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

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.

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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 ◽

10.1186/s12863-020-00955-y ◽

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.

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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

10.21203/rs.3.rs-37023/v2 ◽

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.

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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

10.1101/2020.01.30.926626 ◽

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.

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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

10.22541/au.162683878.89695015/v1 ◽

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.

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Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.20.0189 ◽

2020 ◽

Vol 33 (11) ◽

pp. 1732-1740

Author(s):

Muhammad Abdur Rashid ◽

Prabuddha Manjula ◽

Shakila Faruque ◽

A. K. Fazlul Haque Bhuiyan ◽

Dongwon Seo ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Population Variation ◽

Fixation Index ◽

Indigenous Chicken ◽

Diversity Measures ◽

Red Jungle Fowl

Objective: The objectives of this study were to investigate the genetic diversity, population structure and relatedness among the five chicken populations of Bangladesh using microsatellite markers.Methods: A total of 161 individuals representing 5 chicken populations (non-descript Deshi [ND], naked neck [NN], hilly [HI], Aseel [AS], and red jungle fowl [JF]) were included in this study to investigate genetic diversity measures, population structure, genetic distance and phylogenetic relationships. Genotyping was performed using 16 selected polymorphic microsatellite markers distributed across 10 chromosomes.Results: The average observed and expected heterozygosity, mean number of alleles and polymorphic information content were found to be 0.67±0.01, 0.70±0.01, 10.7 and 0.748, respectively in the studied populations. The estimated overall fixation index across the loci (F), heterozygote deficiency within (FIS) and among (FIT) chicken populations were 0.04±0.02, 0.05 and 0.16, respectively. Analysis of molecular variance analysis revealed 88.07% of the total genetic diversity was accounted for within population variation and the rest 11.93% was incurred with population differentiation (FST). The highest pairwise genetic distance (0.154) was found between ND and AS while the lowest distance was between JF and AS (0.084). Structure analysis depicted that the studied samples can be categorized into four distinct types or varieties (ΔK = 3.74) such as ND, NN, and HI where AS and JF clustered together as an admixed population. The Neighbor-Joining phylogenetic tree and discriminant analysis of principal component also showed close relatedness among three chicken varieties namely AS, HI, and JF.Conclusion: The results reflected that indigenous chicken of Bangladesh still possess rich genetic diversity but weak differentiation among the studied populations. This finding provides some important insight on genetic diversity measures that could support the designing and implementing of future breeding plans for indigenous chickens of Bangladesh.

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Genetic variability and population structure of Saudi Arabia bread wheat (Triticum aestivum L.) by microsatellite markers

Genetika ◽

10.2298/gensr2003943a ◽

2020 ◽

Vol 52 (3) ◽

pp. 943-956

Author(s):

Ibrahem Almohisen

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Saudi Arabia ◽

Population Structure ◽

Genetic Variability ◽

Microsatellite Markers ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Fixation Index ◽

Wheat Landraces

Almohisen A. Ibrahem (2020). Genetic variability and population structure of Saudi Arabia bread wheat (Triticum aestivum L.) by microsatellite markers- Genetika, Vol 52, No.3, 943-956. Wheat (Triticum aestivum L.) is an important cereal crop. Analysis of genetic diversity and population structure in local landraces would improve the wheat breeding program by more efficient use of genetic materials and management of genetic variation. To address this challenge, a set of thirteen Saudi Arabia wheat landraces was used to assess population structure and genetic diversity. Thirteen landraces were genotyped using eighteen microsatellite markers which revealed a clear polymorphism among these genotypes. In total, 136 alleles from a set of eighteen simple sequence repeats (SSRs) loci on a panel of thirteen wheat landraces were detected. All SSRs loci showed a wide range of allele numbers extended from 3 to 11 alleles with an average of 7.5. Genetic diversity, polymorphism information content and minor allele frequency ranged from 0.26 to 0.50, 0.23 to 0.37 and 0.15 to 0.46 with an average 0.43, 0.33 and 0.34, respectively. The results of principal coordinate analysis (PCoA) agreed with the structure analysis. Structure grouped the thirteen landraces into three clear subpopulations. The fixation index (Fst), a measure of population substructure, was 0.217, 0.432 and 0.541 for G2, G1, and G3, respectively. Furthermore, analysis of molecular variance recognized 35% variance among and 65% within populations. The present study showed a high genetic diversity between landraces which can be exploited to produce new bread wheat cultivars.

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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First Records on Genetic Diversity and Population Structure of Algerian Peanut (Arachis hypogaea) Using Microsatellite Markers

Plant Molecular Biology Reporter ◽

10.1007/s11105-021-01305-7 ◽

2021 ◽

Author(s):

Hanène Djeghim ◽

Ines Bellil ◽

Rima Hind Boudchicha ◽

Ali Boumegoura ◽

Douadi Khelifi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Arachis Hypogaea

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Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00168-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Workia Ahmed ◽

Tileye Feyissa ◽

Kassahun Tesfaye ◽

Sumaira Farrakh

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Information Content ◽

Date Palm ◽

Polymorphic Information Content ◽

Phoenix Dactylifera ◽

Mean Value ◽

Date Palms ◽

Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

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