Population Structure of Rhizoctonia oryzae-sativae in California Rice Fields

Six pairs of single-locus microsatellite primers were developed to study the population structure of Rhizoctonia oryzae-sativae, the cause of aggregate sheath spot disease of rice, among and within three rice-growing areas in California over a 3-year period. A high level of gene flow among growing areas was indicated by low population subdivision according to analysis of molecular variance and moderate to no population differentiation between pairs of populations based on the fixation index (FST). Gametic equilibrium of most pairs of microsatellite loci, high numbers of unique multilocus genotypes, and high genotypic diversity indicated extensive sexual recombination within growing areas. Because there was little differentiation among populations in all hierarchical levels, including among growing areas within sampling years, fields within growing areas, and corners within individual fields, a high level of gene flow was revealed in all levels. Basidiospores were likely the main vehicle of gene flow among populations, including short and long distances. Asexual inocula (sclerotia and mycelia) probably overwinter because a few clones were detected over a 2-year period within the same field. A few clones were shared among fields but were not commonly shared among growing areas.

Download Full-text

Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan

Phytopathology ◽

10.1094/phyto-01-19-0031-r ◽

2019 ◽

Vol 109 (10) ◽

pp. 1793-1800 ◽

Cited By ~ 1

Author(s):

Muhammad Rameez Khan ◽

Zia-ur Rehman ◽

Sidra Noreen Nazir ◽

Sangay Tshewang ◽

Suraj Baidya ◽

...

Keyword(s):

Puccinia Striiformis ◽

Gene Diversity ◽

Genotypic Diversity ◽

Himalayan Region ◽

Population Subdivision ◽

Aerial Dispersal ◽

Western Himalayan Region ◽

Nonsignificant Difference ◽

Limited Gene Flow ◽

High Level

The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by FST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Download Full-text

Population Structure Among and Within Iowa, Missouri, Ohio, and South Dakota Populations of Phytophthora sojae

Plant Disease ◽

10.1094/pdis-04-15-0437-re ◽

2016 ◽

Vol 100 (2) ◽

pp. 367-379 ◽

Cited By ~ 12

Author(s):

S. Stewart ◽

A. E. Robertson ◽

D. Wickramasinghe ◽

M. A. Draper ◽

A. Michel ◽

...

Keyword(s):

Gene Flow ◽

South Dakota ◽

Genotypic Diversity ◽

Phytophthora Sojae ◽

Field Variation ◽

Limited Gene Flow ◽

Rps Gene ◽

Pathogen Populations ◽

High Level ◽

Important Disease

Phytophthora root and stem rot, caused by Phytophthora sojae, is an economically important disease of soybean throughout the Midwestern United States. This disease has been successfully managed with resistance (Rps) genes; however, pathogen populations throughout the Midwest have developed virulence to many Rps genes, including those that have not been deployed. To gain a better understanding of the processes that influence P. sojae evolution, the population genetic structure was compared among populations using one isolate collected from 17, 33, and 20 fields in Iowa, Ohio, and South Dakota, respectively, as well as multiple isolates from individual fields in Iowa, Ohio, and Missouri. Genotypic diversity was measured using 21 polymorphic microsatellite (simple-sequence repeat) markers. and pathotype diversity using 15 soybean differentials. For all but three of the populations with low sample size, there was a high level of pathotype diversity and a low to moderate level of genotypic diversity among the populations for both comparisons between states and within-field variation. None of the Rps-gene differentials were resistant to all of the isolates. There were 103 unique multilocus genotypes identified in this study and only 2 were identified from the same field. Although no clones were identified in more than one field, pairwise FST indicated that some gene flow within neighboring fields does occur but not across the region, including fields from neighboring states. These results suggest that there is a strong probability that each state may have their own or several regional populations, as well as provide further evidence of high diversity within this homothallic pathogen which may be due, in part, to limited gene flow, mutation, or outcrossing, and this likely affects the success of deployment of resistance.

