Genetic Diversity and Spread of Thiobencarb Resistant Early Watergrass (Echinochloa oryzoides) in California

Resistance to the thiocarbamates has been selected in early watergrass populations within the rice-growing region of California. To elucidate the processes contributing to the spread of resistance among rice fields, we characterized the genetic diversity and differentiation of thiobencarb-resistant (R) and thiobencarb-susceptible (S) populations across the Central Valley using microsatellite markers. A total of 406 individuals from 22 populations were genotyped using seven nuclear microsatellite primer pairs. Three analytical approaches (unshared allele, Shannon–Weaver, and allelic-phenotype statistics) were used to assess genetic diversity and differentiation in the allohexaploid species. Low levels of genetic variation were detected within populations, consistent with other highly selfing species, with S populations tending to be more diverse than R populations.FSTvalues indicated that populations were genetically differentiated and that genetic differentiation was greater among S populations than R populations. Principal coordinate analysis generated two orthogonal axes that explained 88% of the genetic variance among early watergrass populations and differentiated populations by geographical region, which was associated with resistance phenotype. A Mantel test revealed that genetic distances between R populations were positively correlated with the geographical distances separating populations. Taken together, our results suggest that both short- and long-distance seed dispersal, and multiple local and independent evolutionary events, are involved in the spread of thiobencarb-resistant early watergrass across rice fields in the Sacramento Valley. In contrast, resistance was not detected in early watergrass populations in the San Joaquin Valley.

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Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

Bulletin of Entomological Research ◽

10.1017/s0007485309990538 ◽

2010 ◽

Vol 100 (5) ◽

pp. 521-527 ◽

Cited By ~ 9

Author(s):

K.M. Mikac ◽

N.N. FitzSimmons

Keyword(s):

Genetic Structure ◽

Isolation By Distance ◽

Geographic Distance ◽

Allelic Diversity ◽

Mantel Test ◽

Null Alleles ◽

Dispersal Patterns ◽

Long Distance ◽

Population Comparisons ◽

Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

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Genetic diversity of three Aegla species (Decapoda, Anomura) revealed by AFLP and mtDNA markers

Crustaceana ◽

10.1163/15685403-00003873 ◽

2019 ◽

Vol 92 (4) ◽

pp. 445-462

Author(s):

Bianca L. Zimmermann ◽

Jober V. De Vargas Machado ◽

Sandro Santos ◽

Marlise L. Bartholomei-Santos

Keyword(s):

Genetic Diversity ◽

Distinct Species ◽

Genetic Distances ◽

Species Level ◽

Taxonomic Resolution ◽

Similar Species ◽

Southern Brazil ◽

Low Levels ◽

Management And Conservation ◽

Mtdna Markers

Abstract Representatives of the genus Aegla present a conserved morphology; thus, the increased use of molecular markers has raised many taxonomic issues. We used AFLP and mtDNA to investigate the genetic differentiation and phylogenetic relationships of morphologically similar species with overlapping distribution areas in southern Brazil: A. georginae, A. ludwigi, and A. platensis. While A. platensis is widely distributed, the critically endangered A. georginae and A. ludwigi have limited distributions. Although both markers showed populations with low levels of genetic variability, they differed markedly in revealing relationships between populations; according to AFLP, the genetic distances between A. platensis populations were as high as those between distinct species, a result not observed when considering mtDNA data. We emphasize that the use of multiple lines of evidence is necessary for defining correct levels of genetic diversity and a good species-level taxonomic resolution. Such features are essential for the management and conservation of Aegla species.

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Morpho-phenological diversity among Tunisian natural populations of Brachypodium hybridum

The Journal of Agricultural Science ◽

10.1017/s0021859614000689 ◽

2014 ◽

Vol 153 (6) ◽

pp. 1006-1016 ◽

Cited By ~ 5

Author(s):

M. NEJI ◽

F. GEUNA ◽

W. TAAMALLI ◽

Y. IBRAHIM ◽

M. SMIDA ◽

...

