scholarly journals Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1019 ◽  
Author(s):  
Zhong ◽  
Yang ◽  
Li ◽  
Zhang ◽  
Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
South China ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Jiangxi Province ◽  
Group Method ◽  
Cinnamomum Camphora ◽  
Wild Populations ◽  
Arithmetic Means

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 731-737 ◽  
Author(s):  
N A Barkley ◽  
M L Newman ◽  
M L Wang ◽  
M W Hotchkiss ◽  
G A Pederson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Expressed Sequence Tag ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Expressed Sequence ◽  
Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

scholarly journals Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Haftom Brhane ◽  
Teklehaimanot Haileselassie ◽  
Kassahun Tesfaye ◽  
Cecilia Hammenhag ◽  
Rodomiro Ortiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Finger Millet ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Geographic Regions ◽  
Landrace Accessions ◽  
Expressed Sequence ◽  
Simple Sequence

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers.Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species

2016 ◽  
Vol 154 (7) ◽  
pp. 1254-1269 ◽  
Author(s):  
A. SINGH ◽  
H. K. DIKSHIT ◽  
D. SINGH ◽  
N. JAIN ◽  
M. ASKI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Wild Species ◽  
Expressed Sequence Tag ◽  
Group Method ◽  
Comparative Genomic ◽  
Pair Group ◽  
Ssr Loci ◽  
Related Wild Species ◽  
Expressed Sequence

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to analyse genetic diversity among three Lens species. The SSR loci amplified successfully in wild species, with 94·82% transferability in Lens culinaris subsp. orientalis, 95·4% in Lens nigricans, 98·81% in L. culinaris subsp. odemensis, 94·82% in L. culinaris subsp. tomentosus and 96·55% in Lens ervoides. Ninety-nine alleles (average 3·41 alleles/locus) were detected by 29 SSR markers. Based on the unweighted pair group method with arithmetic mean cluster analysis, all the genotypes were grouped into three clusters at a similarity level of 0·30. The diversity analysis indicated no species-specific clustering of the wild and cultivated species. Wild species L. nigricans and L. culinaris subsp. odemensis, L. culinaris subsp. orientalis and L. ervoides were grouped in Cluster I, whereas the Mediterranean land races of L. culinaris subsp. culinaris and L. culinaris subsp. tomentosus formed a separate group in Cluster II A. Cluster II B comprised L. ervoides, L. culinaris subsp. orientalis and L. culinaris subsp. culinaris. Clusters II C, II D and II F included cultivated Indian lentil genotypes. Cluster II E comprised Indian and Mediterranean germplasm lines. Cluster II F included three early maturing germplasm lines, whereas Cluster III included only two germplasm lines. The functional annotation of SSR-containing unigenes revealed that a majority of genes were involved in an important transport-related function or were a component of metabolic pathways. A high level of polymorphism of EST-SSRs and their transferability to related wild species indicated that these markers could be used for molecular screening, map construction, comparative genomic studies and marker-assisted selection.

scholarly journals Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (6) ◽  
pp. 797-800
Author(s):  
Xiaoli Wang ◽  
Zhiyong Wang ◽  
Li Liao ◽  
Xinyi Zhang ◽  
Changjun Bai
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Warm Season ◽  
Group Method ◽  
Sequence Repeat ◽  
Marker Assisted Breeding ◽  
Arithmetic Means ◽  
Pair Group ◽  
Simple Sequence

Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

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 Genetic diversity within local and introduced cultivars of wheat (Triticum aestivum L.) grown under Mediterranean environment as revealed by AFLP markers

2019 ◽  
Vol 63 (1) ◽  
pp. 25-30
Author(s):  
Mohammed Imad Eddin Arabi ◽  
Amina Shoaib ◽  
Eyad Al-Shehadah ◽  
Mohammed Jawhar
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Aflp Markers ◽  
Group Method ◽  
Wheat Cultivars ◽  
Arithmetic Means

Information on genetic diversity among cultivars is critical in wheat improvement. In this work, heterogeneity within local and introduced cultivars of bread wheat grown in Syria was investigated using amplified fragment length polymorphism (AFLP) markers. The eight primer pairs were used to detect 177 polymorphic bands among the 21 cultivars resulting in an average of 22.13 (57.3%) polymorphic loci per primer pair. Major allelic frequency ranged from 0.50 to 0.75 with a mean 0.64, and estimated gene diversity was 0.45. Values of average polymorphic information content (PIC) for these markers were estimated to be 0.34. This low value might be attributed to the rigorous selection pressure aimed at cultivar purity and associated breeding practices. Dissimilarity values ranged from 0.32 to 0.66 with an average of 0.54, indicating that such techniques sample distinct genome regions. Three major subgroups of wheat cultivars were identified using the unweighted pair-group method with arithmetic means analysis (UPGMA), with all local cultivars falling into one cluster, which was confirmed by a principal component analysis (PCA). The narrow genetic diversity observed among Syrian wheat cultivars suggests the need of broadening the genetic base of wheat breeding materials, including local landraces.

scholarly journals Impact of Plant Breeding on the Genetic Diversity of Cultivated Strawberry as Revealed by Expressed Sequence Tag-derived Simple Sequence Repeat Markers

2009 ◽  
Vol 134 (3) ◽  
pp. 337-347 ◽  
Author(s):  
David Jesús Gil-Ariza ◽  
Iraida Amaya ◽  
José Manuel López-Aranda ◽  
José Federico Sánchez-Sevilla ◽  
Miguel Ángel Botella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Natural Populations ◽  
Group Method ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Strawberry Cultivars

Unlike other important crops analyzed so far for genetic diversity and population structure, the brief history and particularities of the genetics of the cultivated strawberry (Fragaria ×ananassa Duchesne) have limited its genetic characterization. The genomic composition and the pattern of inheritance have not been fully elucidated, although a number of studies have suggested a highly diploidized genome. In this study, the similarity relationships and structure of 92 selected strawberry cultivars with widely diverse origins have been established using simple sequence repeat (SSR) markers derived from expressed sequence tags (EST-SSR markers). Genetic analysis performed by the unweighted pair group method with arithmetic mean clustering revealed a distribution according to both date of cultivar release and breeding for a specific climatic adaptation. Additionally, a model-based clustering approach identified three populations among the strawberry cultivars with an overall FST value of 0.15 to 0.16. Both analyses support a limited differentiation of modern cultivars, most probably as a consequence of the methodology of strawberry breeding. Interestingly, the collection of strawberry cultivars here analyzed showed comparable genetic differentiation to that observed in natural populations of Fragaria chiloensis (L.) Mill., one of its wild ancestors. Our results suggest that breeding has produced a small but significant reduction on the genetic diversity of F. ×ananassa. The panel of 10 EST-SSRs described in this work provided an extremely low probability of confusion (less than 10−11), offering an efficient and accurate method for cultivar identification.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2019 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Genetic Structure ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Group Method ◽  
Arithmetic Means ◽  
Illumina Hiseq ◽  
Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species. Keywords: Conservation, EST-SSRs; Transcriptome; Panax vietnamensis ; Population genetics

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