Download Full-text

Microsatellite analysis of population structure in the shortfin mako (Isurus oxyrinchus)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f03-064 ◽

2003 ◽

Vol 60 (6) ◽

pp. 670-675 ◽

Cited By ~ 70

Author(s):

Aaron W Schrey ◽

Edward J Heist

Keyword(s):

Population Structure ◽

Microsatellite Analysis ◽

Population Subdivision ◽

Mako Shark ◽

The North ◽

Isurus Oxyrinchus ◽

Shortfin Mako ◽

Weak Evidence ◽

Female Dispersal ◽

High Level

Microsatellite analysis of the shortfin mako shark (Isurus oxyrinchus) revealed very weak evidence of population structure. Samples collected from the North Atlantic, South Atlantic, North Pacific, South Pacific, and Atlantic, and Pacific coasts of South Africa were screened at four microsatellite loci. Multilocus measures of population subdivision were much lower than expected (FST = 0.0014, P = 0.1292; RST = 0.0029, P = 0.019). Power analysis revealed that the study had a high level of power (>0.995) to detect the magnitude of FST expected based on a previous study of mtDNA and assumptions of equal male and female dispersal. Thus, integrating the results from microsatellite- and mitochondrial-based studies may provide evidence for gender-biased dispersal for the shortfin mako.

Download Full-text

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

Parasites & Vectors ◽

10.1186/s13071-021-04924-x ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Antonio Acini Vásquez-Aguilar ◽

Arturo Barbachano-Guerrero ◽

Diego F. Angulo ◽

Víctor Hugo Jarquín-Díaz

Keyword(s):

Population Structure ◽

Gene Flow ◽

Population Expansion ◽

Fixation Index ◽

Hepatozoon Canis ◽

Pairwise Comparisons ◽

Distribution Analysis ◽

Population Genetic Analysis ◽

Molecular Variance ◽

The World

Abstract Background Hepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world. Methods We used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed. Results The dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution). Conclusions The current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite. Graphical abstract

Download Full-text

Seasonal Migration and Genetic Population Structure in House Wrens

The Condor ◽

10.1093/condor/102.3.517 ◽

2000 ◽

Vol 102 (3) ◽

pp. 517-528 ◽

Cited By ~ 4

Author(s):

Nidia Arguedas ◽

Patricia G. Parker

Keyword(s):

Population Structure ◽

Gene Flow ◽

Migratory Birds ◽

Seasonal Migration ◽

Population Subdivision ◽

Migratory Behavior ◽

Genetic Population ◽

Neotropical Migrant ◽

House Wrens ◽

Migrant Birds

Abstract Neotropical migrant birds have undergone significant changes in population size, due in part to alterations in the landscape in their breeding range. Some alterations have resulted in the isolation of areas containing optimal habitat for breeding. Isolation between habitat fragments could reduce gene flow between populations, which might result in loss of genetic variation due to genetic drift. To test whether isolation due to distance between populations may affect migratory birds as much as sedentary birds, we used four microsatellite loci as genetic markers to compare gene flow and population structure in migratory and sedentary House Wrens (Troglodytes aedon and T. musculus, respectively). If migratory behavior enhanced gene flow, we expected to find that populations of migratory birds were genetically more similar than populations of sedentary birds, and that gene flow declined more rapidly with distance in sedentary than in migratory populations. Blood samples were collected from 18–25 migratory House Wrens at each of six sites in Ohio separated by distances from 25 to over 300 km, and from 16–20 sedentary House Wrens at each of six sites in Costa Rica, also at distances up to 350 km. We used heterologous microsatellite primers to obtain estimates for RST (population subdivision) and Nm (number of immigrants per generation) in relation to distance between pairs of populations. In the migratory populations, Mantel permutational tests showed no effect of distance on RST or Nm at distances between 25 and 300 km. In the sedentary birds, RST increased and Nm decreased significantly as distance between populations increased from 25 to 300 km. FST values were not different from those obtained using Slatkin's (1995) RST statistics. These results are consistent with our hypothesis that migratory behavior enhances gene flow.

