Virulence Spectrum of Phytophthora infestans and Spatial Distribution of Physiological Races in Northwestern Ethiopia

አህፅሮትድንች ለምግብና ለአመጋግብ ዘዴ ዋስትና በተለይም የምግብ ዋስትና ችግር ባለበት አካባቢ ዋነኛ ምግብ ነው፡፡ ምንም እንኳን ድንች ከፍተኛ ጠቀሜታ ያለው ቢሆንም ፋይቶፍቶራ ኢንፌስታንስ በሚባል ተዋስያን አማካኝነት የሚከሰተው የድንች ምች በሽታ ከፍተኛ ጉዳት በማድረስ ለድንች ማምረት ትልቅ  ማነቆ ነው፡፡ ጥናቱ በሰሜን ምዕራብ ኢትዮጵያ ዋና ዋና የድንች አብቃይ በሆኑ አካባቢዎች ላይ የፋይቶፍቶራ ኢንፌስታንስ በሽታ አምጭ የዝርያ ዓይነቶችን እና ስርጭታቸውን ለመለየት በ2018 የተካሄደ ነው፡፡ በአጠቃላይ 74  ናሙናዎች ተሰብስበው በድንች ቁርጥራጮች ላይ በማባዛት በብላክስ በሽታ ተቋቋሚ የድንች ዘረመሎች ላይ በሽታ አምጭነታቸው ተገምግሟል፡፡ ናሙናዎቹ በሽታውን በሚቋቋሙ ዘረመሎች ላይ ተሞክረው በአሳዩት አፀፋዊ መልስ መሠረት 6፣ 11 እና 16 የተለያዩ ዓይነት በሽታ አምጭ ዝርያዎች በአዊ፣ በደቡብ ጎንደር እና በምዕራብ ጎጃም በቅደም ተከል መሠረት እንደሚገኙ አሳይቷል፡፡ የሻኖን የአይነት ብዛት መለኪያ ውጤት ለሁሉም ናሙናዎች በአጠቃላይ 0.8 ሲሆን ለአዊ፣ ለደቡብ ጎንደር እና ምዕራብ ጎጃም ዞኖች ለየራሳቸው ደግሞ 0.75፣ 0.84 እና 0.92 በቅደም ተከተላቸው መሠረት ነው፡፡ በአጠቃላይ 74ቱም ናሙናዎች የሦስቱም ዞኖች ፑል ተደርገው ሲታይ 27 የተለያዩ ዓይነት በሽታ አምጭ ዝርያዎች እንዳሉ ተለይተዋል፡፡ ምንም አይነት የዝርያ ውስብስብነት የሌለው ናሙና በደቡብ ጎንደር እና ምዕራብ ጎጃም ዞኖች የተገኘ ቢሆንም ከፍተኛ የዝርያ ውስብስብነት 10 የበሽታ አምጭነት ነገር ያላው ዝርያ በደቡብ ጎንደር ተገኝቷል፡፡ በሽታውን ከሚቋቋሙ ዘረመሎች ውስጥ R3, R5, R8 እና R9 አጠቃላይ ከታየው ልዩነት ከፍተኛ አስተዋፅኦ ያበረከቱ ሲሆን R9 እና R5 በጣም ውጤታማ የነበሩ 95% እና 92%  የሚሆኑትን ናሙናዎች በቅደም ተከተል መቋቋም የቻሉ ዘረመሎች ናቸው፡፡ በጠቅላላው ዋና ተቋቋሚ ዘረመል የያዙ የድንች ዝርያዎችን በመጠቀም በሽታውን መከላከል አዳጋች ነው፡፡ ምክንያቱም ሁሉንም ናሙናዎች መቋቋም የቻለ ዘረመል ባለመኖሩ እና ውስብስብ በሽታ አምጭ የዝርያ ዓይነቶች በአካባቢው ተሰራጭተው ስለሚገኙ፡፡  AbstractDespite the importance of potato the late blight disease, caused by the oomycete Phytophthora infestans is most destructive disease for potato production. The study was conducted to identify virulent races and spatial distribution of Phytophthora infestans populations in major potato growing areas of northwestern Ethiopia in 2018. Seventy-four isolates (samples) were collected and multiplied on potato tuber slices and virulence was assessed on Black’s potato differentials. Isolates reaction to differentials revealed 6, 11, and 16 race types at Awi, South Gondar and West Gojam, respectively. Shannon diversity index was 0.80 for the entire isolates but it was 0.75, 0.84 and 0.92 for isolates collected from Awi, South Gondar and West Gojam, respectively. Tewnty-seven physiological races were detected in the pooled population when the 74 isolates from the three populations were combined. Absence of race complexity was found in isolates of South Gondar and West Gojam while the highest race complexity with virulence factors of 10 was found in South Gondar. Differentials, R3, R5, R8, and R9 had larger contribution to the total variability of isolates and R9 and R5 genes were most effective withstood 95% and 92% of isolates. It is concluded that potato varieties resistant to major genes are hardly possible to be used as disease management option due to the absence of R genes resistant to all isolates, the complexity, and distribution of races in the region

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

BACKGROUND: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. RESULTS: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. CONCLUSIONS: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes

Tuber shape and eye depth variation in a diploid family of Andean potatoes.

