Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

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High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily

Plants ◽

10.3390/plants8050116 ◽

2019 ◽

Vol 8 (5) ◽

pp. 116 ◽

Cited By ~ 2

Author(s):

Fiore ◽

Mercati ◽

Spina ◽

Blangiforti ◽

Venora ◽

...

Keyword(s):

Genetic Diversity ◽

Durum Wheat ◽

Extreme Environments ◽

Principal Component ◽

Detailed Knowledge ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Wide Range ◽

Wheat Landraces ◽

Durum Wheat Landraces

During the XX Century, the widespread use of modern wheat cultivars drastically reduced the cultivation of ancient landraces, which nowadays are confined to niche cultivation areas. Several durum wheat landraces adapted to the extreme environments of the Mediterranean region, are still being cultivated in Sicily, Italy. Detailed knowledge of the genetic diversity of this germplasm could lay the basis for their efficient management in breeding programs, for a wide-range range of traits. The aim of the present study was to characterize a collection of durum wheat landraces from Sicily, using single nucleotide polymorphisms (SNP) markers, together with agro-morphological, phenological and quality-related traits. Two modern cv. Simeto, Claudio, and the hexaploid landrace, Cuccitta, were used as outgroups. Cluster analysis and Principal Coordinates Analysis (PCoA) allowed us to identify four main clusters across the analyzed germplasm, among which a cluster included only historical and modern varieties. Likewise, structure analysis was able to distinguish the ancient varieties from the others, grouping the entries in seven cryptic genetic clusters. Furthermore, a Principal Component Analysis (PCA) was able to separate the modern testers from the ancient germplasm. This approach was useful to classify and evaluate Sicilian ancient wheat germplasm, supporting their safeguard and providing a genetic fingerprint that is necessary for avoiding commercial frauds to sustaining the economic profits of farmers resorting to landraces cultivation.

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Molecular techniques in the assessment of genetic relationships between populations of Consolida (Ranunculaceae)

Caryologia ◽

10.36253/caryologia-1235 ◽

2021 ◽

Vol 74 (2) ◽

pp. 149-161

Author(s):

Jing Ma ◽

Wenyan Fan ◽

Shujun Jiang ◽

Xiling Yang ◽

Wenshuai Li ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Morphological Characters ◽

Mantel Test ◽

Molecular Techniques ◽

Group Method ◽

Plant Resources ◽

High Genetic Diversity

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

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Taxonomic revision of Ceropegia sec. Huernia (Asclepiadoideae – Apocynaceae) in Saudi Arabia with four new combinations

10.3897/arphapreprints.e58902 ◽

2020 ◽

Author(s):

Samah Alharbi ◽

Rahmah Al Qthanin

Keyword(s):

Saudi Arabia ◽

Principal Component ◽

Taxonomic Revision ◽

Morphological Characters ◽

New Combinations ◽

Principal Coordinates Analysis ◽

Distribution Maps ◽

Principal Coordinates ◽

Conservation Assessments ◽

Iucn Criteria

This study provides a taxonomic revision for Ceropegia sec. Huernia in the flora of Saudi Arabia. Forty-eight quantitative and qualitative morphological characters were analysed using principal component analysis (PCA), principal coordinates analysis (PCoA) and the unweighted pairs group using mean average (UPGMA) to separate and help delimit taxa. We proposed to reduce the number of names reported in Saudi Arabia from 11 to four species: C. arabica comb. nov.,C. Khalidbinsultanii comb. nov., C. laevis and C. lodarensis. This study also suggested reducing two of Plowes’ new names to a variety level under C. lodarensis (var. foetida comb. nov. and var. rubrosticta comb. nov.). A key to the species, detailed morphological descriptions, illustrations, distribution maps, ecology, etymology and preliminarily conservation assessments following IUCN criteria are provided.

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Molecular and phenotypic diversity among chickpea (Cicer arietinum) genotypes as a function of drought tolerance

Crop and Pasture Science ◽

10.1071/cp17284 ◽

2018 ◽

Vol 69 (2) ◽

pp. 142 ◽

Cited By ~ 4

Author(s):

Supriya Sachdeva ◽

C. Bharadwaj ◽

Vinay Sharma ◽

B. S. Patil ◽

K. R. Soren ◽

...

