scholarly journals Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

2020 ◽  
Author(s):  
Mariano Joly Kpaténon ◽  
Valère Kolawolé Salako ◽  
Sylvain Santoni ◽  
Leila Zekraoui ◽  
Muriel Latreille ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Sub Saharan Africa ◽  
Fixation Index ◽  
Second Phase ◽  
Polymorphism Detection ◽  
Palm Species ◽  
Borassus Aethiopum

AbstractIn Sub-Saharan Africa, the fan palm Borassus aethiopum Mart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource.The present work is a first attempt at characterizing the genetic diversity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity in nine B. aethiopum populations.Our results show that genetic diversity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that sampled B. aethiopum populations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Savè (which also has the highest He) and populations from the North.In light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.

scholarly journals Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mariano Joly Kpatènon ◽  
Kolawolé Valère Salako ◽  
Sylvain Santoni ◽  
Leila Zekraoui ◽  
Muriel Latreille ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
De Novo ◽  
Sub Saharan Africa ◽  
Fixation Index ◽  
Second Phase ◽  
Climatic Regions ◽  
Palm Species ◽  
Borassus Aethiopum

Abstract Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy.

scholarly journals Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

2020 ◽  
Author(s):  
Mariano Joly Kpatènon ◽  
Kolawolé Valère Salako ◽  
Sylvain Santoni ◽  
Leila Zekraoui ◽  
Muriel Latreille ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
De Novo ◽  
Sub Saharan Africa ◽  
Fixation Index ◽  
Second Phase ◽  
Climatic Regions ◽  
Palm Species ◽  
Borassus Aethiopum

Abstract Background: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results: During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions: In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy.

scholarly journals Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

2020 ◽  
Author(s):  
Mariano Joly Kpaténon ◽  
Valère Kolawolé Salako ◽  
Sylvain Santoni ◽  
Leila Zekraoui ◽  
Muriel Latreille ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
De Novo ◽  
Fixation Index ◽  
Second Phase ◽  
Climatic Regions ◽  
Polymorphism Detection ◽  
Borassus Aethiopum ◽  
Collection Sites

Abstract Background: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results: During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. We thus generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it in a second phase for the de novo detection of microsatellite loci. Among the primer pairs designed to target these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity. Across the nine collection sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average value of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation, and accordingly the low number of migrants and the positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. While we globally observe a weak correlation between genetic and geographic distances, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the Northern sites than to samples from the other Central sites. Conclusions: In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Development and characterization of microsatellite markers for two subspecies of Handroanthus chrysanthus

Rodriguésia ◽  
2021 ◽  
Vol 72 ◽  
Author(s):  
Augusta Yadira Cueva-Agila ◽  
Carlos Manchego ◽  
Cristian Bastidas ◽  
Manuel Curto
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Genetic Analysis ◽  
Microsatellite Markers ◽  
High Throughput Sequencing ◽  
Biodiversity Loss ◽  
Important Species ◽  
Polymorphic Microsatellites ◽  
Genetic Diversity And Structure

Abstract An understanding of the genetic diversity and structure of plant species is essential in order to comprehend the degree of biodiversity loss and to develop successful restoration programs. Handroanthus is an important genus that presents one of the most valuable timbers of South America. Handroanthus chrysanthus is an important species distributed in Central and South America. Microsatellite markers are not previously developed for this species. Ten microsatellites for Handroanthus chrysanthus developed using high-throughput sequencing are presented here. The usefulness of these microsatellite loci for the genetic analysis of subspecies H. chrysanthus subsp. chrysanthus (distributed in coastal dry forests) and subspecies H. chrysanthus subsp. meridionalis (distributed in premontane moist forests) is analyzed. At least eight polymorphic microsatellites are useful for each subspecies, seven of which can be used in both subspecies.

