Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers

Abstract Background Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. Results Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. Conclusion Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.

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Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00157-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ghazal Ghobadi ◽

Alireza Etminan ◽

Ali Mehras Mehrabi ◽

Lia Shooshtari

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Wild Relatives ◽

Resolving Power ◽

Start Codon ◽

Aegilops Cylindrica ◽

Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

BMC Genetics ◽

10.1186/1471-2156-13-102 ◽

2012 ◽

Vol 13 (1) ◽

pp. 102 ◽

Cited By ~ 25

Author(s):

Yanxin Zhang ◽

Xiurong Zhang ◽

Zhuo Che ◽

Linhai Wang ◽

Wenliang Wei ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Core Collection ◽

Mini Core Collection ◽

Diversity Assessment

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Genetic diversity of Salvia tomentosa Miller (Lamiaceae) species using Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) molecular markers

Acta Biologica Szegediensis ◽

10.14232/abs.2019.2.135-141 ◽

2020 ◽

Vol 63 (2) ◽

pp. 135-141

Author(s):

Basel Saleh

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Sea Level ◽

Natural Population ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Natural Populations ◽

Mediterranean Species ◽

Marker Index ◽

Minisatellite Dna

Salvia tomentosa Miller (Lamiaceae) a Mediterranean species has an important role in various pharmacological applications. To reveal genetic relationships among S. tomentosa natural populations, 35 samples were collected from different regions of Syria. Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) markers have been investigated for this goal. Td-DAMD assay produced 158 total bands of which 131 (82.911%) were polymorphic with a mean polymorphic information content (PIC) value of 0.264 and a mean marker index (MI) value of 2.269. Clustering profile based on TdDAMD data showed that samples were grouped into two main clusters; the first cluster included Lattakia samples which split into two subclusters regardless their altitudes over the sea level. Whereas, the second cluster included Tartous and Hama samples. Td-DAMD assay successfully discriminate among the tested 35 samples belonged to the S. tomentosa natural population.

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Assessment of genetic diversity in Indian Barnyard millet (Echinochloa spp. complex) using morphological and molecular markers

Journal of Applied and Natural Science ◽

10.31018/jans.v8i3.1016 ◽

2016 ◽

Vol 8 (3) ◽

pp. 1643-1648 ◽

Cited By ~ 1

Author(s):

M. P. Moharil ◽

Dipti Gawai ◽

N. Dikshit ◽

M.S. Dudhare ◽

P. V. Jadhav

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Improvement ◽

Molecular Diversity ◽

Genetic Relationships ◽

Barnyard Millet ◽

Clear Cut ◽

Cultivated Species ◽

High Degree

In the present study, morphological and molecular markers (RAPD primers) were used to analyze the genetic diversity and genetic relationships among 21 accessions of Echinochloa spp. complex comprising the wild and cultivated species collected from Melghat and adjoining regions of Vidarbha, Maharashtra. The availability of diverse genetic resources is a prerequisite for genetic improvement of any crop including barnyard millet. A high degree of molecular diversity among the landraces was detected. Among the 21 genotypes, two major groups (A and B) were formed, at 67.28 % similarity, which clearly encompasses 15 accessions of E. frumentacea and 6 accessions of E. colona. Higher similarity was observed in accessions of E. frumentacea. The accessions IC 597322 and IC 597323 also IC 597302 and IC 597304 showed more than 94% similarity among themselves. The classification of genetic diversity has enabled clear-cut grouping of barnyard millet accessions into two morphological races (E. frumentacea and E. colona).

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Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data

Frontiers in Plant Science ◽

10.3389/fpls.2020.600249 ◽

2020 ◽

Vol 11 ◽

Author(s):

Man Liu ◽

Xin Hu ◽

Xu Wang ◽

Jingjing Zhang ◽

Xubing Peng ◽

...

Keyword(s):

Genetic Diversity ◽

Medicinal Plant ◽

Core Collection ◽

Polymorphic Information Content ◽

Sampling Strategy ◽

Market Demand ◽

Conservation Assessment ◽

Information Index ◽

Ssr Loci ◽

Metabolic Data

Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon’s information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.

