scholarly journals Understanding population differentiation using geographical, morphological and genetic characterization in Erodium cicunium

2020 ◽  
Vol 80 (04) ◽  
Author(s):  
Xingxing Si ◽  
Lei GAO ◽  
Yuwei Song ◽  
Majid Khayatnezhad ◽  
Amir Abbas Minaeifar
Keyword(s):  
Genetic Difference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Population Diversity ◽  
Start Codon ◽  
Principal Coordinates Analysis ◽  
Forage Plants ◽  
Principal Coordinates ◽  
Geographical Populations ◽  
Study Population

Erodium cicunium (Geraniaceae) species are distributed in different habitats of Iran. Some species are of medicinal importance while some are well known weeds and used as forage plants. An investigation was carried out to evaluate 124 randomly collected plants of E. cicunium from 15 geographical populations in 5 provinces to study population structure and for morphological and molecular characters. Start Codon Targeted (SCoT) markers were used to analyse molecular diversity. Analysis of molecular variance (AMOVA) revealed significant genetic difference among the studied populations and also revealed that 60% of total genetic variability was due to within population diversity, while 40% genetic differentiation was recorded among populations. Principal Coordinates Analysis (PCoA) of populations based on morphological characters was not in agreement with Metric Multidimensional Scaling (MDS) plot of molecular data.

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

2018 ◽  
Vol 69 (2) ◽  
pp. 142 ◽  
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).

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

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

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.

scholarly journals Temporal and Spatial Analysis of Forward and Backward Microbial Contamination in a Mars Analog Mission

2021 ◽  
Vol 8 ◽  
Author(s):  
Yael Yair ◽  
Leah Reshef ◽  
Camelia Shopen-Gochev ◽  
Gal Yoffe ◽  
Gil Azulay ◽  
...  
Keyword(s):  
Diversity Index ◽  
Environmental Dna ◽  
Population Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Mars Analog ◽  
Sequencing Platforms ◽  
Contamination Events

As human exploration missions to Mars are on the horizon, microbial cross-contamination remains a key issue to address. These issues can be approached today using advances in molecular metagenomics methods, which include rapid and sensitive sequencing platforms for characterizing microbial populations. Combined with analog missions, these methods provide powerful tools for assessing the challenges associated with planetary exploration. Here, we designed a protocol to monitor forward and backward contamination events and progression in an 11-days Mars analog mission in the Ramon crater in Israel. Forward contamination soil samples were collected daily from three sites–two sites in close proximity to the habitat and one isolated site. Backward contamination was determined in samples from nitrile gloves of six analog astronauts before and after extravehicular activities Temperature, relative humidity and soil composition data were also collected for all sites. Environmental DNA samples were extracted in the main habitat and 16S (bacterial) and 18S (eukaryotic, fungal) rRNA gene amplicons were sequenced and analyzed to study microbial population diversity and composition. Shannon Diversity index analysis and Principal Coordinates analysis (PCoA) of rRNA genes indicated that differences in the diversity and population composition were significant in sites closer to the habitat when compared to a reference site. These samples also demonstrated the introduction of human-associated taxa to the environment. Backward contamination consisted of bacterial taxa found on gloves upon return from EVA and also detected in soil, altogether 44 genera, indicating backward contamination events. To our knowledge, this is the first protocol to utilize advanced molecular technologies to investigate forward and backward contamination in a Mars analog mission.

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

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.

Buddleja caryopteridifolia (Scrophulariaceae), a species to be recognized based on morphology, floral scent and AFLP data

Phytotaxa ◽  
2014 ◽  
Vol 161 (3) ◽  
pp. 181 ◽  
Author(s):  
Xin Zhang ◽  
Gao Chen ◽  
Weichang Gong ◽  
Weibang Sun
Keyword(s):  
Volatile Compound ◽  
Fragment Length Polymorphism ◽  
Floral Scent ◽  
Morphological Characters ◽  
Aflp Data ◽  
Principal Coordinates Analysis ◽  
Separate Species ◽  
Principal Coordinates ◽  
Flora Of China ◽  
Independent Species

Buddleja caryopteridifolia was treated as a synonym of B. crispa in Flora of China. However, it was found that the two entities had different phenologies as well as morphology in the sympatric habitat investigated. Buddleja crispa flowers from mid-March to mid-May while B. caryopteridifolia blooms from early June to mid-September. In this study, the comprehensive comparative analyses of morphological traits, floral scent composition and amplified fragment length polymorphism (AFLP) data were utilized to determine whether B. caryopteridifolia should be recognized as a separate species. Among 13 morphological characters, all but calyx length were significantly different (all p<0.05, t-test) between the two species. Both cluster analysis and principal coordinates analysis (PCoA) of AFLP markers produced two distinct clusters for B. crispa and B. caryopteridifolia. The results of floral scent indicated several differences between B. crispa and B. caryopteridifolia. The main volatile compound of B. crispa was Benzaldehyde, while that of B. caryopteridifolia mostly consisted of trans-β-Ocimene. Therefore, all analyses supported the rehabilitation of B. caryopteridifolia as an independent species.

AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae)

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 90-105 ◽  
Author(s):  
Martina Rex ◽  
Kerstin Patzolt ◽  
Katharina Schulte ◽  
Georg Zizka ◽  
Roberto Vásquez ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Molecular Data ◽  
Aflp Analysis ◽  
Long Distance ◽  
Aflp Data ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Centre Of Diversity ◽  
Branch Lengths ◽  
Species Groups

The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A–L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.

scholarly journals ISSR markers and population differentiations in Erodium ciconium (L.) L'hér ex Aiton

2021 ◽  
Vol 28 (1) ◽  
pp. 61-73
Author(s):  
Xi Fei ◽  
Ruan Xuejun ◽  
Amir Abbas Minaeifar
Keyword(s):  
Population Genetic ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Molecular Data ◽  
Issr Markers ◽  
Mantel Test ◽  
Population Diversity ◽  
Protein Supplements ◽  
Population Genetic Differentiation ◽  
Plant Taxon

Erodium ciconium is an important grazing plant and a source of protein supplements to straw for ruminants in semideserts and wastelands of the Middle East. There is no information on its population genetic structure, genetic diversity, and morphological variability in Iran. We performed molecular data for knowing the population differentiation in this species. For this study, we used 110 randomly collected plants from 15 geographical populations in 6 provinces of Iran. AMOVA test revealed significant genetic difference among the studied populations and also revealed that, 63% of total genetic variability was due to within population diversity while, 37% was due to among population genetic differentiation. Mantel test showed positive significant correlation between genetic distance and geographical distance of the studied populations. Networking, STRUCTURE analyses revealed some degree of gene flow among these populations. Bangladesh J. Plant Taxon. 28(1): 61-73, 2021 (June)

scholarly journals Genetic diversity and morphological variability in Geranium purpureum Vill. (Geraniaceae) of Iran

Genetika ◽  
2017 ◽  
Vol 49 (2) ◽  
pp. 543-557 ◽  
Author(s):  
Somayeh Bozchaloyi ◽  
Masoud Sheidai ◽  
Maryam Keshavarzi ◽  
Zahra Noormohammadi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Morphological Variability ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mantel Test ◽  
Geographical Populations ◽  
Well Differentiated ◽  
Genetic Stratification

Genetic variability and populations, structure were studied in 15 geographical populations of Geranium purpureum Vill. (Geraniaceae). Genetic diversity parameters were determined in these populations. AMOVA and Gst analyses revealed the presence of genetic variability within populations and significant molecular difference among the studied populations. Mantel test showed positive significant correlation between genetic distance and geographical distance of the studied populations. STRUCTURE and K-Means clustering revealed populations, genetic stratification. UPGMA dendrogram of populations based on morphological characters was in agreement with NJ tree of molecular data. These results indicated that geographical populations of G. purpureum are well differentiated both in genetic content as well as morphological characteristics. Consensus tree based on morphological and genetic data separated some of these populations from the others suggesting the existence of ecotypes within this species.

Genetic and morphological diversity in Stachys lavandulifolia (Lamiaceae) populations

Biologija ◽  
2016 ◽  
Vol 62 (1) ◽  
Author(s):  
Masoud Sheidai ◽  
Fatemeh Taban ◽  
Seyed Mehdi Talebi ◽  
Zahra Noormohammadi
Keyword(s):  
Genetic Diversity ◽  
Medicinal Plant ◽  
Gene Diversity ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Population Diversity ◽  
Morphological Data ◽  
Gene Pools ◽  
Germplasm Management ◽  
Geographical Populations

Stachys lavandulifolia Vahl. (Lamiaceae) is an important medicinal plant that grows in different parts of Iran and forms many geographical populations. We have no information on its population genetic structure, genetic diversity, and morphological variability in Iran. Therefore, we planned a genetic and morphological investigation in St. lavandulifolia geographical populations in Iran. The obtained data are important for conservation and germplasm management of this medicinal plant species. Seventy-four plants were randomly collected from 14 geographical populations and studied for genetic diversity (ISSR molecular markers) and morphological variability. The  highest value for gene diversity occurred in populations 1 and 4 (0.133 and 0.129, respectively). The  latitude and altitude were positively correlated with gene diversity and genetic polymorphism while longitude was negatively correlated with them. The Mantel test showed correlation between genetic distance and geographical distance. AMOVA revealed a significant genetic difference among populations and showed that 58% of total genetic variation was due to within-population diversity. The STRUCTURE analysis and K-Means clustering identified two gene pools for St. lavandulifolia. The  consensus tree of both molecular and morphological data identified divergent populations.

Genetic diversity in four cabbage populations based on random amplified polymorphic DNA markers

2005 ◽  
Vol 143 (5) ◽  
pp. 377-384 ◽  
Author(s):  
O. KOUTITA ◽  
K. TERTIVANIDIS ◽  
T. V. KOUTSOS ◽  
M. KOUTSIKA-SOTIRIOU ◽  
G. N. SKARACIS
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Population Diversity ◽  
Group Method ◽  
Jaccard Coefficient ◽  
Gene Frequencies ◽  
Principal Coordinates Analysis ◽  
Arithmetic Average ◽  
Principal Coordinates

Genetic diversity in four local Greek cabbage open-pollinated populations was investigated using RAPD (Random Amplified Polymorphic DNA) DNA markers in 18 individual plants from each population. A total of 24 random primers detected 90 polymorphic bands in the four populations studied, with an average of 3·75 bands/primer. The mean between-population differentiation was close to 40%, leaving 60% for within-population diversity. The individual plants were grouped, based on the Jaccard coefficient, by clustering (Unweighted Pair Group Method and Arithmetic Average – UPGMA) and an ordination (Principal Coordinates Analysis – PCO) methods, resulting in 7 and 6 groups, respectively. In general, there was a notable similarity in the grouping of the individuals with these two methods. In addition, Nei's standard genetic distance between populations, as calculated on the basis of within-population gene frequencies, was employed to group the populations by the UPGMA method. Clustering results were in good agreement with previously reported results based on morphological descriptors applied to the same populations. It was concluded that RAPD markers could be exploited as alternative or supplementary tools to already established methods for the evaluation and classification of cabbage genetic resources.

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