Kevin M. King, Leo Barr, Louise Bousquet, Anna Glaab, Gail Canning, Faye Ritchie, Steven Kildea, Bart A. Fraaije, Jonathan S. West
Plenodomus lingam (Leptosphaeria maculans) and P. biglobosus (L. biglobosa) are fungi causing Phoma leaf spot/stem canker, an international damaging disease of oilseed rape (Brassica napus) and other brassicas. In Europe, fungicides used for disease management are mainly sterol 14α‐demethylase (CYP51) inhibitors (DMIs/azoles); quinone‐outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs) are also used. Decreased DMI sensitivity has emerged in Australian and eastern European P. lingam populations and is mediated by CYP51 promoter inserts resulting in target site overexpression. In this study using in vitro sensitivity testing, we report decreased DMI (prothioconazole‐desthio, mefentrifluconazole) sensitivity in modern western European P. lingam isolates (collected 2022–2023) compared to older baseline (1992–2005) isolates. Around 85% of modern western European P. lingam isolates collected, for which the CYP51 promoter region was sequenced, carried a promoter insert, but target site alterations were not detected. Six different CYP51 promoter inserts were identified, most commonly a 237 bp fragment of the Sahana transposable element. Inserts were associated with an approximately 3‐ to 10‐fold decrease in sensitivity to the DMIs tested. In contrast to P. lingam, PCR screening revealed CYP51 promoter inserts were absent in modern western European P. biglobosus isolates (2021–2023). Combined data indicate P. lingam isolates lacking an insert were similarly (or slightly more) sensitive to the DMIs tested for P. biglobosus, whereas those carrying an insert were slightly less sensitive than P. biglobosus. No evidence for substantive sensitivity shifts to the QoI (pyraclostrobin) or SDHI (boscalid) fungicides tested was obtained for either Plenodomus species.
Plenodomus lingam（Leptosphaeria maculans）和 P. biglobosus（L. biglobosa）是引起 Phoma 叶斑病/茎腐病的真菌，这是一种危害油菜（Brassica napus）和其他黄铜类作物的国际性病害。在欧洲，用于病害防治的杀菌剂主要是甾醇 14α-脱甲基酶（CYP51）抑制剂（DMIs/唑类）；此外还使用醌外抑制剂（QoIs）和琥珀酸脱氢酶抑制剂（SDHIs）。澳大利亚和东欧的林蛙种群对 DMI 的敏感性降低，其原因是 CYP51 启动子插入导致靶位点过度表达。在这项使用体外敏感性测试的研究中，我们报告了与较早的基线（1992-2005 年）分离物相比，现代西欧肺孢子虫分离物（收集于 2022-2023 年）对 DMI（丙硫菌唑-脱硫菌唑、甲氰氟唑）的敏感性降低。在对 CYP51 启动子区域进行测序后，收集到的现代西欧越橘分离物中约有 85% 带有启动子插入物，但未检测到目标位点的改变。共鉴定出 6 个不同的 CYP51 启动子插入片段，最常见的是 Sahana 转座元件的 237 bp 片段。插入物与对所测试的 DMIs 的敏感性降低约 3 到 10 倍有关。与 P. lingam 相反，PCR 筛选发现现代西欧 P. biglobosus 分离物（2021-2023 年）中不存在 CYP51 启动子插入。综合数据表明，缺乏启动子插入物的 P. lingam 分离物对大环孢霉属 DMIs 的敏感性与大环孢霉属相似（或略高），而携带启动子插入物的 P. lingam 分离物的敏感性略低于大环孢霉属。没有证据表明 Plenodomus 物种对 QoI（吡唑醚菌酯）或 SDHI（啶酰菌胺）杀菌剂的敏感性发生了实质性变化。
{"title":"Evolution of decreased sensitivity to azole fungicides in western European populations of Plenodomus lingam (Phoma stem canker on oilseed rape)","authors":"Kevin M. King, Leo Barr, Louise Bousquet, Anna Glaab, Gail Canning, Faye Ritchie, Steven Kildea, Bart A. Fraaije, Jonathan S. West","doi":"10.1111/ppa.13897","DOIUrl":"https://doi.org/10.1111/ppa.13897","url":null,"abstract":"<jats:italic>Plenodomus lingam</jats:italic> (<jats:italic>Leptosphaeria maculans</jats:italic>) and <jats:italic>P. biglobosus</jats:italic> (<jats:italic>L. biglobosa</jats:italic>) are fungi causing Phoma leaf spot/stem canker, an international damaging disease of oilseed rape (<jats:italic>Brassica napus</jats:italic>) and other brassicas. In Europe, fungicides used for disease management are mainly sterol 14α‐demethylase (<jats:italic>CYP51</jats:italic>) inhibitors (DMIs/azoles); quinone‐outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs) are also used. Decreased DMI