Download Full-text

Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190329 ◽

2018 ◽

Vol 19 (3) ◽

pp. 978-988 ◽

Cited By ~ 1

Author(s):

MUTIA RAMADHANIATY ◽

ISDRAJAD SETYOBUDIANDI ◽

HAWIS H. MADDUPPA

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Distance ◽

Haplotype Diversity ◽

Fixation Index ◽

Morphological Identification ◽

Marine Bivalve ◽

Geographical Distance ◽

Environmental Complexity ◽

Saccostrea Cucullata

Ramadhaniaty M, Setyobudiandi I, Madduppa HH. 2018. Morphogenetic and population structure of two species marine bivalve (Ostreidae: Saccostrea cucullata and Crassostrea iredalei) in Aceh, Indonesia. Biodiversitas 19: 978-988. Oysters (Family Ostreidae) are mollusks, with high levels of phenotypic plasticity and wide geographic distribution. Oysters are a challenging group for morphological identification and genetic populations study. Saccostrea cucullata and Crassostrea iredalei are oysters from bivalve class that lives in the intertidal area and mangrove ecosystem. To clarify the morphology, genetic diversity and population structure of the two forms of S. cucullata and C. iredalei, we collected and studied oysters from three locations along the coastal region of Aceh by using morphometric method and 16 S mtDNA sequences analysis. We also added more oysters sequences from China, Japan, and Thailand to determine the connectivity between all populations. Morphometric characteristics of the oyster showed a negative allometric growth pattern, which means the rate of length gain is faster than that of the weight gain. The genetic distance from S. cucullata was 0.0030.004 (Fst = 0.708) and C. iredalei was 0.000 (Fst = 0.971). The long genetic distance and high fixation index (Fst) in the oysters population are caused by the close geographical distance of the species in the three populations. The haplotype diversity value from S. cucullata and C. iredalei were 20 and 3, respectively. The haplotype showed the connectivity among the oyster populations which indicated by the gene flow pattern. The gene flow was affected by geographical distance and environmental complexity.

Download Full-text

Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

Russian Journal of Herpetology ◽

10.30906/1026-2296-1997-4-2-102-114 ◽

2011 ◽

Vol 4 (2) ◽

pp. 102-114 ◽

Cited By ~ 2

Author(s):

Evgenyi N. Panov ◽

Larissa Yu. Zykova

Keyword(s):

Population Structure ◽

Gene Flow ◽

Habitat Preference ◽

Additional Data ◽

Near East ◽

Field Studies ◽

Subspecies Level ◽

Limited Gene Flow ◽

Study Sites ◽

And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

Download Full-text

CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

Animal Breeding and Genetics ◽

10.31073/abg.54.17 ◽

2017 ◽

Vol 54 ◽

pp. 134-140

Author(s):

H. S. Rudoman ◽

V. M. Balatsky ◽

V. Y. Nor ◽

V. O. Vovk

Keyword(s):

