Mahmudul; Rafii, M. Y.; Ramlee, Shairul Izan; Jusoh, Mashitah; Mamun, Al; Halidu, Jamilu

doi:10.1038/s41598-021-93867-5

Cited by 34 publications

(30 citation statements)

References 58 publications

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“…NCSS, LLC.) reported by Khan et al [ 10 ]. To show the graphical relationship among principal axis, eigenvalues, and cumulative variance on a single graph, “scree plot” was created using XLSTAT software (Ver.2014.5.03, Addinsoft) reported by Vidal et al [ 36 ].…”

Section: Methodsmentioning

confidence: 94%

“…To show the graphical relationship among principal axis, eigenvalues, and cumulative variance on a single graph, “scree plot” was created using XLSTAT software (Ver.2014.5.03, Addinsoft) reported by Vidal et al [ 36 ]. Eigen values and PCA biplot were illustrated by the use of JMP ver.16 software (SAS program) reported by Khan et al [ 10 ]. For estimation of the Shannon diversity index, we used Multivariate Statistical Packages (MVSP) ver.…”

Section: Methodsmentioning

confidence: 99%

“…One of the reasons for Bambara groundnut's low yield is the usage of local landraces [ 7 ]. Khaliqi et al [ 8 ] reported that the yield of Bambara groundnut varied from 0.97 ton/ha to 3.12 ton/ha, though it has the ability to produce a higher yield up to 4 to 5 ton/ha under optimum conditions and standard cultivation procedures [ 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

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Unveiling Genetic Diversity, Characterization, and Selection of Bambara Groundnut (Vigna subterranea L. Verdc) Genotypes Reflecting Yield and Yield Components in Tropical Malaysia

Khan

Rafii

Ramlee

et al. 2022

BioMed Research International

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Addressing genetic diversity and application of appropriate breeding strategies are imperative for Bambara groundnut (Vigna subterranea L.) improvement as a newly introduced legume in Malaysia. It has become a “miracle lucrative” legume for Asia and Africa because of its drought resilience, excellent nutritional profiles, and versatile uses. This crop’s progress has been limited owing to a lack of extensive research, marginalization, inadequate knowledge, and a lack of accessible funds, among other concerns. The expansion of this crop is reliant on the assessment and selection of unique and reliable breeding lines in various circumstances. Consequently, the goal of this work is to determine genetic diversity and the relationship between yield-contributing components in 44 Bambara groundnut accessions sourced from the Genebank of Institute of Tropical Agriculture and Food Security (ITAFoS) at Universiti Putra Malaysia (UPM). Three replications were used in the experiment, which was done using a randomized complete block design (RCBD). The data were subjected to ANOVA, PCA, correlation, and heat map cluster analysis; also, genetic parameters and broad-sense heritability estimation were carried out on recorded phenotypic descriptors. All of the investigated variables had a significant variance ( p ≤ 0.05 or 0.01) according to the ANOVA results. Yield per hectare showed a positively strong to perfect significant correlation ( 0.75 ≤ r ≤ 1.00 ; p ≤ 0.01 ) with the yield components viz. fresh pod weight, hundred seed weight, dry pod weight, and dry seed weight. Interestingly, these traits had heritability ≥ 60 % and genetic gain ≥ 20 % , which can be beneficial for direct selection to this crop improvement. The UPGMA clustering revealed five distinct clusters in which genotypes under cluster I, cluster II, and cluster IV produce a greater yield of 5.96%, 7.12%, and 15.05%, respectively, than the grand mean yield of 1927.01 kg/ha. The PCA biplot estimated that PC1 (32.9%) and PC2 (12.9%) would cover 45.8% of the total variance. We discovered 30 promising lines that provide yields per hectare more than 1.8 ton/ha and might be used as parental lines in future breeding operations aimed at improving the grain yield in tropical areas or comparable agroecological zones.

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Section: Methodsmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Unveiling Genetic Diversity, Characterization, and Selection of Bambara Groundnut (Vigna subterranea L. Verdc) Genotypes Reflecting Yield and Yield Components in Tropical Malaysia

Khan

Rafii

Ramlee

et al. 2022

BioMed Research International

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“…The level of genetic closeness between clones based on quality characters was analyzed using the JMP 16.0 program (trial version). The JMP 16.0 program can be used to calculate genetic distance based on the similarity between the objects studied, then arranged in a single unit (cluster analysis) (Khan et al 2021). The end of this analysis will form a dendrogram that describes the extent of the relationship between clones of diversity.…”

Section: Discussionmentioning

confidence: 99%

Quality diversity of 35 tea clones (Camellia sinensis var. sinensis) processed for green tea