sensitivity has emerged in Australian and eastern European <jats:italic>P. lingam</jats:italic> populations and is mediated by <jats:italic>CYP51</jats:italic> promoter inserts resulting in target site overexpression. In this study using in vitro sensitivity testing, we report decreased DMI (prothioconazole‐desthio, mefentrifluconazole) sensitivity in modern western European <jats:italic>P. lingam</jats:italic> isolates (collected 2022–2023) compared to older baseline (1992–2005) isolates. Around 85% of modern western European <jats:italic>P. lingam</jats:italic> isolates collected, for which the <jats:italic>CYP51</jats:italic> promoter region was sequenced, carried a promoter insert, but target site alterations were not detected. Six different <jats:italic>CYP51</jats:italic> promoter inserts were identified, most commonly a 237 bp fragment of the <jats:italic>Sahana</jats:italic> transposable element. Inserts were associated with an approximately 3‐ to 10‐fold decrease in sensitivity to the DMIs tested. In contrast to <jats:italic>P. lingam</jats:italic>, PCR screening revealed <jats:italic>CYP51</jats:italic> promoter inserts were absent in modern western European <jats:italic>P. biglobosus</jats:italic> isolates (2021–2023). Combined data indicate <jats:italic>P. lingam</jats:italic> isolates lacking an insert were similarly (or slightly more) sensitive to the DMIs tested for <jats:italic>P. biglobosus</jats:italic>, whereas those carrying an insert were slightly less sensitive than <jats:italic>P. biglobosus</jats:italic>. No evidence for substantive sensitivity shifts to the QoI (pyraclostrobin) or SDHI (boscalid) fungicides tested was obtained for either <jats:italic>Plenodomus</jats:italic> species.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"59 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140312688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jack L. Scanlan, Alexander Idnurm, Angela P. Van de Wouw
Fungicide resistance is often conferred through the mutation of genes encoding fungicide targets or proteins that remove fungicides from cells, but mechanisms can vary widely between taxa. Discovering the specific resistance alleles present in pathogen populations is essential for monitoring the evolution and movement of resistant genotypes. In this study, we explored the genomic basis of demethylase inhibitor (DMI) resistance in Leptosphaeria maculans, the main pathogen of the canola crop Brassica napus. Using an international collection of over 200 genome‐sequenced isolates, we assayed in vitro sensitivity to the DMI tebuconazole and conducted a genome‐wide association study on a variant set including single‐nucleotide polymorphisms (SNPs), small indels and structural variants. The main resistance allele identified was a 237 bp remnant transposable element insertion in the promoter of the erg11/CYP51 DMI target gene in a large proportion of isolates from Europe, an allele known to confer DMI resistance in Australia. Several associated loci were identified, none of which are commonly linked to DMI resistance in other phytopathogens. We also found little to no relationship between DMI tolerance and baseline growth rate, suggesting minimal fitness effects of fungicide resistance in these isolates. This study indicates common DMI resistance alleles in L. maculans are shared across continents and erg11/CYP51 coding mutations, which are near‐ubiquitous in other fungal pathogens, may not underpin DMI resistance in this species. Furthermore, that resistance occurs frequently in numerous canola‐growing regions suggests management is essential for growers.
