scholarly journals Comparative transcriptomes and genetic diversity assessment of two Sichuan peppers (Zanthoxylum bungeanum and Zanthoxylum armatum)

2019 ◽  
Author(s):  
Yangchuan Deng ◽  
Li Xiang ◽  
Wei Gong ◽  
Tingyu Ma ◽  
Li Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Distances ◽  
Transcriptome Data ◽  
Zanthoxylum Armatum ◽  
Diversity Assessment ◽  
Two Samples ◽  
Ssr Primers ◽  
Medicinal Properties ◽  
Zanthoxylum Bungeanum

Abstract Background: Species of Zanthoxylum (Sichuan pepper) are diverse and valuable economic trees that have been cultivated across Asia for thousands of years for their aromatic and medicinal properties. The current lack of transcriptome and EST-SSR data for these species represents a constraint with regards to identifying increasingly more diverse cultivars in China. This study was conducted to compare the transcriptome profiles of two Zanthoxylum species (Z. bungeanum and Z. armatum) and develop the EST-SSR markers to assess the genetic diversity in Sichuan pepper. Results: A total of 36.76 G high-quality clean data were screened for subsequent analysis. For Z. bungeanum and Z. armatum, 64,944 and 75,669 unigenes were obtained, respectively. After comparing different databases, we found that the highest number of unigenes (43,3198 and 49,638 for Z. bungeanum and Z. armatum, respectively) were annotated using the NR database. In addition, six pairs of EST-SSR markers were selected to determine the genetic diversity of 125 samples of three Zanthoxylum species. A population clustering dendrogram indicated that there was an average of four samples per population, with the number of allelic genes (Na) ranging from 1 to 1.4510 (average of 1.1462). The number of effective allelic genes (Ne) ranged from 1 to 1.2744 (average of 1.0971), whereas genetic diversity (Nei) ranged from 0 to 0.1486 (average of 0.05512) and Shannon genetic diversity (I) ranged from 0 to 0.2177 (average 0.08123). In individual clustering dendrograms, the 125 samples were divided into five cohorts. Cohort I contained Z. bungeanum and its varieties, cohort II included Z. armatum and its varieties, cohort III contained mostly Z. piperitum and two other Z. bungeanum samples, and cohorts IV and V each contained only two samples, with genetic distances of 0 to 1.14 between them. Conclusion: In this study, we analyzed the comparative transcriptome data of two Zanthoxylum species, for which we assessed genetic diversity using EST-SSR primers derived from their EST information. The genetic diversity of 125 samples obtained from the three Zanthoxylum species Z. bungeanum, Z. armatum and Z. piperitum was relatively low, which can probably be attributed to apomixis.

scholarly journals Genetic Diversity and Relationships of Terebinth (Pistacia terebinthus L.) Genotypes Growing Wild in Turkey

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 671
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
Sezai Ercisli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
In Silico ◽  
Germplasm Collection ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Average ◽  
Principal Coordinates ◽  
Two Samples ◽  
Pistacia Terebinthus

Genetic diversity and relationships of 54 wild-grown terebinths (Pistacia terebinthus L.) were determined using 40 SSR (simple sequence repeat) markers (38 in silico polymorphic SSR markers and 2 SSR markers). In silico polymorphic SSR analysis, 430 alleles were identified. The number of alleles per locus ranged from 3 to 25 with a mean value of 11 alleles per locus. The values of polymorphism information content (PIC) ranged from 0.34 (CUPOhBa4344) to 0.91 (CUPSiBa4072) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), the Structure, and Principal Coordinates (PCoA) based clustering. The structure analysis and UPGMA clustering of the genotypes depicted two major clusters. PCoA results supported cluster analysis results. The dendrogram revealed two major clusters. Forty-two samples were obtained from the Kazankaya canyon and 12 samples from the Karanlıkdere region. The two regions are 130 km apart from each other but in a dendrogram, we did not find geographical isolation. The results proved the efficiency of SSRs for genetic diversity analysis in the terebinth. Based on the results, SSRs can be applied as a trustworthy tool for the evaluation of genetic diversity in terebinth genotypes. Molecular analysis on the terebinth genotypes in this study will promote the germplasm collection and the selection of the populations in future studies on terebinths for genetic mapping, genetic diversity, germplasm characterization, and rootstock breeding.

scholarly journals Genetic Diversity in Finger Millet Landraces revealed by RAPD and SSR Markers

2020 ◽  
Vol 8 (1) ◽  
pp. 1-11
Author(s):  
Bal Krishna Joshi ◽  
Darbin Joshi ◽  
Surya Kanta Ghimire
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Finger Millet ◽  
Rapd Marker ◽  
Principal Component ◽  
Genetic Potential ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Nei's Genetic Distance