Genetic Structure ◽

Information Content ◽

Analysis Of Variance ◽

Farm Animals ◽

Daily Weight Gain ◽

Fixation Index ◽

Its Sequencing ◽

Large White ◽

Stage Of Development ◽

High Level

One of the top priorities at the present stage of development of pig breeding remains the development of a set of measures aimed at increasing the resistance animals to various diseases, especially – to colibacteriosis .One of the recent and effective approaches to prevent colibacillosis is using markers of selection; it involves pig genotyping by genome locuses. Chosen locuses are associated with animal sensitivity to the disease and selection of the results of genotyping of animals with increased resistance. Due to researches, one of such locuses is alpha-fukozyltrasferаza 1 gene (FUT1). Gene FUT1 is located in chromosome 6. As a result of its sequencing in the swine breeds of Large White and Swedish Landrace, single-nucleotide polymorphism (g.307 G > A SNP) has been detected. AA genotype determines the resistance of animals to colibacteriosis, while AG and GG genotypes are susceptible to this disease. According to the results of previous studies, the positive effect of allele A was determined not only on the resistance of pigs to colibacteriosis, but also on indicators of fattening and meat productivity and on reproductive performance. In Ukraine, the studies of polymorphism FUT1 g.307 G > A SNP were held fragmentedly and only on certain populations of Ukrainian Meat and Large White breed but without establishing its association with the indicators of productivity of pigs. The aim of our work was to study the genetic structure of Ukrainian Large White breeds, type 1 and the establishment of association. g. 307 G > A SNP FUT1 gene with pigs indicators of productivity. For research the 96 samples of hair were used. DNA isolation from samples with biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by method of Jorgensen et al. (2006). Using DNA analysis of this breeds locus FUT1 was determined by genetic structure. Allele frequency of allele G (0,573) and allele A (0,427) was established The distribution of genotype frequencies was not statistically significantly different from the theoretically expected, calculated by the Hardy-Weinberg criterion. Thus, according to the locus of FUT1 g.307 G > A, the breeds investigated are in a state close to the genetic equilibrium. The negative value of the fixation index by the locus FUT1 g.307 G > A indicates an excess of heterozygotes in the population, and hence the lack of targeted selection for this marker. The valuation was performed by calculating the PIC (polymorphic information content) – information content of polymorphism marker. In the analyzed pig herd for this marker, the PIC has an average value (0,367), which indicates the high level of polymorphism of the given locus and is favorable for the possibility of conducting a search for links between individual genotypes and indicators of productivity. To establish the association g.307 G > A SNP FUT1 gene with indicators of animal productivity, a one-way analysis of variance of the experimental data was used. Based on the results of a one-way analysis of variance, a significant effect of the genotypes of the FUT1gene (g.1849 G > C) on the indicator of the average daily weight gain (р ≤ 0,001), the thickness of the bacon at the level of the VI-VII vertebrae (p ≤ 0.01), reaching live weight of 100 kg (р ≤ 0,001) and breeding index of fattening qualities (р ≤ 0,01) was found. The parameter of the influence of the genetic factor on the test feature was 28,54%, 10,4%, 33,4% and 8,8% respectively. According to the investigated indicators of productivity, animals with genotype AA, which determines resistance to colibacteriosis, dominated the animals with genotypes GG and AG. Based on the results of our research and pre-published data, the multiple effect of the g.307 G > A SNP FUT1 gene is observed, which is associated with the indicators of productivity, which again confirms the polygenicity of the quantitative trait loci of farm animals. Taking into account a high level of polymorphism of the investigated gene and reliable associations of genotypes with indicators of productivity found, it can be recommended to carry out breeding of pigs using genetic information of the g.307 G > A SNP gene FUT1.

Download Full-text

Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

Parasites & Vectors ◽

10.1186/s13071-019-3740-0 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Maysa Tiemi Motoki ◽

Dina Madera Fonseca ◽

Elliott Frederic Miot ◽

Bruna Demari-Silva ◽

Phoutmany Thammavong ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Aedes Albopictus ◽

Isolation By Distance ◽

Genetic Locus ◽

Lao Pdr ◽

Phylogenetic Network ◽

Population Expansion ◽

Recent Population Expansion ◽

The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

Download Full-text

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Grimar Abdiel Perez ◽

Pumipat Tongyoo ◽

Julapark Chunwongse ◽

Hans de Jong ◽

Anucha Wongpraneekul ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Germplasm Collection ◽

Snp Markers ◽

Fixation Index ◽

Breeding Programs ◽

Total Fixation ◽

Unrooted Phylogenetic Tree ◽

Luffa Acutangula ◽

Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

Download Full-text