Keyword(s):

Drought Tolerance ◽

Phenotypic Diversity ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Similarity Coefficients ◽

Principal Coordinates Analysis ◽

Breeding Programs ◽

Average Value ◽

Principal Coordinates

Diversity as a function of drought tolerance may be identified by morphological characters, and molecular tools used to find the most divergent genotypes for breeding programs for drought tolerance in future. The narrow genetic base of chickpea can be circumvented by using diverse lines in breeding programs. Forty chickpea genotypes were studied for their morphological and molecular diversity with an objective of identifying the most diverse drought-tolerant lines. In total, 90 alleles were detected with 3.6 alleles per locus. Polymorphism information content (PIC) values ranged from 0.155 to 0.782 with an average value of 0.4374 per locus. The size of amplified products ranged from 160 bp to 390 bp. Primer TA136 with eight alleles showed the highest PIC value of 0.7825, indicating its ability to differentiate the genotypes at molecular level. DARwin neighbour-joining tree analysis based on dissimilarity estimates was done for the molecular data and sequential agglomerative hierarchical non-overlapping (SAHN) grouping for the morphological data. It could clearly discriminate the tolerance and the sensitivity of genotypes. Two-dimensional principal coordinates analysis (PCoA) plot indicated good diversity for drought tolerance. The genetic similarity coefficients ranged from 0.115 (genotypes BGD72 to ICCV 5308) to 0.828 (genotypes ICCV 10316 to ICCV 92337).

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Taxonomic revision of Ceropegia sect. Huernia (Asclepiadoideae, Apocynaceae) in Saudi Arabia with three new combinations

PhytoKeys ◽

10.3897/phytokeys.174.58867 ◽

2021 ◽

Vol 174 ◽

pp. 47-80

Author(s):

Samah A. Alharbi ◽

Rahmah N. Al-Qthanin

Keyword(s):

Saudi Arabia ◽

Principal Component ◽

Taxonomic Revision ◽

Morphological Characters ◽

New Combinations ◽

Principal Coordinates Analysis ◽

Distribution Maps ◽

Principal Coordinates ◽

Conservation Assessments ◽

Iucn Criteria

This study provides a taxonomic revision for Ceropegia sect. Huernia in the flora of Saudi Arabia. Forty-six quantitative and qualitative morphological characters were analysed using principal component analysis (PCA), principal coordinates analysis (PCoA) and the unweighted pairs group using mean average (UPGMA) to separate and help delimit taxa. We propose to reduce the number of species reported in Saudi Arabia from 11 to four: C. khalidbinsultaniicomb. nov., C. laevis, C. lodarensis and C. macrocarpa. This study also suggested reducing two names to varietal level under C. lodarensis (var. foetidacomb. nov. and var. rubrostictacomb. nov.). A key to the species, detailed morphological descriptions, illustrations, distribution maps, ecology, etymology and preliminary conservation assessments are provided that follow IUCN criteria.

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GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v20n1.2019.p1-8 ◽

2019 ◽

Vol 20 (1) ◽

pp. 1

Author(s):

Riry Prihatini ◽

Tri Budiyanti ◽

Noflindawati Noflindawati

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Accurate Method ◽

Morphological Characters ◽

Morphological Characterization ◽

Fruit Shape ◽

Morphological Data ◽

Group Method ◽

Pair Group

<p class="abstrakinggris">Diverse papaya (<em>Carica</em> sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.</p>

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Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

Plant Genetic Resources ◽

10.1017/s1479262118000096 ◽

2018 ◽

Vol 16 (5) ◽

pp. 469-477 ◽

Cited By ~ 5

Author(s):

Georgios F. Tsanakas ◽

Photini V. Mylona ◽

Katerina Koura ◽

Anthoula Gleridou ◽

Alexios N. Polidoros

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Variability ◽

Morphological Analysis ◽

Phenotypic Variability ◽

Market Price ◽

Genetic Distances ◽

Reaction Products ◽

Principal Coordinates Analysis ◽

Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

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Resolving the Tetrastigma loheri s. l. Species Complex (Vitaceae) in the Philippines: No Evidence for Recognizing More than One Species

Systematic Botany ◽

10.1600/036364421x16312067913327 ◽

2021 ◽

Author(s):

