Molecular Diversity, Haplotype Distribution and Gene Flow of Bipolaris Sorokiniana Fungus Causing Spot Blotch Disease in Different Wheat Growing Zones

2021 ◽  
Author(s):  
Prem Lal Kashyap ◽  
sudheer Kumar ◽  
Anju Sharma ◽  
Ravi Shekhar Kumar ◽  
Sunita Mahapatra ◽  
...  
Keyword(s):  
Gene Flow ◽  
Balancing Selection ◽  
Population Expansion ◽  
Bipolaris Sorokiniana ◽  
Spot Blotch ◽  
Moderate Level ◽  
Common Source ◽  
Source Population ◽  
Internal Transcribed Spacer Region ◽  
Haplotypic Diversity

Abstract Bipolaris sorokiniana (BS) is an economically important fungal pathogen causing spot blotch of wheat (Trtiticum aestivum) and found in all wheat growing zones of India. Very scanty and fragmentary information is available on its genetic diversity. The current research is the first detailed report on the geographic distribution and evolution of BS population in five geographically distinct wheat growing zones [North Western Plain Zone (NWPZ), North Eastern Plain zone (NEPZ); North Hill Zone (NHZ), Southern Hill Zone (SHZ) and Peninsular Zone (PZ)] of India, studied by performing nucleotide sequence comparison of internal transcribed spacer region of 183 isolates. A moderate to high levels of haplotypic diversity was noticed in different wheat growing zones. Phylogenetic analysis suggests that B. sorokiniana exist in two distinct lineages as all isolates under study were grouped in two different clades and found analogous to the findings of haplotypic and median joining network analysis. The genetic parameters revealed the existence of 59 haplotypes with three major haplotypes (H_2, H_3, and H_25) which showed star-like structure network surrounded by several single haplotypes, revealing high frequency of the mutations ((Eta = 2 – 437) in total analyzed population. H_3 was observed as a predominant haplotype and prevalent in all the five zones. Moderate level of genetic differentiation was found between NEPZ and PZ (Fst = 0.563), whereas it was low between NEPZ and NHZ (Fst = -0.062). High level of gene flow was noticed between NWPZ and NEPZ (Nm = 14.32), while it was found minimum between SZ and NHZ (Nm = 0.50). Moreover, negative score of neutrality statistics (Tajima’s D and Fu’s FS test) for NWPZ, PZ and SHZ populations, suggested recent population expansion in these zones. However, positive score for both the neutrality tests observed in NEPZ and NHZ indicated the dominance of balancing selection in structuring their population. Recombination events were observed in the NWPZ, NEPZ and NHZ population, while it was absent in SHZ and PZ population. Thus, the lack of any specific genetic population structure in all the zones indicates for the expansion history only from one common source population i.e. NWPZ, a mega zone of wheat production in India. Overall, it seems that the predominance of individual haplotypes with a moderate level of genetic variation and men mediated movement of contaminated seed and dispersal of inoculum, mutations and recombination as prime evolutionary processes play essential role in defining the genetic structure of BS population.

scholarly journals Molecular Diversity and Evolutionary Processes of Alternaria solani in Brazil Inferred Using Genealogical and Coalescent Approaches

2009 ◽  
Vol 99 (6) ◽  
pp. 765-774 ◽  
Author(s):  
Valdir Lourenço ◽  
Andrés Moya ◽  
Fernando González-Candelas ◽  
Ignazio Carbone ◽  
Luiz A. Maffia ◽  
...  
Keyword(s):  
Gene Flow ◽  
Nucleotide Diversity ◽  
Early Blight ◽  
Balancing Selection ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Alternaria Solani ◽  
Interesting Case ◽  
Evolutionary Processes ◽  
Tomato Plants

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

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

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.

scholarly journals First report of Bipolaris sorokiniana causing spot blotch of lentil in Algeria

2021 ◽  
Vol 43 (2) ◽  
Author(s):  
M. El Amine Kouadri ◽  
A. Amine Bekkar ◽  
S. Zaim
Keyword(s):  
Bipolaris Sorokiniana ◽  
Spot Blotch ◽  
First Report

Characterization of elite bread wheat (Triticum aestivum L.) germplasm for spot blotch Bipolaris sorokiniana (Sacc.) Shoemaker resistance

2021 ◽  
pp. 1-8
Author(s):  
Deep Shikha ◽  
Chandani Latwal ◽  
Elangbam Premabati Devi ◽  
Anupama Singh ◽  
Pawan K. Singh ◽  
...  
Keyword(s):  
Abiotic Stress Tolerance ◽  
Bipolaris Sorokiniana ◽  
Triticum Aestivum L ◽  
Spot Blotch ◽  
Biotic And Abiotic Stress ◽  
Wheat Varieties ◽  
Effective Measure ◽  
Breeding Lines ◽  
Elite Breeding Lines ◽  
Germplasm Accessions

