Genetic Variation Among Natural Populations of Tilletia controversa and T. bromi

Isolates of Tilletia controversa and T. bromi were sampled from wheat and two Bromus species hosts, respectively, in the Pacific Northwest, and genetic variation within and among populations was determined. Fifty-one random amplified polymorphic DNA markers from eleven primers were treated as phenotypic 1 and 0 character state data to estimate similarities and analyze molecular variance (AMOVA) among populations and as putative genetic loci to carry out analyses of gene diversity. Phenotypic analysis of T. controversa and T. bromi isolates revealed two distinct clusters that were 37% similar. The T. bromi cluster was subdivided further into two groups, corresponding to host, with 40% similarity. Cluster analysis based on allele frequencies produced similar results and also supported two T. bromi groups based on host. No evidence of natural hybridization and introgression was detected between the T. controversa and T. bromi populations. Both AMOVA and gene diversity analyses detected moderate levels of differentiation among T. controversa populations, whereas T. bromi populations were highly differentiated. The level of genetic differentiation observed between the T. bromi populations on different Bromus species hosts supports the hypothesis that a high degree of host specificity exists in the wild grass-infecting smuts. We speculate that the higher level of genetic differentiation among the T. bromi populations compared with the T. controversa populations on wheat may be due to selection by a more genetically diverse host population.

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RAPD Analysis of Genetic Variation Within and Among Four Natural Populations of Betula maximowicziana

Silvae Genetica ◽

10.1515/sg-2004-0042 ◽

2004 ◽

Vol 53 (1-6) ◽

pp. 234-239 ◽

Cited By ~ 9

Author(s):

Yoshiaki Tsuda ◽

S. Goto ◽

Y. Ide

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Global Analysis ◽

Random Amplified Polymorphic Dna ◽

Economic Value ◽

Geographic Distance ◽

Natural Populations ◽

Fundamental Information ◽

Betula Maximowicziana ◽

Amova Analysis

SummaryBetula maximowicziana is a long-lived pioneer tree species in cool temperate forests that plays an important role in the forest ecosystem and has high economic value. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variation of four natural populations of B. maximowicziana (three in central Honshu and the other in Hokkaido) to obtain fundamental information on this natural resource. Sixty-one reproductive amplified bands were obtained with 23 primers. Of these 61 bands, 22 were monomorphic and 39 were polymorphic. The level of genetic variation within each population may be very similar, because the population rankings according to number of polymorphic loci, Shannon’s indices and intra-population genetic variance revealed no definite patterns. Global analysis of AMOVA (analysis of molecular variance) showed that genetic variation among populations accounted for 15.6% of the total variation, with the remainder (84.4%) occurring within population. These results demonstrate that genetic differentiation among the four populations is moderate. Hierarchical AMOVA analysis showed that variation among regions (Hokkaido and central Honshu) accounted for 10.4% of the total genetic variation, suggesting that regional genetic differentiation is relatively high. Significant correlations between pairwise ΦPTvalues and geographic distance were detected, and results of both a neighbor-joining dendrogram based on pairwise ΦPTvalues, and principal coordinate analysis (PCO) based on a Euclidean metric revealed that the Furano population in Hokkaido was genetically different from the three populations in central Honshu. The data obtained in this study should have important implications for the conservation and management of regional genetic variation of B. maximowicziana.

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Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Journal of Plant Pathology ◽

10.1007/s42161-021-00759-8 ◽

2021 ◽

Author(s):

Rui Zang ◽

Ying Zhao ◽

Kangdi Guo ◽

Kunqi Hong ◽

Huijun Xi ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Fusarium Oxysporum ◽

Diversity Index ◽

Gene Diversity ◽

Pcr Amplification ◽

Bitter Gourd ◽

Diseased Plant ◽

Variation Analysis ◽

Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

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Molecular Markers Dispute the Existence of the Afro-Andean Group of the Bean Angular Leaf Spot Pathogen, Phaeoisariopsis griseola

Phytopathology ◽

10.1094/phyto.2002.92.6.580 ◽

2002 ◽

Vol 92 (6) ◽

pp. 580-589 ◽

Cited By ~ 30

Author(s):

George S. Mahuku ◽

María Antonia Henríquez ◽

Jaime Munõz ◽

Robin A. Buruchara

Keyword(s):

Genetic Differentiation ◽

Leaf Spot ◽

Multiple Correspondence Analysis ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Point Mutations ◽

