Global Hierarchical Gene Diversity Analysis Suggests the Fertile Crescent Is Not the Center of Origin of the Barley Scald Pathogen Rhynchosporium secalis

A total of 1,366 Rhynchosporium secalis isolates causing scald on barley, rye, and wild barley (Hordeum spontaneum) were assayed for restriction fragment length polymorphism loci, DNA fingerprints, and mating type, to characterize global genetic structure. The isolates originated from 31 field populations on five continents. Hierarchical analysis revealed that more than 70% of the total genetic variation within regions was distributed within a barley field. At the global level, only 58% of the total genetic variation was distributed within fields, while 11% was distributed among fields within regions, and 31% was distributed among regions. A significant correlation was found between genetic and geographic distance. These findings suggest that gene flow is common at the local level while it is low between regions on the same continent, and rare between continents. Analyses of multilocus associations, genotype diversity, and mating type frequencies indicate that sexual recombination is occurring in most of the populations. We found the highest allele richness in Scandinavia followed by Switzerland. This suggests that R. secalis may not have originated at the center of origin of barley, the Fertile Crescent, nor in a secondary center of diversity of barley, Ethiopia.

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Genetic Structure of Rhynchosporium secalis in Australia

Phytopathology ◽

10.1094/phyto.1999.89.8.639 ◽

1999 ◽

Vol 89 (8) ◽

pp. 639-645 ◽

Cited By ~ 93

Author(s):

B. A. McDonald ◽

J. Zhan ◽

J. J. Burdon

Keyword(s):

Genetic Structure ◽

Gene Diversity ◽

Sampling Site ◽

Geographic Distance ◽

South Australia ◽

Rflp Markers ◽

Rhynchosporium Secalis ◽

Fungal Isolates ◽

Fungal Populations ◽

Average Gene

Restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Australian field populations of the barley scald pathogen Rhynchosporium secalis. Fungal isolates were collected by hierarchical sampling from five naturally infected barley fields in different geographic locations during a single growing season. Genetic variation was high in Australian R. secalis populations. Among the 265 fungal isolates analyzed, 214 distinct genotypes were identified. Average genotype diversity within a field population was 65% of its theoretical maximum. Nei's average gene diversity across seven RFLP loci was 0.54. The majority (76%) of gene diversity was distributed within sampling site areas measuring ≈1 m2; 19% of gene diversity was distributed among sampling sites within fields; and 5% of gene diversity was distributed among fields. Fungal populations from different locations differed significantly both in allele frequencies and genotype diversities. The degree of genetic differentiation was significantly correlated with geographic distance between populations. Our results suggest that the R. secalis population in Western Australia has a different genetic structure than populations in Victoria and South Australia.

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Temporal components of genetic variation in migrating and wintering American wigeon

Canadian Journal of Zoology ◽

10.1139/z93-313 ◽

1993 ◽

Vol 71 (11) ◽

pp. 2229-2235 ◽

Cited By ~ 15

Author(s):

Olin E. Rhodes Jr. ◽

Loren M. Smith ◽

Ronald K. Chesser

Keyword(s):

Genetic Variation ◽

Gene Diversity ◽

High Plains ◽

Genetic Characteristics ◽

Total Genetic Variation ◽

Breeding Populations ◽

Wintering Waterfowl ◽

Breeding Grounds ◽

Average Proportion ◽

Wintering Population

Data from allele frequencies of wintering American wigeon (Anas americana) from the Southern High Plains (SHP) of Texas were used to monitor changes in genetic characteristics of the wintering population through time, and to estimate the average proportion of total genetic variation partitioned among parent breeding populations. Wigeon were surveyed electrophoretically for genetic variation at 25 biochemical loci. Changes in total gene diversity were observed throughout the study period (5 October 1988 to 15 March 1989) at numerous loci. Significant temporal changes in the genetic composition of the wintering population were detected, and a minimum of 7% of the total genetic variation in these wigeon was thought to be partitioned among the breeding populations represented on the SHP. A new influx of migrating wigeon, weather-related movements of wigeon, or spatial subdivision of breeding populations on the SHP may be responsible for shifts observed in the genetic characteristics of the wintering population. Significant heterozygote deficiencies in the sample of wintering wigeon suggest that this species maintains some degree of genetic structure on the breeding grounds. Genetic data collected from wintering waterfowl may provide minimum expectations of the degree of genetic subdivision among breeding populations and may help waterfowl biologists to detect changes in the composition of wintering waterfowl populations through time.