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Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

BMC Genomics ◽

10.1186/s12864-019-5824-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Paul I. Otyama ◽

Andrew Wilkey ◽

Roshan Kulkarni ◽

Teshale Assefa ◽

Ye Chu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Core Collection ◽

Mini Core Collection ◽

The U.S

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Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Genetics Research ◽

10.1017/s0016672307008695 ◽

2007 ◽

Vol 89 (2) ◽

pp. 93-106 ◽

Cited By ~ 37

Author(s):

NOELLE A. BARKLEY ◽

ROB E. DEAN ◽

ROY N. PITTMAN ◽

MING L. WANG ◽

CORLEY C. HOLBROOK ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Data Set ◽

Mini Core Collection ◽

Genomic Ssr ◽

Cultivated Peanut ◽

The Mean ◽

Wild Accessions ◽

Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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SPAR Markers-Assisted Assessment of Genetic Diversity and Population Structure in Finger Millet (Eleusine Coracana (L.) Gaertn) Mini-Core Collection

Journal of Crop Science and Biotechnology ◽

10.1007/s12892-018-0034-0 ◽

2018 ◽

Vol 21 (5) ◽

pp. 469-481 ◽

Cited By ~ 2

Author(s):

Subramani Pandian ◽

Karuppasamy Marichelvam ◽

Lakkakula Satish ◽

Stanislaus Antony Ceasar ◽

Shunmugiah Karutha Pandian ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Finger Millet ◽

Eleusine Coracana ◽

Mini Core Collection

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Comparison of Genetic Variation of Anthurium (Anthurium andraeanum) Cultivars Using SCoT, CDDP and RAPD Markers

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v28i2.39676 ◽

2018 ◽

Vol 28 (2) ◽

pp. 171-182 ◽

Cited By ~ 2

Author(s):

Abbas Saidi ◽

Zahra Daneshvar ◽

Zohreh Hajibarat

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Molecular Markers ◽

Rapd Markers ◽

Start Codon ◽

Similarity Matrix ◽

Random Amplification ◽

Anthurium Andraeanum ◽

Rapd Polymorphism

To evaluate the genetic diversity among 10 cultivars of anthurium were performed using three molecular markers such as Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP), and Random Amplification of Polymorphic DNA (RAPD). Polymorphism index content (PIC) was calculated 0.39, 0.42 and 0.37 for RAPD, SCoT and CDDP, respectively. This result showed all the three molecular markers had almost an identical potential in estimating genetic diversity. Cluster analysis using SCoT, CDDP and RAPD divided the cultivars to three distinct clusters. The similarity matrix obtained through SCoT and CDDP was positively significantly correlated (r = 0.76, p < 0.01). This is the first report in which the efficiency of two targeted DNA region molecular markers (SCoT and CDDP) together with RAPD technique have been compared with each other in a set of anthurium cultivras. Results suggested that SCOT, CDDP and RAPD fingerprinting techniques are of sufficient ability to detect polymorphism in anthurium cultivars. Plant Tissue Cult. & Biotech. 28(2): 171-182, 2018 (December)

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Genetic analysis of mango landraces from Mexico based on molecular markers

Plant Genetic Resources ◽

10.1017/s147926210932434x ◽

2009 ◽

Vol 7 (03) ◽

pp. 244-251 ◽

Cited By ~ 9

Author(s):

Didiana Gálvez-López ◽

Sanjuana Hernández-Delgado ◽

Maurilio González-Paz ◽

Enrique Noe Becerra-Leor ◽

Miguel Salvador-Figueroa ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Geographical Origin ◽

Genetic Recombination ◽

Genetic Relationships ◽

Mangifera Indica ◽

Aflp Analysis ◽

Significant Genetic Differentiation ◽

Simple Sequence

Genetic diversity and relationships among 112 mango (Mangifera indica) plants native to 16 states of Mexico and four controls [three mango cultivars (Ataulfo, Manila and Tommy Atkins) and one accession ofMangifera odorata] were evaluated based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Mango germplasm shows broad dispersion through Mexico and genetically similar germplasm from different agroecological regions has previously been found by our group. Both AFLP and SSR analyses indicated high genetic similarity among mango populations that were clustered in two major groups: mangos from Gulf of Mexico coastline and mangos from Pacific Ocean coastline and locations far away from the sea. The highest genetic diversity was found within plants from each state, and significant genetic differentiation (FST = 0.1921, AFLPs and 0.1911, SSRs) was also observed among mango populations based on geographical origin and genetic status (cultivars versus landraces). Heterozygosity values ranged from low (0.38) to moderate (0.68), and no heterozygote deficits were found. The highest genetic variability was found in mango populations from Tabasco, Michoacán and Oaxaca. Data suggested that mangoes are subjected to natural or induced pollination, so segregation as well as genetic recombination plays major roles on genetic diversification of Mexican mangos. AFLP analysis was more robust than SSR for determining the genetic relationships among mango landraces from Mexico.

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