{"title":"Genome‐wide mapping in an international isolate collection identifies a transcontinental erg11/CYP51 promoter insertion associated with fungicide resistance in Leptosphaeria maculans","authors":"Jack L. Scanlan, Alexander Idnurm, Angela P. Van de Wouw","doi":"10.1111/ppa.13898","DOIUrl":"https://doi.org/10.1111/ppa.13898","url":null,"abstract":"Fungicide resistance is often conferred through the mutation of genes encoding fungicide targets or proteins that remove fungicides from cells, but mechanisms can vary widely between taxa. Discovering the specific resistance alleles present in pathogen populations is essential for monitoring the evolution and movement of resistant genotypes. In this study, we explored the genomic basis of demethylase inhibitor (DMI) resistance in <jats:italic>Leptosphaeria maculans</jats:italic>, the main pathogen of the canola crop <jats:italic>Brassica napus</jats:italic>. Using an international collection of over 200 genome‐sequenced isolates, we assayed in vitro sensitivity to the DMI tebuconazole and conducted a genome‐wide association study on a variant set including single‐nucleotide polymorphisms (SNPs), small indels and structural variants. The main resistance allele identified was a 237 bp remnant transposable element insertion in the promoter of the <jats:italic>erg11</jats:italic>/<jats:italic>CYP51</jats:italic> DMI target gene in a large proportion of isolates from Europe, an allele known to confer DMI resistance in Australia. Several associated loci were identified, none of which are commonly linked to DMI resistance in other phytopathogens. We also found little to no relationship between DMI tolerance and baseline growth rate, suggesting minimal fitness effects of fungicide resistance in these isolates. This study indicates common DMI resistance alleles in <jats:italic>L</jats:italic>. <jats:italic>maculans</jats:italic> are shared across continents and <jats:italic>erg11</jats:italic>/<jats:italic>CYP51</jats:italic> coding mutations, which are near‐ubiquitous in other fungal pathogens, may not underpin DMI resistance in this species. Furthermore, that resistance occurs frequently in numerous canola‐growing regions suggests management is essential for growers.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"14 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140316839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Idesia polycarpa is a woody oil plant with great development and application prospects. However, stem canker disease of I. polycarpa was frequently observed in Henan and Hubei provinces of China in 2020–2022. The seriousness of the disease caused a large number of trees deaths, which affected seedling production and fruit yield, restricting the development of the I. polycarpa industry. We performed isolation, purification and pathogenicity analysis of canker samples. Pathogenicity tests reproduced typical canker disease symptoms on detached branches of I. polycarpa. Based on morphological observations, conidial morphology and phylogenetic analysis of isolates with high similarity to the rDNA internal transcribed spacer (ITS), EF‐1α and TUB2 sequences screened in GenBank by BLAST, the pathogen of canker disease on I. polycarpa was identified as Botryosphaeria dothidea. This is the first report of B. dothidea as the pathogen of stem canker of I. polycarpa.
鸢尾是一种木本油料植物，具有广阔的开发和应用前景。然而，2020-2022 年，中国河南、湖北等省频繁发生油桐茎腐病。该病严重时造成大量苗木死亡，影响了苗木产量和果实产量，制约了鸢尾产业的发展。我们对腐烂病样本进行了分离、纯化和致病性分析。致病性试验再现了 I. polycarpa 分离枝条上典型的腐烂病症状。根据形态观察、分生孢子形态以及与 BLAST 在 GenBank 中筛选到的 rDNA 内部转录间隔序列（ITS）、EF-1α 和 TUB2 序列高度相似的分离物的系统进化分析，确定 I. polycarpa 腐烂病的病原体为 Botryosphaeria dothidea。这是首次报道 B. dothidea 是 I. polycarpa 茎腐烂病的病原体。
{"title":"Botryosphaeria dothidea causes stem canker of Idesia polycarpa in China","authors":"Lisha Fang, Tianjiao Zheng, Jian Feng, Wenyan Zhi, Yanmei Wang, Zhi Li, Qifei Cai, Xiaodong Geng, Zhen Liu","doi":"10.1111/ppa.13895","DOIUrl":"https://doi.org/10.1111/ppa.13895","url":null,"abstract":"<jats:italic>Idesia polycarpa</jats:italic> is a woody oil plant with great development and application prospects. However, stem canker disease of <jats:italic>I. polycarpa</jats:italic> was frequently observed in Henan and Hubei provinces of China in 2020–2022. The seriousness of the disease caused a large number of trees deaths, which affected seedling production and fruit yield, restricting the development of the <jats:italic>I</jats:italic>. <jats:italic>polycarpa</jats:italic> industry. We performed isolation, purification and pathogenicity analysis of canker samples. Pathogenicity tests reproduced typical canker disease symptoms on detached branches of <jats:italic>I</jats:italic>. <jats:italic>polycarpa</jats:italic>. Based on morphological observations, conidial morphology and phylogenetic analysis of isolates with high similarity to the rDNA internal transcribed spacer (ITS), <jats:italic>EF‐1α</jats:italic> and <jats:italic>TUB2</jats:italic> sequences screened in GenBank by BLAST, the pathogen of canker disease on <jats:italic>I</jats:italic>. <jats:italic>polycarpa</jats:italic> was identified as <jats:italic>Botryosphaeria dothidea</jats:italic>. This is the first report of <jats:italic>B</jats:italic>. <jats:italic>dothidea</jats:italic> as the pathogen of stem canker of <jats:italic>I</jats:italic>. <jats:italic>polycarpa</jats:italic>.