BACKGROUND: Tuber appearance is highly variable in the Andean cultivated potato germplasm. The diploid backcross mapping population ‘DMDD’ derived from the recently sequenced genome ‘DM’ represents a sample of the allelic variation for tuber shape and eye depth present in the Andean landraces. Here we evaluate the utility of morphological descriptors for tuber shape for identification of genetic loci responsible for the shape and eye depth variation. RESULTS: Subjective morphological descriptors and objective tuber length and width measurements were used for assessment of variation in tuber shape and eye depth. Phenotypic data obtained from three trials and male–female based genetic maps were used for quantitative trait locus (QTL) identification. Seven morphological tuber shapes were identified within the population. A continuous distribution of phenotypes was found using the ratio of tuber length to tuber width and a QTL was identified in the paternal map on chromosome 10. Using toPt-437059, the marker at the peak of this QTL, the seven tuber shapes were classified into two groups: cylindrical and non-cylindrical. In the first group, shapes classified as ‘compressed’, ‘round’, ‘oblong’, and ‘long-oblong’ mainly carried a marker allele originating from the male parent. The tubers in this group had deeper eyes, for which a strong QTL was found at the same location on chromosome 10 of the paternal map. The non-cylindrical tubers classified as ‘obovoid’, ‘elliptic’, and ‘elongated’ were in the second group, mostly lacking the marker allele originating from the male parent. The main QTL for shape and eye depth were located in the same genomic region as the previously mapped dominant genes for round tuber shape and eye depth. A number of candidate genes underlying the significant QTL markers for tuber shape and eye depth were identified. CONCLUSIONS: Utilization of a molecular marker at the shape and eye depth QTL enabled the reclassification of the variation in general tuber shape to two main groups. Quantitative measurement of the length and width at different parts of the tuber is recommended to accompany the morphological descriptor classification to correctly capture the shape variation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0213-0) contains supplementary material, which is available to authorized users

The Top 10 oomycete pathogens in molecular plant pathology

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.Keywords: microbiology, diversity, genomics, oomycetes plant patholog

Diversity, Pathogenicity, and Current Occurrence of Bacterial Wilt Bacterium Ralstonia solanacearum in Peru

The current bacterial wilt infestation level in the potato fields in the Peruvian Andes was investigated by collecting stem samples from wilted plants and detecting Ralstonia solanacearum. In total 39 farmers’ fields located in the central and northern Peru between the altitudes 2111 and 3742 m above sea level were sampled. R. solanacearum was detected in 19 fields, and in 153 out of the 358 samples analyzed. Phylogenetic analysis using the partial sequence of the endoglucanase gene on strains collected in Peru between 1966 and 2016 from potato, pepper, tomato, plantain or soil, divided the strains in phylotypes I, IIA, and IIB. The Phylotype IIB isolates formed seven sequevar groups including the previously identified sequevars 1, 2, 3, 4, and 25. In addition to this, three new sequevars of phylotype IIB were identified. Phylotype IIA isolates from Peru clustered together with reference strains previously assigned to sequevars 5, 39, 41, and 50, and additionally one new sequevar was identified. The Phylotype I strain was similar to the sequevar 18. Most of the Peruvian R. solanacearum isolates were IIB-1 strains. In the old collection sampled between 1966 and 2013, 72% were IIB-1 and in the new collection at 2016 no other strains were found. The pathogenicity of 25 isolates representing the IIA and IIB sequevar groups was tested on potato, tomato, eggplant and tobacco. All were highly aggressive on potato, but differed in pathogenicity on the other hosts, especially on tobacco. All IIA strains caused latent infection on tobacco and some strains also caused wilting, while IIB strains caused only few latent infections on this species. In conclusion, high molecular diversity was found among the R. solanacearum strains in Peru. Most of the variability was found in areas that are no longer used for potato cultivation and thus these strains do not pose a real threat for potato production in the country. Compared to the previous data from the 1990s, the incidence of bacterial wilt has decreased in Peru. The epidemics are likely caused by infected seed tubers carrying the clonal brown rot strain IIB-1

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