Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Rajinder Singh ◽  
Noorhariza Zaki ◽  
Ngoot-Chin Ting ◽  
Rozana Rosli ◽  
Soon-Guan Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Polymorphic Information Content ◽  
Strong Association ◽  
Geographic Location ◽  
Group Method ◽  
Pair Group ◽  
High Level ◽  
Nucleotide Repeats

AbstractA total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

scholarly journals Estimation of Genetic Diversity in Genus Mentha Collected From Azad Jammu And Kashmir, Pakistan

2019 ◽  
Author(s):  
Fozia Abasi ◽  
Israr Ahmad ◽  
Sami Ullah khan ◽  
Khawaja Shafique Ahmad ◽  
Aneela Ulfat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Means ◽  
Jammu And Kashmir ◽  
Pair Group ◽  
High Level

ABSTRACTMints are perennial aromatic herbs used both for medicinal and aromatic purposes. Flora of Pakistan has reported six species of genus Mentha. Taxonomy of genus Mentha is more complex and confusing due to inter specific hybridization. The present research is the first documented report from Pakistan for the purpose to dissect Mentha specimens using molecular tools. A total of 17 SCoT and SSR markers used to dissect genetic diversity among 41 Mentha specimens. The results revealed substantial variation among Mentha specimens. The molecular data analyzed through NTSYS and Power marker software’s. Dendrogram constructed on the base of similarity coefficients generated using weighted pair group method of arithmetic means (UPGMA) recorded high level of polymorphism. Polymorphic Information Content (PIC) for molecular markers recorded in the range of 5-8. Mean genetic distance (GD) was estimated in the range from 0.35% to 100%. The minimum and maximum GD recorded in one combination each as P2-P4 and M41-P10. The present study was explored the efficiency of SCoT and SSR markers for evaluating the genetic diversity of medicinal plants. The present research was concluded that both morphological and molecular dendrogram determined considerable level of diversity among Mentha species. Furthermore, specific primers and DNA chloroplast technology could be needed for further molecular analysis to refine the data more up to varietal level.

scholarly journals Molecular characterization of mulberry genotypes and species in Turkey

2020 ◽  
Vol 48 (2) ◽  
pp. 549-557 ◽  
Author(s):  
Emine ORHAN ◽  
Meleksen AKIN ◽  
Sadiye P. EYDURAN ◽  
Sezai ERCISLI
Keyword(s):  
Ssr Markers ◽  
Phenotypic Diversity ◽  
Polymorphic Information Content ◽  
Morus Alba ◽  
Group Method ◽  
Pair Group ◽  
Morus Nigra ◽  
Similarity Ratio ◽  
White Mulberry ◽  
High Level

Mulberries are one of the most important traditional fruit in Turkey and either consumed fresh or processed into several traditional products. Mulberry trees (genotypes) belong to Morus alba L., Morus nigra L., and Morus rubra L. shows high phenotypic diversity. In this study, 26 genotypes of Morus nigra, 21 genotypes of Morus rubra and 26 genotypes and landraces of Morus alba sampled from different parts of eastern Anatolia region in Turkey were fingerprinted using 16 simple sequence repeat (SSR) markers. Among SSR markers, the number of alleles per locus ranged from 2 (SS01, SS05) to 11 (MulSTR3) with an average of 5.19. A total of 83 alleles were obtained for the 16 SSR markers. The polymorphic information content ranged from 0.43 to 0.84 with an average of 0.61 per locus. In this study, MulSTR3, MulSTR5, MulSTR6, SS04 and SS20 were found to be the most useful SSR markers to detect genetic differences between mulberry species, genotypes and landraces. Genetic similarity ratio ranged from 0.24 to 0.94 with a mean similarity value of 0.41 indicating a high level of polymorphism among the mulberry species, genotypes and landraces. Clustering based on Jaccard's similarity coefficient and an unweighted pair group method with arithmetic mean (UPGMA) revealed 3 main clusters that corresponded with species. The results of the present study indicate that white mulberry landraces and genotypes were more diverse than the red and black mulberry genotypes. Therefore, white mulberry genotypes can be a good source for the mulberry-breeding programme due to its better genetic diversity as well as its high economical and yield properties.

Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

2015 ◽  
Vol 14 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Ndenum S. Shitta ◽  
Michael T. Abberton ◽  
Adenubi I. Adesoye ◽  
Daniel B. Adewale ◽  
Olaniyi Oyatomi
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Arithmetic Average ◽  
African Yam Bean ◽  
Pair Group ◽  
Ssr Primers ◽  
Nutritional Qualities ◽  
High Level ◽  
Average Cluster

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

scholarly journals Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1748
Author(s):  
Brenda I. Guerrero ◽  
M. Engracia Guerra ◽  
Sara Herrera ◽  
Patricia Irisarri ◽  
Ana Pina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Group Method ◽  
Japanese Plum ◽  
Pair Group ◽  
Prunus Salicina ◽  
Wide Range ◽  
High Level ◽  
Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

scholarly journals Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

2019 ◽  
Author(s):  
Jacob Popoola ◽  
James Agbolade ◽  
Abiodun Ajiboye ◽  
Omotolani Akinola ◽  
Francis Lewu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sub Saharan Africa ◽  
Group Method ◽  
Parkia Biglobosa ◽  
Arithmetic Average ◽  
Ecological Zones ◽  
Pair Group

African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

scholarly journals ANALISIS DIVERSITAS GENETIK AKSESI KELAPA SAWIT KAMERUN BERDASARKAN MARKA SSR

2020 ◽  
Vol 19 (4) ◽  
pp. 194 ◽  
Author(s):  
I MADE TASMA ◽  
SEKAR ARUMSARI
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Information Content ◽  
Ssr Markers ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Group Method ◽  
Pair Group ◽  
Elaeis Guineensis Jacq ◽  
Analysis System