Genetic diversity assessment is the preliminary work for development of variety and conservation of diversity. Finger millet is a very important crop in Nepal however, its genetic potential has not been fully utilized. Genetic diversity was assessed in forty landraces of finger millet using 9 RAPD and 5 SSR markers. These landraces were collected from Kaski and Dhading districts. None of single primers of these RAPD and SSR could separate all 40 landraces. The average number of bands were 6.33 and 7.8 per RAPD and SSR primers respectively. Mean polymorphism information content was of 0.314 for RAPD and 0.37 for SSR. Primer OPA-4 produced the highest number of bands and the lowest numbers of bands were produced by OPA-16. Among the SSR primers, SSR-06 produced the highest number of polymorphic bands and UGEP-53 produced the lowest bands. RAPD based dendrogram has generated four clusters and SSR based dendrogram has generated two clusters. In both dendrogram and principal component analyses, Purbeli landrace was found unique locating separately in the cluster and scatter plot. Nei's genetic distance produced by RAPD and SSR primers was similar that is 0.327 by RAPD and 0.296 by SSR markers. Genetic distance produced by SSR markers was higher than distance produced by RAPD marker. These landraces were from two districts and therefore have shown intermediate diversity. These molecular marker-based findings should would be more useful if we could link with agromorphological traits. Inclusion of large number of landraces collected from different areas are required to get higher level diversity in addition to associate genetic diversity with geographical sites. Groupings of these landraces could be useful for selecting landraces in breeding program as well as planning conservation program.

scholarly journals Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Raphael Adu-Gyamfi ◽  
Ruth Prempeh ◽  
Issahaku Zakaria
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Analysis Of Variance ◽  
Morphological Data ◽  
Northern Ghana ◽  
Land Races ◽  
Diversity Assessment ◽  
Parental Lines ◽  
Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

scholarly journals SSR DNA marker aided genetic diversity assessment of selected willow clones

Genetika ◽  
2013 ◽  
Vol 45 (2) ◽  
pp. 527-536 ◽  
Author(s):  
N.B. Singh ◽  
S. Joshi ◽  
P. Choudhary ◽  
J.P. Sharma
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Dna Marker ◽  
Similarity Coefficient ◽  
Gene Pools ◽  
Morphometric Traits ◽  
Genetic Base ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Clustering Pattern

Around 100 clones of tree willows were subjected for nursery screening twice on morphometric traits. Genetic diversity was assessed in twenty-five genetically superior willow clones hailing from six countries using 16 SSR primers. Fourteen primers amplified the DNA but only ten showed polymorphism. Total 34 bands were scored, out of that 27 were found to be polymorphic and 7 were monomorphic. Three primers showed 100% polymorphism whereas 79.4% polymorphism was recorded in total. The dendrogram obtained from SSR markers revealed that clone SE-69-002 (S. matsudana) and NZ-1040 (S. matsudana X S. alba) as most similar clones (Jaccards coefficient of 0.97), and clone PN-721(S. matsudana X S. alba) and PN-731 (S. nigra), as most divergent clones (Jaccards coefficient of 0.63). All the genotypes were grouped into 4 distinct clusters. On the basis of similarity coefficient analysis the first cluster comprised of 11 genotypes, the second cluster have 8 genotypes where as third one has only one genotype and fourth cluster retained five genotypes. The clustering pattern further indicated that the geographic distribution may not be the reflection of genetic diversity in willow clones. Genotypes with high molecular diversity could be used in breeding programme in order to obtain heterotic hybrids and development of gene pools with broad genetic base. The genotype specific bands developed by the SSR primers could also be used for identification of cultivar.

scholarly journals Divergência genética entre acessos de mentrasto do Estado do Tocantins através de marcadores RAPD

2013 ◽  
Vol 4 (4) ◽  
pp. 290-298
Author(s):  
Elainy Martins Oliveira ◽  
Waldesse Oliveira Junior ◽  
Jaqueline Oliveira ◽  
Henrique Guilhon De Castro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Geographic Location ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Ageratum Conyzoides ◽  
Genetic Studies ◽  
Low Degree ◽  
Medicinal Properties ◽  
Degree Of Association

Ageratum conyzoides (Asteraceae) is known in Brazil for its medicinal properties being mainly used as painkiller and anti-inflammatory. Due to the existence of few genetic studies for this species, this work aimed to characterize the genetic diversity among nine accessions from different sites at Tocantins state, to provide information about its genetic resources. Similarity coefficients obtained varied from 48% to 80%, result of amplification of 102 fragments, of which 72 (70.5%) were polymorphic. Groupment analysis allowed the differentiation in three groups. One of them was distinguished because it presented the highest similarity among all, being composed by ANA and NAT (80% similarity). In general, these data showed there is low degree of association between the geographic location of the accessions and the genetic distances. So, the collected accession ns in Tocantins state presented considerable genetic variability and the efficiency of RAPD markers for such characterization was here proven.

scholarly journals Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers

2008 ◽  
Vol 51 (1) ◽  
pp. 183-192 ◽  
Author(s):  
Silvia Graciele Hülse de Souza ◽  
Valéria Carpentieri-Pípolo ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Paulo Maurício Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Zea Mays L ◽  
Inbred Lines ◽  
Pedigree Data ◽  
Dice Coefficient ◽  
Quantitative Characters ◽  
Maize Inbred Lines ◽  
Ssr Primers ◽  
Selection Of

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

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 Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yuejin Zhang ◽  
Yuanyuan Chen ◽  
Ruihong Wang ◽  
Ailin Zeng ◽  
Michael K. Deyholos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Information Index ◽  
Polyporus Umbellatus ◽  
Ssr Primers ◽  
Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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