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"48 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140200057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Downy mildew caused by Sclerospora graminicola is a systemic disease that affects the yield and quality of foxtail millet. This obligate biotrophic oomycete manipulates host physiology and immune processes through numerous effectors. A thorough comprehension of effector biology is crucial to unravel disease mechanisms and understand host plant resistance. In this study, bioinformatic analyses revealed 498 potentially secreted proteins in S. graminicola, of which 62 were identified as RXLR effectors; 46 RXLR‐encoding genes exhibited upregulated expression during the early stages of infection. To elucidate the functions of these secreted proteins, a heterogeneous expression system was developed using Nicotiana benthamiana. Twenty‐one RXLR effectors secreted by S. graminicola were transiently expressed in N. benthamiana, of which four could suppress INF1‐triggered cell death. Various defence responses in N. benthamiana were attenuated, including inhibition of defence gene expression, reduction of reactive oxygen species (ROS) accumulation and diminished callose deposition. The expression of SG_RXLR41 also enhanced the growth of Phytophthora capsici on N. benthamiana leaves. These findings indicate that S. graminicola facilitates infection and expansion through the secretion of multiple RXLR effectors, and SG_RXLR41 is an important virulence‐related effector that is involved in manipulating plant immunity by suppressing cell death.
{"title":"Identification of candidate RXLR effectors from downy mildew of foxtail millet pathogen Sclerospora graminicola and functional analysis of SG_RXLR41","authors":"Nuo Zhang, Zhixian Ren, Jinye Wang, Linjie Nan, Yurong Sun, Baojun Zhang, Jichun Jia","doi":"10.1111/ppa.13899","DOIUrl":"https://doi.org/10.1111/ppa.13899","url":null,"abstract":"Downy mildew caused by <jats:italic>Sclerospora graminicola</jats:italic> is a systemic disease that affects the yield and quality of foxtail millet. This obligate biotrophic oomycete manipulates host physiology and immune processes through numerous effectors. A thorough comprehension of effector biology is crucial to unravel disease mechanisms and understand host plant resistance. In this study, bioinformatic analyses revealed 498 potentially secreted proteins in <jats:italic>S</jats:italic>. <jats:italic>graminicola</jats:italic>, of which 62 were identified as RXLR effectors; 46 RXLR‐encoding genes exhibited upregulated expression during the early stages of infection. To elucidate the functions of these secreted proteins, a heterogeneous expression system was developed using <jats:italic>Nicotiana benthamiana</jats:italic>. Twenty‐one RXLR effectors secreted by <jats:italic>S</jats:italic>. <jats:italic>graminicola</jats:italic> were transiently expressed in <jats:italic>N</jats:italic>. <jats:italic>benthamiana</jats:italic>, of which four could suppress INF1‐triggered cell death. Various defence responses in <jats:italic>N</jats:italic>. <jats:italic>benthamiana</jats:italic> were attenuated, including inhibition of defence gene expression, reduction of reactive oxygen species (ROS) accumulation and diminished callose deposition. The expression of SG_RXLR41 also enhanced the growth of <jats:italic>Phytophthora capsici</jats:italic> on <jats:italic>N</jats:italic>. <jats:italic>benthamiana</jats:italic> leaves. These findings indicate that <jats:italic>S</jats:italic>. <jats:italic>graminicola</jats:italic> facilitates infection and expansion through the secretion of multiple RXLR effectors, and SG_RXLR41 is an important virulence‐related effector that is involved in manipulating plant immunity by suppressing cell death.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"23 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140200101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander Idnurm, Alec J. McCallum, Angela P. Van de Wouw
Microbes can overcome the ability of plant resistance genes to confer protection against disease by mutating their corresponding avirulence genes. The fungus Leptosphaeria maculans causes blackleg disease on canola crops and subverts Brassica napus resistance genes through several DNA mutation mechanisms. One of these is repeat‐induced point (RIP) mutation, which can ‘leak’ into the avirulence genes from the adjacent repetitive sequences that the mutation process is targeting. Here, we identified populations of L. maculans in Australia that have extensive RIP mutations in the avirulence gene AvrLm2 and show that this has been triggered by a duplication of the gene and surrounding DNA that includes the distant (>55 kb in total) AvrLm6 gene. This finding provides another mechanism of mutation by which pathogens can overcome host resistance, and more broadly contributes to understanding the complex balance between gene duplication and genome defence.