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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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Significant genetic differences among Heterodera schachtii populations within and among sugar beet production areas

Nematology ◽

10.1163/15685411-00003297 ◽

2020 ◽

Vol 22 (2) ◽

pp. 165-177 ◽

Cited By ~ 1

Author(s):

Rasha Haj Nuaima ◽

Johannes Roeb ◽

Johannes Hallmann ◽

Matthias Daub ◽

Holger Heuer

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Spatial Scales ◽

Geographic Distance ◽

Heterodera Schachtii ◽

Parasitic Nematodes ◽

Neutral Genetic Variation ◽

Production Areas

Summary Characterising the non-neutral genetic variation within and among populations of plant-parasitic nematodes is essential to determine factors shaping the population genetic structure. This study describes the genetic variation of the parasitism gene vap1 within and among geographic populations of the beet cyst nematode Heterodera schachtii. Forty populations of H. schachtii were sampled at four spatial scales: 695 km, 49 km, 3.1 km and 0.24 km. DGGE fingerprinting showed significant differences in vap1 patterns among populations. High similarity of vap1 patterns appeared between geographically close populations, and occasionally among distant populations. Analysis of spatially sampled populations within fields revealed an effect of tillage direction on the vap1 similarity for two of four studied fields. Overall, geographic distance and similarity of vap1 patterns of H. schachtii populations were negatively correlated. In conclusion, the population genetic structure was shaped by the interplay between the genetic adaptation and the passive transport of this nematode.

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Allele Diversity of Hordein-Coding Loci Hrd A and Hrd B in Cultivated (Hordeum vulgare L.) and Wild (Hordeum spontaneum C. Koch) Barley from Syria (as a Part of the Fertile Crescent)

Russian Journal of Genetics ◽

10.1134/s1022795418110121 ◽

2018 ◽

Vol 54 (11) ◽

pp. 1293-1301 ◽

Cited By ~ 2

Author(s):

A. A. Pomortsev ◽

S. V. Boldyrev ◽

E. V. Lyalina

Keyword(s):

Hordeum Vulgare ◽

Hordeum Spontaneum ◽

Hordeum Vulgare L ◽

Fertile Crescent

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Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers

Molecular Ecology ◽

10.1111/j.1365-294x.1993.tb00104.x ◽

1993 ◽

Vol 2 (3) ◽

pp. 151-159 ◽

Cited By ~ 110

Author(s):

I. K. DAWSON ◽

K. J. CHALMERS ◽

R. WAUGH ◽

W. POWELL

Keyword(s):

Genetic Variation ◽

Rapd Markers ◽

Hordeum Spontaneum

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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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Genetic studies revealed differences between European and North American populations of Calypogeia azurea

Biodiversity Research and Conservation ◽

10.1515/biorc-2016-0010 ◽

2016 ◽

Vol 42 (1) ◽

pp. 19-26 ◽

Cited By ~ 2

Author(s):

Katarzyna Buczkowska ◽

Alina Bączkiewicz ◽

Patrycja Gonera

Keyword(s):

