scholarly journals Assessment of genetic diversity and structure of Bambara groundnut [Vigna subterranea (L.) verdc.] landraces in South Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adré Minnaar-Ontong ◽  
Abe S. Gerrano ◽  
Maryke T. Labuschagne
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Ssr Markers ◽  
Southern Africa ◽  
Crop Improvement ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Legume Crop ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

AbstractWith its drought tolerant and protein-rich properties, Bambara groundnut [Vigna subterranea (L.) Verdc.], an indigenous African legume crop can contribute immensely to food security. This miracle crop is used as food and for the enhancement of soil fertility in South Africa. Knowledge on the genetic diversity and structure among the Bambara groundnut landraces can pave the way for the effective use and cultivation of this crop in southern Africa, especially South Africa. The aim of this study was to assess the genetic diversity and structure among Bambara groundnut landraces collected across South Africa and compared to a limited number of accessions from southern Africa using SSR markers. Seventy-eight Bambara groundnut accessions were genotyped using 19 Bambara specific SSR markers. SSR loci explored in this study, were all polymorphic. A total of 127 alleles were detected with a mean of 6.7 alleles per locus. Allele diversity and frequency among genotypes varied from 0.21 to 0.85 with an average of 0.62 per locus. Genetic variation as described by the analysis of molecular variance indicated higher genetic diversity (92%) within landraces than between (8%) different landraces. Population structure analysis showed that three subpopulations existed, and most of the South African accessions were restricted to one subpopulation, indicating that Bambara landraces has the ability to form unique haplotypes in different environments. Information harnessed in this study is helpful for further use in breeding programs for crop improvement.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers

Genome ◽  
2011 ◽  
Vol 54 (11) ◽  
pp. 898-910 ◽  
Author(s):  
P. Somta ◽  
S. Chankaew ◽  
O. Rungnoi ◽  
P. Srinives
Keyword(s):  
Ssr Markers ◽  
Gene Diversity ◽  
Bambara Groundnut ◽  
West African ◽  
Azuki Bean ◽  
Vigna Subterranea ◽  
East African ◽  
The West ◽  
Legume Crop ◽  
Population Structure Analysis

Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean.

scholarly journals Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1479
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Dhiman Biswas ◽  
Jennifer Ann Harikrishna ◽  
Yuxuan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Comparative Mapping ◽  
In Silico ◽  
Large Scale ◽  
Crop Improvement ◽  
Musa Spp ◽  
Population Structure Analysis ◽  
A Genome ◽  
Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Md Mahmudul Hasan Khan ◽  
Mohd Y. Rafii ◽  
Shairul Izan Ramlee ◽  
Mashitah Jusoh ◽  
Md Al Mamun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Sustainability ◽  
Crop Improvement ◽  
Principal Component ◽  
Issr Markers ◽  
Bambara Groundnut ◽  
Fixation Index ◽  
Vigna Subterranea ◽  
Information Index ◽  
Issr Primers

AbstractAs a new crop in Malaysia, forty-four Bambara groundnut (Vigna subterranea L. verdc.) genotypes were sampled from eleven distinct populations of different origins to explore the genetic structure, genetic inconsistency, and fixation index. The Bambara groundnut, an African underutilized legume, has the capacity to boost food and nutrition security while simultaneously addressing environmental sustainability, food availability, and economic inequalities. A set of 32 ISSRs were screened out of 96 primers based on very sharp, clear, and reproducible bands which detected a total of 510 loci with an average of 97.64% polymorphism. The average calculated value of PIC = 0.243, RP = 5.30, H = 0.285, and MI = 0.675 representing the efficiency of primer set for genetic differentiation among the genotypes. The ISSR primers revealed the number of alleles (Na = 1.97), the effective number of alleles (Ne = 1.38), Nei's genetic diversity (h = 0.248), and a moderate level of gene flow (Nm = 2.26) across the genotypes studied. The estimated Shannon’s information index (I = 0.395) indicates a high level of genetic variation exists among the accessions. Based on Nei’s genetic dissimilarity a UPMGA phylogenetic tree was constructed and grouped the entire genotypes into 3 major clusters and 6 subclusters. PCA analysis revealed that first principal component extracted maximum variation (PC1 = 13.92%) than second principal component (PC2 = 12.59%). Bayesian model-based STRUCTURE analysis assembled the genotypes into 3 (best ΔK = 3) genetic groups. The fixation-index (Fst) analysis narrated a very great genetic diversity (Fst = 0.19 to 0.40) exists within the accessions of these 3 clusters. This investigation specifies the effectiveness of the ISSR primers system for the molecular portrayal of V. subterranea genotypes that could be used for genetic diversity valuation, detection, and tagging of potential genotypes with quick, precise, and authentic measures for this crop improvement through effective breeding schemes.