<p>ABSTRAK<br />Diversitas genetik aksesi kelapa sawit Indonesia saat ini sangat<br />rendah. Dalam usaha meningkatkan keragaman genetik telah dilakukan<br />eksplorasi plasma nutfah di pusat keragaman genetik kelapa sawit di<br />Kamerun. Tujuan dari penelitian ini untuk mengetahui diversitas genetik<br />dan tingkat polimorfisme berdasarkan marka SSR aksesi-aksesi kelapa<br />sawit Kamerun. Bahan tanaman yang digunakan 49 aksesi kelapa sawit<br />Kamerun, Afrika yang ditanam di Kebun Sumber Daya Genetik (SDG)<br />Sawit Sijunjung, Sumatera Barat. DNA genomik diisolasi dari tiap<br />individu aksesi menggunakan protokol isolasi DNA untuk tanaman<br />bergetah. DNA dianalisis menggunakan 20 marka SSR. Dendrogram<br />kekerabatan dikonstruksi menggunakan metode Unweighted Pair Group<br />Method Arithmetic (UPGMA) melalui software NTSYS-pc (Numerical<br />Taxonomy and Multivariate Analysis System) versi 2.1-pc. Hasil penelitian<br />menunjukkan nilai polimorfisme information content (PIC) marka SSR<br />tinggi sebesar 0,80 (berkisar 0,63-0,91). Jumlah alel yang terdeteksi per<br />marka SSR berkisar antara 4-15 alel per lokus SSR (rata-rata 8,75).<br />Analisis filogenetik 49 aksesi menghasilkan diversitas genetik 12,5-<br />54,72% (kemiripan genetik 55,28-87,50%). Pada diversitas genetik<br />54,72%, aksesi Kamerun terbagi menjadi tujuh kelompok masing-masing<br />terdiri dari 9, 28, 4, 2, 1, 2, dan 3 aksesi. Aksesi dengan diversitas genetik<br />tinggi dan berada pada klaster berbeda, potensial digunakan sebagai calon<br />tetua dalam program pemuliaan kelapa sawit.<br />Kata kunci: Elaeis guineensis Jacq., diversitas genetik, plasma nutfah,<br />marka SSR</p><p>ABSTRACT<br />Genetic diversity of the Indonesian oil palm collection is very low.<br />To improve their genetic variability, exploration from the oil palm center<br />of origins has been done in Kamerun. The objectives of this study were to<br />determine genetic and polymorphism level of the SSR markers Cameroon-<br />originated oil palm accessions. Genetic materials used were 49 Cameroon-<br />originated oil palm accessions collected at Sijunjung Oil Palm Germplam<br />Collection Station, West Sumatera. Genomic DNA was isolated using a<br />protocol for isolating DNA from leaves rich with latex. DNA was analyzed<br />using 20 SSR markers. A dendogram was constructed using the<br />Unweighted Pair Group Method Arithmetic (UPGMA) method through the<br />Numerical Taxonomy and Multivariate Analysis System software<br />(NTSYS-pc) version 2.1-pc. Results showed that the polimorfisme<br />information content (PIC) values of the SSR markers used was high, 0.80<br />(range from 0.63-0.91). The average number of the SSR alleles detected<br />was also high, 8.75 alleles (range from 4-15 alleles per SSR locus).<br />Phylogenetic analysis of the 49 oil palm accessions resulted genetic<br />diversity of 12.5-54.72% (genetic similarity of 55.28-87.50%). At genetic<br />diversity 54.72%, the 49 accessions were divided into seven clusters, each<br />consisted of 9, 28, 4, 2, 1, 2, and 3 accesions, respectively. Accessions<br />with high genetic diversity and located at different clusters may be useful<br />as parent candidates in the future oil palm breeding programs.<br />Key words: Elaeis guineensis Jacq., genetic diversity, germplasm, SSR<br />markers</p>

scholarly journals Optimal use of SSR markers for varietal identification of upland cotton

2015 ◽  
Vol 50 (7) ◽  
pp. 571-581 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Ana Luíza Ramos Cazé ◽  
Michelle Garcia da Silva ◽  
Vanessa Cavalcante Almeida ◽  
Fernanda Oliveira da Cunha Magalhães ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Discrimination Power ◽  
Arithmetic Average ◽  
Pair Group ◽  
Varietal Identification ◽  
The World ◽  
The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

scholarly journals SSR Markers Reveal the Genetic Diversity of Asian Cercis Taxa at the U.S. National Arboretum

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 498-502 ◽  
Author(s):  
Chandra S. Thammina ◽  
David L. Kidwell-Slak ◽  
Stefan Lura ◽  
Margaret R. Pooler
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
The United States ◽  
Group Method ◽  
Cercis Canadensis ◽  
Landscape Plant ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Eastern Redbud ◽  
The U.S

The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than 20 cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily Cercis chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has a diverse collection of Cercis germplasm collected in North America and Asia. Fourteen genomic simple sequence repeat (genomic-SSR) markers were used to analyze the genetic diversity of 53 accessions of Asian Cercis taxa from our collection, including C. chinensis, Cercis chingii Chun, Cercis gigantea ined., Cercis glabra Pamp., Cercis racemosa Oliv., and Cercis yunnanensis Hu and W. C. Cheng. SSR markers detected an average of 5.7 alleles per locus with a range of two to nine alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient. Four major clusters were identified. Accessions tended to group by taxa or provenance, but with some notable exceptions caused either by misidentification or nomenclatural confusion in the species. This information will be used for collection management and for making decisions in the breeding program to maximize genetic diversity of cultivated Cercis.

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