Angular Leaf Spot ◽

Gene Pools ◽

Phaeoisariopsis Griseola ◽

Intergenic Spacer Region

Coevolution of the angular leaf spot pathogen, Phaeoisariopsis griseola, with its common bean host has been demonstrated, and P. griseola isolates have been divided into Andean and Mesoamerican groups that correspond to defined bean gene pools. Recent characterization of P. griseola isolates from Africa has identified a group of isolates classified as Andean using random amplified polymorphic DNA (RAPD), but which are able to infect some Mesoamerican differential varieties. These isolates, designated Afro-Andean, have been identified only in Africa. Random amplified microsatellites, RAPD, and restriction digestion of amplified ribosomal intergenic spacer region were used to elucidate the relationships among the Afro-Andean, Andean, and Mesoamerican groups of P. griseola. Cluster and multiple correspondence analysis of molecular data separated isolates into Andean and Meso-american groups, and the Afro-Andean isolates clustered with Andean isolates. Analysis of molecular variance ascribed 2.8% of the total genetic variation to differences between Afro-Andean and Andean isolates from Africa. Gene diversity analysis revealed no genetic differentiation (GST = 0.004) between Afro-Andean and Andean isolates from Africa. However, significant levels of genetic differentiation (GST = 0.39) were observed between Afro-Andean or Andean isolates from Africa and Andean isolates from Latin America, revealing significant geographical differentiation within the Andean lineage. Results from this study showed that Afro-Andean isolates do not constitute a new P. griseola group and do not represent long-term evolution of the pathogen genome, but rather are likely the consequents of point mutations in genes for virulence. This finding has significant implications in the deployment of resistant bean genotypes.

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RAPD ANALYSIS OF GENETIC VARIATION IN NATURAL POPULATIONS OF AEGILOPS SP. FROM SOUTH ADRIATIC

AGROFOR ◽

10.7251/agreng1801035d ◽

2018 ◽

Vol 3 (1) ◽

Author(s):

Miodrag DIMITRIJEVIĆ ◽

Sofija PETROVIĆ ◽

Borislav BANJAC ◽

Goran BARAĆ

Keyword(s):

Genetic Variation ◽

Food Production ◽

Rapd Markers ◽

Rapd Analysis ◽

Gene Diversity ◽

Rapd Marker ◽

Natural Populations ◽

Genetic Structuring ◽

Potential Source ◽

Novel Approach

New challenges that food production is facing, requires novel approach inagricultural strategy. The scissors of growing demand for food and the limits of theEarth's resources are forcing plant breeders to run for the new borders, utilizing allthe available genetic variation in order to create fruitful and economically soundcultivars. Aegilops sp. (Poaceae) is a potential source of genetic variation for wheatimprovement. RAPD marker analysis was used in order to distinguish and evaluatedifferent genotypes of Aegilops sp. population samples from the collectiongathered during few years’ expeditions in South Adriatic, along the coastal, littoraland the inland parts of Montenegro. Ten randomly amplified polymorphic DNAmarkers (RAPDs) were tested: OPA-05, OPA-08, OPB-06, OPA-02, OPA-07,OPA-25, OPB-07, OPB-18, OPC-06, OPC-10 to examine genetic structuring on 18samples of 6 populations of different Aegilops sp. According to global AMOVA,75% of total gene diversity was attributable mostly to diversity within population(ΦPT =0.205 p=0.001), indicating that the groups of studied goat grass populationswere seemingly to differing genetically. In contrast, 25% of the variation camefrom variation among populations. According to PCoA, the distribution of 18 goatgrass accessions by Principal Coordinate Analysis shows 3 distinct groups. PCoaxis 1, PCo axis 2, and PCo axis 3 account for 20.8%, 18.2% and 14.1% of thevariation, respectively. The results showed that RAPD markers could be aconvenient tool for investigating genetic variation and for detecting geneticstructuring of populations. Genetic variability formed under natural selection wasentrenched.

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Spatial Structure and Genetic Variation of a Mangrove Species (Avicennia marina (Forssk.) Vierh) in the Farasan Archipelago

Forests ◽

10.3390/f11121287 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1287

Author(s):

Rahmah N. Al-Qthanin ◽

Samah A. Alharbi

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Species Conservation ◽

Natural Populations ◽

Avicennia Marina ◽

Conservation Strategies ◽

Isolated Populations ◽

Mangrove Species ◽

Population Genetic Differentiation ◽

Sea Currents

Avicennia marina (Forssk.) Vierh is distributed in patches along the Farasan archipelago coast and is the most common mangrove species in the Red Sea. However, to date, no studies have been directed towards understanding its genetic variation in the Farasan archipelago. In this investigation, genetic variations within and among natural populations of Avicennia marina in the Farasan archipelago were studied using 15 microsatellite markers. The study found 142 alleles on 15 loci in nine populations. The observed (Ho) and expected (He) heterozygosity values were 0.351 and 0.391, respectively, which are much lower than those of earlier studies on A. marina in the Arabian Gulf. An inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (FST = 0.301) was similar to other mangrove species. Our findings suggest that the sea current direction and coastal geomorphology might affect genetic dispersal of A. marina. The more isolated populations with fewer connections by sea currents exhibited lower genetic variation and differentiation between populations. The genetic clustering of populations fell into three main groups—Group 1 (populations of Farasan Alkabir Island), Group 2 (populations of Sajid Island), and Group 3 (mix of one population of Farasan Alkabir Island and a population of Zifaf Island). More genetic variation and less genetic differentiation occurred when the population was not isolated and had a direct connection with sea currents. Both of these factors contributed to limited propagule dispersal and produced significant structures among the population. It is expected that the results of this research will be useful in determining policy and species-conservation strategies and in the rehabilitation of A. marina mangrove stands on the Farasan islands in an effort to save this significant natural resource.

