Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

2019 ◽  
Vol 26 ◽  
pp. 127-136 ◽  
Author(s):  
Seyed M. Talebi ◽  
Reza Rezakhanlou ◽  
Alex V. Matsyura
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
Conservation Status ◽  
Molecular Study ◽  
Medicinal Species ◽  
High Genetic Diversity ◽  
Genetic Groups ◽  
Nj Tree ◽  
Two Populations

Salvia nemorosa is widely distributed in different parts of Iran, while, there is no information about its population genetic structure and genetic diversity. The current information of its potential protection or conservation status in Iran is almost absent and unclear. Our investigation was the first molecular study of this medicinal species. We performed analysis of genetic variability and population structure of 11 populations of S. nemorosa in Iran using ISSR technique. We revealed intra and inter-population genetic diversity in the studied populations. Genetic parameters widely varied among the studied populations and confirmed their high genetic diversity. Moreover, AMOVA test showed significant molecular variation among and within the populations. The arrangement of populations and their individuals in NJ tree, PCA and MDS plots was in agreement with AMOVA results and individuals of five groups were overlapped. The Nm value showed low amount of gene flow among the populations. Based on STRUCTURE analysis and UPGMA tree of genetic distance, six genetic groups were identified among the studied populations, while two populations had significant differences and could be definite as ecotypes.

scholarly journals Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
José David Rangel-Medrano ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
High Genetic Diversity ◽  
The Family ◽  
The Mean

ABSTRACT The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F’ST=0.013 - 0.017, P > 0.05, D’est= -0.004 - 0.023, P > 0.05; P. magnus: F’ST= 0.031, P= 0.055; D’est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

2021 ◽  
Vol 43 (1) ◽  
pp. 38-42
Author(s):  
Kavungal Priya ◽  
◽  
Indira . ◽  
Vadakkethil Balakrishnan Sreekumar ◽  
Renuka . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Ghats ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Western Ghats Of India ◽  
The Mean ◽  
Two Parameters ◽  
Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

scholarly journals Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

2009 ◽  
Vol 99 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Laura I. Weber ◽  
Cintia G. Hildebrand ◽  
Anderson Ferreira ◽  
Gustavo Pedarassi ◽  
José A. Levy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Significant Degree ◽  
Southern Brazil ◽  
High Genetic Diversity ◽  
Low Degree ◽  
Faecal Samples ◽  
High Level ◽  
Degree Of Differentiation ◽  
Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

Species delimitation and population structure in three Onosma (Boraginaceae) species

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Masoud Sheidai ◽  
Samira Sadeghi ◽  
Mahnaz-Arab Ameri ◽  
Ahmad-Reza Mehrabeian
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Species Delimitation ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Morphological Diversity ◽  
Mantel Test ◽  
Geographical Distance ◽  
Nj Tree ◽  
Issr Molecular Markers

AbstractThe present study aimed to reveal genetic diversity and population structure in three Onosma species i.e., Onosma bulbotrichum DC., O. elwendicum Wettst. and O. sericeum Willd. (Boraginaceae) growing in Iran. This study was performed to check if the ISSR molecular markers could be used in the Onosma species delimitation. We also investigated the infra-specific morphological variability and if we can identify infra-species taxonomic forms. The present study revealed within species genetic and morphological diversity. ISSR data could delimit the studied species as they were separated from each other in NJ tree, maximum parsimony and STRUCTURE analysis. AMOVA and Hickory tests produced significant genetic difference among the studied species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations for all three species. Reticulation analysis and Nm estimation showed gene flow among these populations. We could identify a few ISSR loci that are adaptive. Data obtained can be used in conservation of these medicinal plants in Iran.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

scholarly journals Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 135 ◽  
Author(s):  
Jingxue Zhang ◽  
Miaoli Wang ◽  
Zhipeng Guo ◽  
Yongzhuo Guan ◽  
Jianyu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Cynodon Dactylon ◽  
Latitudinal Gradients ◽  
Wind Pollination ◽  
Ploidy Levels ◽  
Sexual And Asexual Reproduction ◽  
Genetic Pattern

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.

scholarly journals Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Moein Khojasteh ◽  
S. Mohsen Taghavi ◽  
Pejman Khodaygan ◽  
Habiballah Hamzehzarghani ◽  
Gongyou Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Global Scale ◽  
Population Diversity ◽  
Bacterial Leaf Streak ◽  
High Genetic Diversity ◽  
Center Of Origin ◽  
Content Type ◽  
Xanthomonas Translucens ◽  
Insight Into

ABSTRACT This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens—have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

scholarly journals Genetic Diversity and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1193
Author(s):  
Clementine Namazzi ◽  
Julius Pyton Sserumaga ◽  
Swidiq Mugerwa ◽  
Martina Kyalo ◽  
Collins Mutai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Crop Production ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Model Based Clustering ◽  
High Gene ◽  
Nj Tree ◽  
Improvement Programs ◽  
The Tropics

Brachiaria (syn. Urochloa) grass is an important tropical forage of African origin that supports millions of livestock and wildlife in the tropics. Overgrazing, conversion of grasslands for crop production and non-agricultural uses, and the introduction of improved forages have threatened the natural diversity of Brachiaria grass in Uganda. This study established a national collection of Brachiaria ecotypes in Uganda and analyzed them for genetic diversity and population structure using 24 simple sequence repeats (SSR) markers. These markers had a high discriminating ability with an average polymorphism information content (PIC) of 0.89 and detected 584 alleles in 99 ecotypes. Analysis of molecular variance revealed a high within populations variance (98%) indicating a high gene exchange or low genetic differentiation (PhiPT = 00.016) among the ecotype populations. The Bayesian model based clustering algorithm showed three allelic pools in Ugandan ecotypes. The principal component analysis (PCA) of ecotypes, and Neighbor-joining (NJ) tree of ecotypes and six commercial cultivars showed three main groups with variable membership coefficients. About 95% of ecotype pairs had Rogers’ genetic distance above 0.75, suggesting most of them were distantly related. This study confirms the high value of these ecotypes in Brachiaria grass conservation and improvement programs in Uganda and elsewhere.

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