Keyword(s):

Genetic Diversity ◽

Geographic Distribution ◽

Phenotypic Diversity ◽

Average Length ◽

Natural Populations ◽

Negative Relationship ◽

Mantel Test ◽

Population Variation ◽

Long Distance ◽

Temperate Cereal

SUMMARYBrachypodium hybridum belongs to the Poaceae grass subfamily. It has a close genetic relationship with temperate cereal crops, which means that it can be used as a model for temperate cereal and grass crops. In order to improve knowledge on the genetic diversity of this species, 145 lines of B. hybridum representative of nine populations and all the ecoregions of Tunisia were characterized on the basis of 18 morpho-phenologic features. The results show a considerable variation between populations and ecoregions in all traits studied. Variation was relatively higher for reproductive than vegetative traits. The majority of traits showed very low to high heritability with low border value for average length of spikelet (ALS) and an average value of 0·64. It is noticeable that high values of heritability were observed for most vegetative descriptors, with low values for reproductive ones. Differentiation between populations (QST) varied from 0·02 for ALS to 0·78 for average length of leaves with a mean value across traits of 0·4, which confirms the wide intra-population variation in Tunisian natural population of B. hybridum. Pairwise QST showed that the greatest differentiation among populations was registered between Ain Drahem and Jbel Zaghouan and the smallest between Haouria and Raoued. Overall, the Ain Draham population showed the largest differentiation from the rest of the populations. To infer the effect of geographic distribution of the species, a Mantel test was applied between observed pairwise differentiation and geographic distance between populations and between ecoregions: the results show a positive, but not significant, relationship. In addition a significant negative relationship was found between phenotypic diversity and altitude, indicating that genetic diversity decreased with increasing altitude. Taken together, the high levels of intra-population variation and the lack of correlation between genetic differentiation and geographic distribution suggest a potentially important rate of long-distance seed dispersal and confirm the role played by natural selection in the population structure of Tunisian natural populations of B. hybridum.

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Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm by RAPD markers

Genetika ◽

10.2298/gensr2102783q ◽

2021 ◽

Vol 53 (2) ◽

pp. 783-798

Author(s):

Xiaohui Qian ◽

Shahram Mehri

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Morphological Characters ◽

Mantel Test ◽

Pistacia Vera ◽

High Genetic Diversity ◽

Horticultural Crops ◽

Genetic Structure Of Populations ◽

Geographical Distances ◽

Species Adaptability

Assessing the genetic diversity in the population is the prerequisite to start and develop plant breeding projects. Pistacia vera is considered as a commercial species of Pistacia genus. In Iran, Pistachio export is in the second place in terms of non-oil exports and in the first place among horticultural crops. Therefore, we collected and analyzed 11 pistachio genotype (Pistacia vera), from two provinces of Iran regions. Our aims were 1) to assess genetic diversity among some of Irainian pistachio cultivars 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Akbari cultivars depicted unbiased expected heterozygosity (UHe) in the range of 0.028. Shannon information was high (0.49) in Seifadini cultivars. Akbari cultivars howed the lowest value, 0.029. The observed number of alleles (Na) ranged from 0.261 to 2.700 in Shahpasand cultivars and Kalehghoochi cultivars. The effective number of alleles (Ne) was in the range of 1.021-1.800 for Akbari cultivars and Moosaabadi cultivars .Gene flow (Nm) was relatively low (0.38) in pistachio cultivars. The Mantel test showed correlation (r = 0.33, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the among some of Irainian pistachio cultivars 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 pistachio cultivars.