Genetic Variation ◽

North America ◽

Genetic Distance ◽

Gene Diversity ◽

Oil Bodies ◽

Genetic Studies ◽

Isozyme Loci ◽

The Mean ◽

Different Parts ◽

Nei's Genetic Distance

Abstract Calypogeia azurea, a widespread, subboreal-montane liverwort species, is one of a few representatives of the Calypogeia genus that are characterized by the occurrence of blue oil bodies. The aim of the study was to investigate the genetic variation and population structure of C. azurea originating from different parts of its distribution range (Europe and North America). Plants of C. azurea were compared with C. peruviana, another Calypogeia species with blue oil bodies. In general, 339 gametophytes from 15 populations of C. azurea were examined. Total gene diversity (HT) estimated on the basis of nine isozyme loci of C. azurea at the species level was 0.201. The mean Nei’s genetic distance between European populations was equal to 0.083, whereas the mean genetic distance between populations originating from Europe and North America was 0.413. The analysis of molecular variance (AMOVA) showed that 69% of C. azurea genetic variation was distributed among regions (Europe and North America), 15% - among populations within regions, and 16% - within populations. Our study revealed that C. azurea showed genetic diversity within its geographic distribution. All examined samples classified as C. azurea differed in respect of isozyme patterns from C. peruviana.

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Genetic diversity in wild and hatchery populations of stinging catfish (Heteropneustes fossilis Bloch) revealed by RAPD analysis

Journal of Bio-Science ◽

10.3329/jbs.v19i0.13005 ◽

2012 ◽

Vol 19 ◽

pp. 81-87

Author(s):

Md Nazrul Islam ◽

Abhishak Basak ◽

Dr Ashrafullah ◽

Md Samsul Alam

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Gene Diversity ◽

Similarity Index ◽

Heteropneustes Fossilis ◽

Wild Populations ◽

Polymorphic Loci

Context: DNA fingerprinting using genetic markers such as Random Amplification of Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), microsatellite (Simple sequence repeat), Amplified Fragment Length Polymorphism (AFLP) etc. can be successfully used to reveal genetic variation within and among different populations. Objective: The aim of the present study was to assess genetic diversity in two wild and one hatchery populations of stinging catfish Heteropneustes fossilis by RAPD fingerprinting. Materials and Methods: A total of 90 live fish (H. fossilis), 30 from each source, were collected from a beel in Patuakhali, a beel in Jessore and Rupali Hatchery, Mymensingh. Genomic DNA was extracted from fin tissues. The concentration of DNA was estimated using a spectrophotometer. Fifteen decamer primers of random sequence from three kits (six from kit A, seven from kit B and two from kit C) (Operon technologies, Inc., Alameda, CA, USA) were screened on sub-samples of one randomly chosen H. fossilis DNA sample from the each population to test their suitability for amplifying RAPDs. The amplified products from each sample were separated by electrophoresis on 1.4% agarose gel containing ethidium bromide. The sizes of the bands were calculated using the software DNAFRAG and the sizes in base pair (bp) were used for identification of the bands (RAPD markers). The similarity index values (SI) between the RAPD fingerprint of any two individuals on the same gel were calculated from RAPD band sharing. Results: A total of 28 RAPD bands were obtained using four decamer random primers, among which 21 bands were polymorphic. The percentage of polymorphic loci, intra-population similarity indices and Nei's gene diversity values were 85.71%, 78.75 and 0.304±0.183 for Jessore population, 83.71%, 82.62 and 0.280±0.159 for Patuakhali population, 82.14%, 85.25 and 0.271±0.165 for Rupali hatchery population, respectively. The overall gene flow (Nm) among the populations was 5.755. The highest inter-similarity (Sij) was found between Patuakhali - Rupali hatchery populations. Among the three populations, the highest genetic distance (0.069) was found between Jessore and Patuakhali population. Considering polymorphic loci, intrapopulation similarity index and gene diversity the genetic variation in the Jessore population was higher than the other two populations. The genetic variation of the hatchery population was found to be lower than the two wild populations. Conclusion: The result of the present study can be used as baseline information regarding the genetic variation and population structure before undertaking any breeding programme. Study indicated that the genetic variation in the hatchery populations were slightly lower than those of the wild populations. DOI: http://dx.doi.org/10.3329/jbs.v19i0.13005 J. bio-sci. 19 81-87, 2011

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