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Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

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Evolution during seed production for ecological restoration? A molecular analysis of 19 species finds only minor genomic changes

10.1101/2021.11.03.467064 ◽

2021 ◽

Author(s):

Malte Conrady ◽

Christian Lampei ◽

Oliver Bossdorf ◽

Walter Durka ◽

Anna Bucharova

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Ecological Restoration ◽

Seed Production ◽

Large Scale ◽

Gene Diversity ◽

Natural Populations ◽

Genetic Change ◽

Breeding Systems ◽

Wild Plants

A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change. We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations grown from these sources. We then linked the magnitudes of genetic changes to the species breeding systems and seed dormancy, to understand the roles of these traits in genetic change. The propagation of native seeds for ecosystem restoration changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions, and the propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible species, probably as a result of increased outcrossing in the monocultures. Synthesis and applications: Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may even increase the adaptive potential of propagated seeds, which makes them especially suitable for ecological restoration. However, we have been working with seeds from Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.

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Genetic Differentiation in Natural Populations of Grevillea robusta

Australian Journal of Botany ◽

10.1071/bt96073 ◽

1997 ◽

Vol 45 (4) ◽

pp. 669 ◽

Cited By ~ 11

Author(s):

C. E. Harwood ◽

G. F. Moran ◽

J. C. Bell

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Natural Populations ◽

Grevillea Robusta ◽

Distance Analysis ◽

Riverine Habitat ◽

Natural Range ◽

Isozyme Loci ◽

The Difference ◽

Genetic Distance Analysis

Genetic variation in 23 natural populations of Grevillea robusta A.Cunn. from across the natural range of the species was examined using 20 isozyme loci assayed in young seedlings. Mean expected heterozygosity per population, He , varied from 0.080 to 0.131 with an average of 0.105. The genetic diversity of individual populations did not appear to be related to their ecological characteristics (araucarian vine forest or riverine habitat types) or their geographic locations. A genetic distance analysis indicated a significant separation of the populations into two regional groups, eight from the northern part of the natural range and the remaining 15 from central and southern areas. Between-population differences accounted for 17.9% of the total genetic variation, one-third of which was attributable to the difference between the two regional groups. Most alleles at the 20 loci occurred across most or all of the geographic range. This, and the low level of genetic differentiation between populations, suggest that genetic exchange between populations has been maintained, despite the pattern of natural distribution of the species in small, separated populations.

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Genetic Structure of Cronartium ribicola Populations in Eastern Canada

Phytopathology ◽

10.1094/phyto.1999.89.10.915 ◽

1999 ◽

Vol 89 (10) ◽

pp. 915-919 ◽

Cited By ~ 26

Author(s):

K. Et-touil ◽

L. Bernier ◽

J. Beaulieu ◽

J. A. Bérubé ◽

A. Hopkin ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Distribution Systems ◽

Gene Diversity ◽

Isolation By Distance ◽

Random Amplified Polymorphic Dna ◽

Cronartium Ribicola ◽

Eastern Canada ◽

Long Distance ◽

Evolutionary Forces

The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (Ht = 0.386) was present within populations (Hw = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (Fst = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA φst = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

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Genetic Differentiation Studies among Natural Populations of Tilapia zillii

Notulae Scientia Biologicae ◽

10.15835/nsb749649 ◽

2015 ◽

Vol 7 (4) ◽

pp. 423-429

Author(s):

Tofunmi E. OLADIMEJI ◽

Michael O. AWODIRAN ◽

Olaniyi O. KOMOLAFE

Keyword(s):

Genetic Differentiation ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Principal Component ◽

Genetic Distances ◽

Morphological Studies ◽

Tilapia Zillii ◽

Meristic Counts ◽

Ctab Method ◽

Group Relationships

The population structure of Tilapia zillii (Gervais 1848) from three reservoirs in Nigeria, Osun State (Opa, Osu and Igun) was determined by employing morphological and molecular (Random Amplified Polymorphic DNA) methods. For morphological studies, 25 morphometric measurements and six meristic counts were recorded on 40 individuals within each population. Principal Component Analysis (PCA) was performed on the morphometric and meristic data using the PAST software. For RAPD studies, genomic DNA was extracted from caudal fin tissue using CTAB method and five primers were used to initiate PCR amplifications. All the clusters produced by the Principal components analysis (PCA) of the morphometric and meristic parameters overlapped indicating a low level of genetic differentiation between the three populations of T. zillii studied. The UPGMA cluster diagram from RAPD analysis identified two major genotypic groups with inter and intra group relationships. All individuals in the first cluster were from the Osu reservoir, while individuals from Opa and Igun reservoirs constituted the second cluster. Nei’s unbiased measure of genetic distances was 0.8532, 0.7321 and 0.7111 for Osu, Igun and Opa populations respectively. This revealed that Opa and Igun populations were genetically closer, while Osu populations is distant from them. The results suggest that the RAPD technique could be used to differentiate populations of T. zillii. However, additional methods such as microsatellite and sequence analysis can be used to maximize the efficiency of genetic differentiation studies.

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