Abstract Genetic resources are of paramount importance for developing improved crop varieties, particularly for biotic and abiotic stress tolerance. Spot blotch (SB) is a destructive foliar disease of wheat prevalent in warm and humid regions of the world, especially in the eastern parts of South Asia. For the management of this disease, the most effective measure is the development of resistant cultivars. Thus, the present investigation was carried out to confirm SB resistance in 200 germplasm accessions based on phenotypic observations and molecular characterization. These elite breeding lines obtained from the International Centre for Maize and Wheat Improvement, Mexico, are developed deploying multiple parentages. These lines were screened for SB resistance in the field under artificially created epiphytotic conditions during 2014–15 and 2015–16 along with two susceptible checks (CIANO T79 and Sonalika) and two resistant checks (Chirya 3 and Francolin). Eighty-two out of 200 germplasm accessions were found resistant to SB and resistance in these lines was confirmed with a specific SSR marker Xgwm148. Three accessions, VORONA/CNO79, KAUZ*3//DOVE/BUC and JUP/BJY//URES/3/HD2206/HORK//BUC/BUL were observed possessing better resistance than the well-known SB-resistant genotype Chirya3. These newly identified resistant lines could be used by wheat breeders for developing SB-resistant wheat varieties.

scholarly journals Molecular Mapping of Loci Conferring Susceptibility to Spot Blotch and Resistance to Powdery Mildew in Barley Using the Sequencing-Based Genotyping Approach

2020 ◽  
Vol 110 (2) ◽  
pp. 440-446 ◽  
Author(s):  
Yueqiang Leng ◽  
Mingxia Zhao ◽  
Jason Fiedler ◽  
Antonín Dreiseitl ◽  
Shiaoman Chao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Molecular Mapping ◽  
Recombinant Inbred Lines ◽  
Major Gene ◽  
Bipolaris Sorokiniana ◽  
Spot Blotch ◽  
Blumeria Graminis ◽  
Seedling Stage ◽  
Barley Cultivars ◽  
Trait Locus

Spot blotch (SB) caused by Bipolaris sorokiniana and powdery mildew (PM) caused by Blumeria graminis f. sp. hordei are two important diseases of barley. To map genetic loci controlling susceptibility and resistance to these diseases, a mapping population consisting of 138 recombinant inbred lines (RILs) was developed from the cross between Bowman and ND5883. A genetic map was constructed for the population with 852 unique single nucleotide polymorphism markers generated by sequencing-based genotyping. Bowman and ND5883 showed distinct infection responses at the seedling stage to two isolates (ND90Pr and ND85F) of Bipolaris sorokiniana and one isolate (Race I) of Blumeria graminis f. sp. hordei. Genetic analysis of the RILs revealed that one major gene (Scs6) controls susceptibility to Bipolaris sorokiniana isolate ND90Pr, and another major gene (Mla8) confers resistance to Blumeria graminis f. sp. hordei isolate Race I, respectively. Scs6 was mapped on chromosome 1H of Bowman, as previously reported. Mla8 was also mapped to the short arm of 1H, which was tightly linked but not allelic to the Rcs6/Scs6 locus. Quantitative trait locus (QTL) analysis identified two QTLs, QSbs-1H-P1 and QSbs-7H-P1, responsible for susceptibility to spot blotch caused by Bipolaris sorokiniana isolate ND85F in ND5883, which are located on chromosome 1H and 7H, respectively. QSbs-7H-P1 was mapped to the same region as Rcs5, whereas QSbs-1H-P1 may represent a novel allele conferring seedling stage susceptibility to isolate ND85F. Identification and molecular mapping of the loci for SB susceptibility and PM resistance will facilitate development of barley cultivars with resistance to the diseases.

scholarly journals The best of both worlds: Shortcutting evolution through adaptive hybridization in hares

2021 ◽  
Author(s):  
Jaakko L.O. Pohjoismäki ◽  
Craig Michell ◽  
Riikka Levänen ◽  
Steve Smith
Keyword(s):  
Gene Flow ◽  
Balancing Selection ◽  
Uncoupling Protein ◽  
Lepus Europaeus ◽  
Genetic Introgression ◽  
The Novel ◽  
Mountain Hare ◽  
Uncoupling Protein 1 ◽  
Expansion Load ◽  
Candidate Loci

Abstract Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), is likely of adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can ease its expansion load through hybridization and obtain beneficial alleles to shortcut evolutionary adaptation to the novel environmental conditions.

scholarly journals First Report of Spot Blotch Caused by Bipolaris sorokiniana on Winter Rye in Kentucky

Plant Disease ◽  
2021 ◽  
Author(s):  
Danilo Neves ◽  
Bill Bruening ◽  
Carrie A Knott ◽  
Chad Lee ◽  
Carl Bradley
Keyword(s):  
Flag Leaf ◽  
Morphological Characteristics ◽  
Bipolaris Sorokiniana ◽  
Spot Blotch ◽  
Winter Rye ◽  
Glycerol Solution ◽  
Conidial Suspension ◽  
Potential Yield ◽  
First Report ◽  
Plastic Bag