scholarly journals Keragaman Genetik Kacang Bogor (Vigna subterranea L. Verdc.) Berdasarkan Marka SSR (Simple Sequence Repeat)

2017 ◽  
Vol 44 (3) ◽  
pp. 279
Author(s):  
Zikril Illahi ◽  
Ni Made Armini Wiendi ◽  
Dan Sudarsono
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Distances ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Sequence Repeat ◽  
Phylogenic Tree ◽  
Legume Crop ◽  
Population Structure Analysis ◽  
Simple Sequence ◽  
Underutilized Legume

<em></em><em>ABSTRACT<br /><br />Bambara groundnut (Vigna subterranea L. Verdc.) is an important underutilized legume crop in Indonesia. The aim of this research is to study genetic diversity of bambara groundnut from Sukabumi and Sumedang, West Java, Indonesia. This study used 107 bambara groundnut accessions, which consisted of 57 accessions from Sukabumi and 50 accessions from Sumedang. We use five simple sequence repeat (SSR) to analyze the accessions. Totally nine alleles were detected, with a mean of 1.8 alleles per locus. Allelic and gene diversities were higher in Sumedang (1.8 alleles per locus and 0.119) than in Sukabumi population (1.4 alleles per locus and 0.020), respectively. We constructed a phylogenic tree by Neighbor-Joining analysis based on genetic distances (DA) and showed the tree divided bambara groundnut accessions into two broad groups according to the origin of samples (Sukabumi and Sumedang). Results from the phylogenic tree are in line with those from the population structure analysis.<br /> <br />Keywords: allele diversity, bambara groundnut, genetic distance, under utilized legume<br /><br /></em>

GENETIC DIVERSITY IN BAMBARA GROUNDNUT (Vigna subterranean) AS REVEALED BY MOLECULAR WEIGHTS OF THE SEEDS’ PROTEINS

2018 ◽  
Vol 30 (2) ◽  
pp. 19-28
Author(s):  
A. J. Oludare ◽  
J. I. Kioko ◽  
A. A. Akeem ◽  
A. T. Olumide ◽  
K. R. Justina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Seed Proteins ◽  
Electrophoretic Analysis ◽  
Protein Characterization ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Phylogenetic Relatedness ◽  
Molecular Weights ◽  
National Centre ◽  
Standard Marker

Nine accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,syn. Voandzeia subterranea (L.) Thouars ex DC.)  obtained from National Centre for Genetic Resources and Biotechnology (NACGRAB), Ibadan, Oyo state, were assessed for their genetic and phylogenetic relatedness through electrophoretic analysis of the seed proteins. 0.2g of the seeds were weighed and macerated with mortar and pestle in 0.2M phosphate buffer containing 0.133M of acid (NaH2PO4) and 0.067 of base (Na2HPO4) at pH 6.5. Protein characterization with standard marker revealed that the seeds of the nine accessions contained proteins (B.S.A, Oval Albumin, Pepsinogen, Trypsinogen and Lysozyme) with molecular weights ranging from 66kda and above, 45 – 65 kDa, 44 – 33 kda, 32-24 kDa and 23-14 kDa, respectively. The student T-test revealed that accessions B, C, E, F, H and I have molecular weights not significantly different from one another (P<0.05) while samples A, D and G showed significantly different values (P>0.05). All the accessions had at least two proteins and two major bands in common. The study revealed intra-specific similarities and genetic diversity in protein contents among the nine accessions of Bambara groundnut (Vigna subterraranea (L.) Verdc.syn

Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 995-999 ◽  
Author(s):  
H I Amadou ◽  
P J Bebeli ◽  
P J Kaltsikes
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Bambara Groundnut ◽  
International Institute ◽  
Tropical Agriculture ◽  
Vigna Subterranea ◽  
Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

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