Prayoga¹,

SYAHRIAN²,

RAHADI³

et al. 2022

Biodiversitas

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Abstract. Prayoga MK, Syahrian H, Rahadi VP, Atmaja MIP, Maulana H, Anas. 2022. Quality diversity of 35 tea clones (Camellia sinensis var. sinensis) processed for green tea. Biodiversitas 23: 810-816. The development of sinensis clones in Indonesia is still focused on increasing productivity and until now there has been no study on the level of genetic similarity and diversity based on quality characters. Therefore, the purpose of this study was to examine the level of kinship and genetic diversity of 35 sinensis clones from the collection of the Indonesia Research Institute for Tea and Cinchona. The study consisted of two stages, testing the content of chemical compounds (polyphenols and caffeine) and organoleptic testing. The material used in both tests was fresh shoots consisting of peko + 3 young leaves (P+3). In organoleptic testing, shoots of 35 sinensis variety clones were first processed into green tea. Furthermore, the processed green tea was tested organoleptically by three credible panelists. The data from the test results of chemical and organoleptic compounds were then tested statistically to get the coefficient of variation (CV), which indicates data diversity. The level of genetic closeness between clones based on quality characters was analyzed using the JMP 16.0 program (trial version), then arranged into clusters. To see the contribution of each parameter to the quality diversity of 35 sinensis clones, a principal component analysis (PCA) was carried out. The results of this study indicate that there are four main clusters grouping the 35 sinensis clones tested. The first cluster excels in the character of taste and aroma, the second cluster excels in appearance, seductive colour, and infusion, the third cluster excels in the character of polyphenols, while the fourth cluster excels in the character of caffeine. The characters that contributed to the genetic diversity of the 35 clones tested were caffeine, appearance, and aroma.

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“…ISSR markers generate more phylogenetically relevant polymorphic fragments than other types of molecular markers, including Simple Sequence Repeats (SSR), Sequence Related Amplified Polymorphisms (SRAP), and Random Amplified Polymorphic DNA (RAPD) [16]. In addition, the genetic data provided by ISSR markers are more consistent with morphological variability and the evolutionary history of the morphotypes [17]. ISSR markers are also simple to use, have good reproducibility, and can distinguish among similar genotypes [18].…”

Section: Introductionmentioning

confidence: 99%

Clematis Genetic Diversity and Hybrid Identification using ISSR Markers

Wang

Lin

et al. 2022

Preprint

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Background Clematis taxa are diverse, with high ornamental value. However, these plants have a complicated genetic background and a long growth period. Thus, molecular identifications are necessary to shorten the breeding cycle. Result Here, the genetic diversity of 17 parental taxa (five wild species and 12 Texas cultivars) were analyzed using inter simple sequence repeat (ISSR) markers. We obtained 108 alleles using 12 ISSR primers (an average of 9 alleles per primer). Genetic parameters, including the number of alleles (Na), the effective number of alleles (Ne), Nei's genetic diversity (H), and Shannon's diversity (I), suggested that these 17 taxa were highly diverse. Phylogenetic analysis recovered the 17 taxa in two large clades: one cluster included all of the cultivars, as well as Clematis pinnata, C. brevicaudata, and C. tubulosa; the second cluster included C. fusca and C. reticulata . The pairwise genetic distances between all cultivars were 0.421–2.368, suggesting that these cultivars may have derived from closely related species. We next performed five crosses between parental taxa and used ISSR markers to validate the authenticity of the 15 hybrid offspring. ISSR primers amplified bands specific to the male parents of each cross. Male parent-specific bands were identified in 11 of the 15 offspring; these 11 offspring were identified as true hybrids. The remaining progeny were considered self-hybrids due to the absence of male parent-specific bands. Conclusion Our results demonstrated that ISSR molecular markers may be useful tools for the verification of true Clematis hybrids. ISSR-based genetic diversity analyses, early hybrid identification, and marker assisted selection of Clematis taxa may improve breeding efficiency, excavate key genes associated with important traits, promote the development of new varieties, and shorten the breeding cycle

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DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system

Cited by 34 publications

References 58 publications

Unveiling Genetic Diversity, Characterization, and Selection of Bambara Groundnut (Vigna subterranea L. Verdc) Genotypes Reflecting Yield and Yield Components in Tropical Malaysia

Unveiling Genetic Diversity, Characterization, and Selection of Bambara Groundnut (Vigna subterranea L. Verdc) Genotypes Reflecting Yield and Yield Components in Tropical Malaysia

Quality diversity of 35 tea clones (Camellia sinensis var. sinensis) processed for green tea

Clematis Genetic Diversity and Hybrid Identification using ISSR Markers

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