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Parasite (Schistosoma mansoni) and host (Biomphalaria glabrata) genetic diversity: population structure in a fragmented landscape

Parasitology ◽

10.1017/s0031182001007727 ◽

2001 ◽

Vol 122 (5) ◽

pp. 545-554 ◽

Cited By ~ 38

Author(s):

C. SIRE ◽

J. LANGAND ◽

V. BARRAL ◽

A. THÉRON

Keyword(s):

Genetic Diversity ◽

Schistosoma Mansoni ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Rattus Rattus ◽

Biomphalaria Glabrata ◽

Genetic Distances ◽

Snail Host ◽

Fragmented Landscape ◽

Geographical Distances

Random amplified polymorphic DNA (RAPD) markers were used to quantify genetic diversity within and between 5 populations ofSchistosoma mansoniwithin its definitive host (Rattus rattus) and the 5 corresponding populations of the snail intermediate host (Biomphalaria glabrata) from a limited endemic area of murine schistosomiasis on the island of Guadeloupe. Analysis of molecular variance (AMOVA) and canonical correspondence analysis (CCA) were used to test the significance of genetic differentiation between populations. Both methods gave similar results. Of total gene diversity, 15.1% (AMOVA) and 18.8% (CCA) was partitioned between localities forS. mansoniwith an absence of association between genetic and geographical distances. Geographical localities accounted for 20.5% (CCA) of the total diversity forB. glabratapopulations. The genetic distances between pairs of parasite populations were not correlated with the genetic distances between the corresponding pairs of snail host populations. Such strong patterns of local differentiation of both parasite and snail populations are consistent with predictions based on metapopulation dynamics and may have implications on host–parasite susceptibility relationship through local adaptation processes.

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Assessing Genetic Diversity of Canada Thistle (Cirsium arvense) in North America with Microsatellites

Weed Science ◽

10.1614/ws-d-09-00070.1 ◽

2010 ◽

Vol 58 (4) ◽

pp. 387-394 ◽

Cited By ~ 9

Author(s):

Tracey A. Bodo Slotta ◽

Michael E. Foley ◽

Shaioman Chao ◽

Ruth A. Hufbauer ◽

David P. Horvath

Keyword(s):

Genetic Diversity ◽

Invasive Species ◽

North America ◽

North American ◽

Isolation By Distance ◽

Genetic Distances ◽

Population Diversity ◽

Canada Thistle ◽

Long Distance ◽

Distance Analysis

Invasive species such as Canada thistle pose a significant threat to ecosystems. The risk of introducing invasive species has increased with human activities, and the effects of such events have economic and aesthetic impacts. Native to Europe, Canada thistle is now established throughout temperate North America. Although there is documentation of early occurrences to North America, little is known on how it has become established in diverse habitats or how it continues to spread. We examined genetic diversity within and among nearly 1,700 Canada thistle individuals from 85 North American locations with the use of seven microsatellite markers in order to address these questions. PAUP and STRUCTURE programs were used to assess genetic diversity and relationships within and between populations. Populations exhibited greater within-population diversity (> 60%) than expected for a reported clonally reproducing species. Total diversity of sampled locations in North America (0.183) was less than previously reported for European locations (0.715), but the greater mean difference between North American populations (0.264 relative to 0.246 from England) suggests strong founder effects or restriction of gene flow influencing individual populations. Furthermore, analyses identified numerous instances where individuals from geographically distant regions clustered together, indicating long-distance translocation of propogules. However, isolation by distance analysis showed significant correlation between location and population genetic distances (r = 0.1917, P = 0.006). Within populations, nearly 92% of individuals sampled harbored unique multilocus genotypes, strongly suggesting that sexual reproduction is common. Within populations, analysis of genetic structure indicated significant admixture of genotypes throughout the invasive range in North America. The recurrent distribution of seed throughout North America has led to a highly diverse gene pool and increased the adaptive success Canada thistle to a wide variety of habitats. Future technologies developed for control of Canada thistle should consider this diversity.

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Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genetika ◽

10.2298/gensr2101393b ◽

2021 ◽

Vol 53 (1) ◽

pp. 393-405

Author(s):

Dezhong Bi ◽

Dan Chen ◽

Majid Khayatnezhad ◽

Zohreh Hashjin ◽

Zifa Li ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Morphological Characters ◽

Mantel Test ◽

High Genetic Diversity ◽

Genetic Structure Of Populations ◽

Geographical Distances ◽

Species Adaptability ◽

Hypericum Species

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum 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 Hypericum species.