Potential for domestication of Borassus aethiopum Mart., a wild multipurpose palm species in Sub-Saharan Africa

2019 ◽  
Vol 66 (5) ◽  
pp. 1129-1144
Author(s):  
V. K. Salako ◽  
A. M. Kégbé ◽  
F. J. Chadaré ◽  
K. M. Kafoutchoni ◽  
A. Amagnidé ◽  
...  
Keyword(s):  
Sub Saharan Africa ◽  
Palm Species ◽  
Sub Saharan ◽  
Borassus Aethiopum

scholarly journals Assessment of genetic variation in Bapedi sheep using microsatellite markers

2020 ◽  
Vol 50 (2) ◽  
pp. 318-324
Author(s):  
A. Maqhashu ◽  
N.O. Mapholi ◽  
H.A. O’Neill ◽  
K.A. Nephawe ◽  
F.V. Ramukhithi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
South African ◽  
Agricultural Research ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Fixation Index ◽  
Indigenous Sheep ◽  
Agricultural Research Council

This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep. Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep

scholarly journals De novo developed microsatellite markers in gill parasites of the genus Dactylogyrus (Monogenea): revealing the phylogeographic pattern of population structure in the generalist parasite Dactylogyrus vistulae

2021 ◽  
Author(s):  
Michal Benovics ◽  
Lenka Gettová ◽  
Andrea Simková
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Parasite Species ◽  
De Novo ◽  
High Genetic Diversity ◽  
Genetic Studies ◽  
The North ◽  
Gill Parasites ◽  
Modern Population

Approaches using microsatellite markers are considered the gold standard for modern population-genetic studies. However, though they have found application in research into various platyhelminth taxa, they remained substantially underutilized in the study of monogeneans. In the present study, a newly-developed set of 24 microsatellite markers was used to investigate the genetic diversity of the generalist monogenean species D. vistulae. The analyzed parasite specimens were collected from 13 cyprinoid species from 11 sites in the Apennine and Balkan peninsulas. A total of 159 specimens were genotyped at each of the loci and the number of alleles per locus ranged from 2 to 16, with a mean number of 6.958 alleles per locus. Exceptionally high genetic diversity was observed among D. vistulae individuals in the southern Balkans, suggesting that this region might represent the center of diversification of the genus in Europe, from where Dactylogyrus parasites expanded into the north. The initial clustering analysis divided all investigated specimens into three major clusters; however, the results of the subsequent analyses revealed the existence of various subpopulations, suggesting that the population structure of D. vistulae is associated with the diversification of their cyprinoid hosts. In addition, partition of the parasite population was observed in regions of the sympatric occurrence of two host species, indicating that these hosts may represent a barrier to gene flow, even for generalist parasite species.

scholarly journals Microsatellites for detecting inconsistencies in Capsicum cultivars registration in Brazilian database: more than meets the eye

2019 ◽  
Vol 37 (3) ◽  
pp. 285-293
Author(s):  
Carlos Diego de O Azevedo ◽  
Rosana Rodrigues ◽  
Cláudia P Sudré
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Molecular Analysis ◽  
Microsatellite Loci ◽  
Principal Coordinate Analysis ◽  
Fixation Index ◽  
National Register ◽  
Genetic Purity ◽  
Low Genetic Diversity ◽  
Capsicum Spp

ABSTRACT In Brazil, cultivars are registered by National Register of Cultivars (RNC), which besides enabling commercialization of cultivar propagative material, also guarantees the producers genetic purity and identity of propagules. However, it is possible that the information about registration and commercialization of some cultivars is inaccurate. This study aims to analyze the use of microsatellite markers to detect inconsistencies in data of Capsicum spp. cultivars obtained from the official database (CultivarWeb). Seven cultivars were evaluated, three of them were through genetic identity analysis (Amarela Comprida, De Cayenne and Cayenne Long Slin) and the others were used as standard for the species C. annuum, C. frutescens and C. chinense. Thirty-three microsatellite loci were polymorphic and presented 76 alleles (an average of 2.3 alleles/locus). Fixation Index (F) showed high homozygosis and estimators of genetic diversity (Ho and I) presented low genetic diversity among cultivars. The molecular analysis, represented in a dendrogram and in Principal Coordinate Analysis Chart (PCOA), showed that the investigated cultivars belong to C. annuum, contrary to what is registered in CultivarWeb, which indicates that such cultivars belong to the species C. frutescens. Thus, the authors recommend that the data in the CultivarWeb should be checked and enhanced.

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