Jasper John A. Obico ◽

Julie F. Barcelona ◽

Vincent Bonhomme ◽

Marie Hale ◽

Pieter B. Pelser

Keyword(s):

Genetic Diversity ◽

Species Complex ◽

Species Recognition ◽

Principal Component ◽

The Philippines ◽

Geometric Morphometric ◽

Putative Species ◽

Principal Coordinates ◽

Multiple Species ◽

Vegetative Characters

Tetrastigma loheri (Vitaceae) is a vine species native to Borneo and the Philippines. Because it is a commonly encountered forest species in the Philippines, T. loheri is potentially suitable for studying patterns of genetic diversity and connectivity among fragmented forestecosystems in various parts of this country. However, previous research suggests that T. loheri is part of a species complex in the Philippines (i.e. the T. loheri s. l. complex) that potentially also contains Philippine plants identified as T. diepenhorstii, T. philippinense, T. stenophyllum, andT. trifoliolatum. This uncertainty about its taxonomic delimitation can make it challenging to draw conclusions that are relevant to conservation from genetic studies using this species. Here, we tested the hypothesis that T. loheri s. l. is composed of more than one species in the Philippines.For this, we used generalized mixed Yule coalescent (GMYC) and Poisson tree process (PTP) species delimitation models to identify clades within DNA sequence phylogenies of T. loheri s. l. that might constitute species within this complex. Although these methods identified several putative species, these are statistically poorly supported and subsequent random forest analyses using a geometric morphometric leafshape dataset and several other vegetative characters did not result in the identification of characters that can be used to discriminate these putative species morphologically. Furthermore, the results of principal component and principal coordinates analyses of these data suggest the absence of morphological discontinuities within the species complex. Under a unified species concept that uses phylogenetic and morphological distinction as operational criteria for species recognition, we therefore conclude that the currently available data do not support recognizing multiple species in the T. loheri s. l. complex. This implies that T. loheri is best considered as a single, morphologically variable specieswhen used for studying patterns of genetic diversity and connectivity in the Philippines.

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A Systematic Analysis of the Alpine Saxifrage Complex (Saxifragaceae) in the Canadian Arctic Islands Using Morphology and Chloroplast DNA Data

The Canadian Field-Naturalist ◽

10.22621/cfn.v118i3.1 ◽

2004 ◽

Vol 118 (3) ◽

pp. 326 ◽

Cited By ~ 5

Author(s):

Caroline Healy ◽

Lynn J. Gillespie

Keyword(s):

Morphological Variability ◽

Canadian Arctic ◽

Principal Component ◽

Distinct Species ◽

Morphological Characters ◽

Sympatric Species ◽

Sensu Stricto ◽

Morphological Data ◽

Systematic Analysis ◽

Site Analysis

The Saxifraga nivalis complex displays significant ecological, morphological and cytological variation. Most European studies suggest that the S. nivalis complex comprises two distinct species: Saxifraga nivalis sensu stricto and Saxifraga tenuis. However, the presence of intermediate morphotypes, inconsistencies in chromosomal counts and variability in morphological keys and descriptions have led to different taxonomic interpretations of the complex in North America. This study investigated the systematics of Canadian Arctic Island members of this complex from 157 specimens using 23 morphological characters. Principal component analysis of the morphological data revealed two adjacent clusters, corresponding to the two taxa and consistent with a close morphological similarity and the presence of hybrids. A preliminary restriction site analysis of five non-coding regions of the chloroplast genome, trnH-trnK, trnT-trnF, trnF-trnV, trnV-rbcL and rbcL-ORF106, was conducted using 21 restriction endonucleases. This analysis indicated a length difference between the trnT-trnF region of S. nivalis and that of S. tenuis, but no difference in restriction sites for any of the assayed regions. These results confirm that in the Canadian Arctic, the S. nivalis complex consists of two closely related, largely sympatric species, with notable morphological variability, and possible hybrids.

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Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽

10.3390/genes10020097 ◽

2019 ◽

Vol 10 (2) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Xiaofeng Chi ◽

Faqi Zhang ◽

Qingbo Gao ◽

Rui Xing ◽

Shilong Chen

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Gene Flow ◽

Tibetan Plateau ◽

Environmental Changes ◽

Restricted Gene Flow ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

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