微生物可以通过突变相应的无毒基因来克服植物抗病基因的防病能力。Leptosphaeria maculans 真菌会引起油菜作物黑胫病，并通过几种 DNA 变异机制破坏甘蓝型油菜的抗性基因。其中之一是重复诱导点突变（RIP），它可以从突变过程所针对的邻近重复序列 "泄漏 "到抗病基因中。在这里，我们发现澳大利亚的L. maculans种群的无毒基因AvrLm2中存在广泛的RIP突变，并表明这是由该基因及其周围DNA的重复引发的，其中包括遥远的（总计55 kb）AvrLm6基因。这一发现提供了病原体克服宿主抗性的另一种突变机制，更广泛地有助于理解基因复制与基因组防御之间的复杂平衡。
{"title":"No safe haven: Loss of avirulence in the plant pathogen Leptosphaeria maculans by DNA duplication and repeat‐induced point mutation","authors":"Alexander Idnurm, Alec J. McCallum, Angela P. Van de Wouw","doi":"10.1111/ppa.13889","DOIUrl":"https://doi.org/10.1111/ppa.13889","url":null,"abstract":"Microbes can overcome the ability of plant resistance genes to confer protection against disease by mutating their corresponding avirulence genes. The fungus <jats:italic>Leptosphaeria maculans</jats:italic> causes blackleg disease on canola crops and subverts <jats:italic>Brassica napus</jats:italic> resistance genes through several DNA mutation mechanisms. One of these is repeat‐induced point (RIP) mutation, which can ‘leak’ into the avirulence genes from the adjacent repetitive sequences that the mutation process is targeting. Here, we identified populations of <jats:italic>L</jats:italic>. <jats:italic>maculans</jats:italic> in Australia that have extensive RIP mutations in the avirulence gene <jats:italic>AvrLm2</jats:italic> and show that this has been triggered by a duplication of the gene and surrounding DNA that includes the distant (>55 kb in total) <jats:italic>AvrLm6</jats:italic> gene. This finding provides another mechanism of mutation by which pathogens can overcome host resistance, and more broadly contributes to understanding the complex balance between gene duplication and genome defence.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"2013 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rodrigo S. Silva, Josias C. Faria, Rosana P. Vianello, Paula Arielle M. R. Valdisser, Helton S. Pereira, Leonardo C. Melo, Patrícia V. Pinheiro, Thiago Lívio P. O. Souza
Although cowpea mild mottle virus (CPMMV) has been reported in Brazil since 1983, it has only become a significant concern for researchers and farmers in recent years. The objective of this work was to investigate the genetic basis of CPMMV tolerance, mapping and reporting the first loci associated with this trait in common bean (cv. BRS Sublime). Phenotypic assays were carried out on 180 individual plants (F2 generation) and 180 F2:3 progenies comprising 12 plants per family and their parents (BRS Sublime, tolerant parent × CNFCT 16207, susceptible parent). CPMMV was mechanically inoculated and symptoms were evaluated at 35 days after inoculation, using a 1–5 scoring scale. A linkage map was constructed using 1695 single‐nucleotide polymorphism (SNP) and SilicoDArT markers that segregated in the F2 and F2:3 generations as expected. Markers were distributed across 11 common bean chromosomes, resulting in a total length of 2864 cM, with an average distance between markers of 1.8 cM. Phenotypic observations revealed that tolerance in cv. BRS Sublime is controlled by a single dominant gene. The main effect quantitative trait locus (QTL; CPMMV.Pv08) associated with CPMMV tolerance was identified in the terminal region on chromosome 8 (Pv08). This QTL explained approximately 77% of phenotypic variation, indicating that the inheritance of tolerance to CPMMV is monogenic, controlled by a major locus. As far as we know, this study represents the first investigation into the inheritance and genetic mapping of CPMMV tolerance in common bean, with potential for the development of elite lines with multiple virus resistance/tolerance.