The Kentucky distilling industry ranks as one of the state’s largest industries and continues to expand. In 2017, the Kentucky distilling industry was responsible for approximately $235 million in state and local tax revenues (Coomes and Kornstein, 2019). Rye (Secale cereale L.) grains are a vital component for production of some distilled spirits. Although winter rye is produced on relatively few hectares in Kentucky currently, a recent initiative has supported expanding production to help meet the growing demand of local distilleries. University of Kentucky winter rye research field trials were visited in Caldwell and Logan Counties, KY in May 2018, and in Fayette County, KY in May 2019. Leaves were collected that had dark brown, oval to irregular-shaped lesions with definite margins and yellow halos. Symptoms were present on approximately 50% to 80% of the flag leaves, with severity ranging from 5% to 30% of the flag leaf area affected. Leaves were surface-disinfested by soaking in a 2% NaOCl solution for 1 min and rinsed twice in sterilized water and then placed in a humidity chamber (plastic bag with moist paper towels) at room temperature (approximately 24°C) to induce fungal sporulation. Seventeen single-spore isolates were obtained and stored at -80°C in 15% glycerol solution. Isolates were grown on potato dextrose agar under 12 h cycles of white light/darkness for 5 days. Colonies were gray to black. Conidia that formed were mostly straight or slightly curved, dark olivaceous brown, 3-7 septate, and 41.0-90.4 × 15.2-29.3 µm. Based on the symptoms observed on the collected leaves and these morphological characteristics similar to those described by Chang and Hwang (2000) and Manamgoda et al. (2014), the fungus was tentatively identified as Bipolaris sorokiniana (Sorokin) Shoemaker. The sequence of internal transcribed spacer regions (ITS) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were used to identify three isolates (18Bs004, 18Bs111 and 19Bs064) using primer ITS1/ITS4 (White et al. 1990) and GPD1/GPD2 (Berbee et al. 1999), respectively. The sequences were deposited in GenBank with accession numbers MT457817, MT457818 and MZ066635 for ITS sequences and MZ073644 to MZ073646 for GAPDH sequences. BLAST searches with ITS and GAPDH sequences matched 100% identity (344/344 bp and 515/515 bp for ITS and GAPDH sequences, respectively) to B. sorokiniana (GenBank accession No. MT254731 and MH844813, respectively). To prove pathogenicity, a conidial suspension (1 × 105 conidia/ml) was used to inoculate 15-day-old cultivar ‘Serafino’ winter rye plants in the greenhouse. Leaves of 8 plants were inoculated with 50 ml of the conidial suspension using a spray bottle. Plants were covered with a transparent plastic bag for 48 h, and symptoms were observed 10 days after inoculation. Leaf lesions, similar to those described above, were present on all inoculated plants, but no symptoms were observed on non-inoculated control plants. Bipolaris sorokiniana was reisolated from symptomatic leaves and the identity of the pathogen was confirmed based on the morphology previously described. To our knowledge, this is the first report of spot blotch caused by B. sorokiniana on winter rye in Kentucky, but B. sorokiniana has been reported on rye in the neighboring state of Virginia (Roane 2009). Kentucky produces approximately 150,000 and 4,000 ha of winter wheat (Triticum aestivum) and winter barley (Hordeum vulgare) annually, respectively, which are both known hosts of B. sorokiniana (Kumar et al. 2002). An isolate of B. sorokiniana from rye was reported by Ghazvini and Tekauz (2007) to be less virulent on barley differential lines. Further research is needed to better understand spot blotch distribution, susceptibility in winter rye cultivars, and potential yield and quality loss implications in winter rye production and end use. It is unknown how susceptible various winter rye cultivars grown in Kentucky are to spot blotch.

scholarly journals Population genomics of the emerging forest pathogen Neonectria neomacrospora

2020 ◽  
Author(s):  
Knud Nor Nielsen ◽  
Shyam Gopalakrishnan ◽  
Thorfinn Sand Korneliussen ◽  
Mikkel Skovrind ◽  
Kimmo Sirén ◽  
...  
Keyword(s):  
Population Genomics ◽  
Population Expansion ◽  
European Population ◽  
Ice Age ◽  
Source Population ◽  
Forest Pathogen ◽  
Comprehensive Collection ◽  
American Source ◽  
Last Ice Age ◽  
Ornamental Trees

ABSTRACTThe fungal pathogen Neonectria neomacrospora is of increasing concern in Europe where, within the last decade, it has caused substantial damage to forest stands and ornamental trees of the genus Abies (Mill.). Using whole-genome sequencing of a comprehensive collection of isolates, we show the extent of three major clades within N. neomacrospora, which most likely diverged around the end of the last Ice Age. We find it likely that the current European epidemic of N. neomacrospora was founded from a population belonging to the east North American clade. All European isolates (1957-2019) had a common evolutionary history, but substantial and asymmetrical gene flow from the larger American source population could be detected. The European population shows multiple signs of having gone through a bottleneck and subsequent population expansion.

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