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Genetic diversity of Lonicera L. (Caprifoliaceae) estimated by molecular markers and morphological characters

Genetika ◽

10.2298/gensr2102651m ◽

2021 ◽

Vol 53 (2) ◽

pp. 651-662

Author(s):

Xin Ma ◽

Huailiang Tian ◽

Haiou Xia ◽

Z Zeenat

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Morphological Characters ◽

Mantel Test ◽

High Genetic Diversity ◽

Changing Environments ◽

Genetic Structure Of Populations ◽

Geographical Distances ◽

Species Adaptability

Members of Lonicera are characterized by opposite, narrowly elliptic to obovate leaves, white, yellow, reddish, or purple-red corolla with capitate stigma and undulate calyx margin. In Flora Iranica, Wendelbo (1965) classified 19 species of the Lonicera into two subgenera (Chamaecerasus and Lonicera) and three sections, namely Isoxylosteum, Isika and Coeloxylosteum. The four studied species belong to subgenus Chamaecerasus and sections Isika and Coeloxylosteum. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Lonicera genetic diversity. Therefore, we collected and analyzed three species from 2 provinces regions. Overall, 45 plant specimens were collected. Our aims were 1) to assess genetic diversity among Lonicera species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. The Mantel test showed correlation (r=0.66, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Lonicera 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 Lonicera species.

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Genetic diversity of the rare Asian plant, Trigonobalanus doichangensis (Fagaceae)

Australian Journal of Botany ◽

10.1071/bt05113 ◽

2007 ◽

Vol 55 (1) ◽

pp. 10 ◽

Cited By ~ 10

Author(s):

Weibang Sun ◽

Chunyan Han ◽

Lianming Gao ◽

Carol A. Wilson

Keyword(s):

Genetic Diversity ◽

Species Diversity ◽

Genetic Distances ◽

Western China ◽

Chinese Populations ◽

Population Conservation ◽

The Family ◽

Geographical Distances ◽

Rare And Endangered ◽

Range Of Values

Trigonobalanus doichangensis is a national rare and endangered fagaceous plant of China. It is currently restricted to five sites, four in Yunnan province in south-western China and one in northern Thailand. We investigated the genetic diversity of T. doichangensis to provide information for the effective preservation of the genetic diversity of the species. Randomly amplified polymorphic DNA (RAPD) markers were used to assess the genetic variation and structure in each of the five extant populations. Sixteen primers produced 157 fragments, of which 83 (53%) were polymorphic. The estimated species diversity of T. doichangensis, although lower than for most fagaceous species, was within the range of values that have been reported for the family. The presence of private and/or uncommon fragments in each population, the presence of unique phenotypes in all individuals sampled, and estimates of relatively high populational fixation and low gene flow indicated that the species diversity present was mostly distributed among the five isolated extant populations. Pairwise genetic distances between populations were not correlated with geographical distances as depicted by the resolution of one of the Chinese populations as most similar to the Thailand population. Conservation of this species should include preservation of each of the five distinct extant populations.

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Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China

PLoS ONE ◽

10.1371/journal.pone.0241452 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241452

Author(s):

Chen Wang ◽

Xiang Ma ◽

Mingxun Ren ◽

Liang Tang

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Decline ◽

Hainan Island ◽

Mantel Test ◽

Long Distance ◽

Endangered Tree ◽

Important Indicator ◽

Endangered Tree Species ◽

Model Based Clustering

Hopea hainanensis Merrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber, H. hainanensis has suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatened Hopea species, H. hainanensis exhibited reduced overall genetic diversity and increased population differentiation (AMOVA: FST = 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assigned H. hainanensis individuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances (r = 0.040, p = 0.418). The observed genetic structure suggests that long-distance gene flow occurred among H. hainanensis populations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered species H. hainanensis are proposed.

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