{"title":"Inheritance and genetic mapping of the first CPMMV tolerance locus in common bean","authors":"Rodrigo S. Silva, Josias C. Faria, Rosana P. Vianello, Paula Arielle M. R. Valdisser, Helton S. Pereira, Leonardo C. Melo, Patrícia V. Pinheiro, Thiago Lívio P. O. Souza","doi":"10.1111/ppa.13892","DOIUrl":"https://doi.org/10.1111/ppa.13892","url":null,"abstract":"Although cowpea mild mottle virus (CPMMV) has been reported in Brazil since 1983, it has only become a significant concern for researchers and farmers in recent years. The objective of this work was to investigate the genetic basis of CPMMV tolerance, mapping and reporting the first loci associated with this trait in common bean (cv. BRS Sublime). Phenotypic assays were carried out on 180 individual plants (F<jats:sub>2</jats:sub> generation) and 180 F<jats:sub>2:3</jats:sub> progenies comprising 12 plants per family and their parents (BRS Sublime, tolerant parent × CNFCT 16207, susceptible parent). CPMMV was mechanically inoculated and symptoms were evaluated at 35 days after inoculation, using a 1–5 scoring scale. A linkage map was constructed using 1695 single‐nucleotide polymorphism (SNP) and SilicoDArT markers that segregated in the F<jats:sub>2</jats:sub> and F<jats:sub>2:3</jats:sub> generations as expected. Markers were distributed across 11 common bean chromosomes, resulting in a total length of 2864 cM, with an average distance between markers of 1.8 cM. Phenotypic observations revealed that tolerance in cv. BRS Sublime is controlled by a single dominant gene. The main effect quantitative trait locus (QTL; CPMMV.Pv08) associated with CPMMV tolerance was identified in the terminal region on chromosome 8 (Pv08). This QTL explained approximately 77% of phenotypic variation, indicating that the inheritance of tolerance to CPMMV is monogenic, controlled by a major locus. As far as we know, this study represents the first investigation into the inheritance and genetic mapping of CPMMV tolerance in common bean, with potential for the development of elite lines with multiple virus resistance/tolerance.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"73 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Johanna Wong‐Bajracharya, John Webster, Luciano A. Rigano, Pragya Kant, Anna Englezou, Fridtjof Snijders, Rebecca Roach, Cuiping Wang, Monica Kehoe, Rachel Mann, Fiona E. Constable, Toni A. Chapman
Xylella fastidiosa is a plant‐pathogenic bacterium that poses a serious threat to the production of economically important plant species including grapes, almonds, olives and a broad range of amenity plants, causing significant economic losses worldwide. While multiple molecular detection assays have been developed for X. fastidiosa, there is a lack of molecular tools available for detection and differentiation of the closely related pear pathogen, Xylella taiwanensis. In this study, we present a novel conventional PCR assay with primers that can amplify both Xylella species. The amplified product could be sequenced and used for discrimination between the two species and the subspecies within the fastidiosa species. This PCR assay was designed using a genome‐informed approach to target the ComEC/Rec2 gene of both Xylella species, ensuring a higher specificity than other previously developed PCR assays. A test performance study across five national plant diagnostic laboratories in Australia and New Zealand demonstrated this assay's high sensitivity and specificity to all known species and subspecies within the Xylella genus. This PCR assay can be used for Xylella identification at the species and subspecies level and is compatible with Sanger sequencing and nanopore sequencing for rapid turnaround time. The newly developed conventional PCR assay presented here offers rapid detection and accurate identification of both Xylella species from plant, insect vector or bacterial samples, enabling timely implementation of biosecurity measures or disease management responses.
{"title":"All‐in‐one Xylella detection and identification: A nanopore sequencing‐compatible conventional PCR","authors":"Johanna Wong‐Bajracharya, John Webster, Luciano A. Rigano, Pragya Kant, Anna Englezou, Fridtjof Snijders, Rebecca Roach, Cuiping Wang, Monica Kehoe, Rachel Mann, Fiona E. Constable, Toni A. Chapman","doi":"10.1111/ppa.13877","DOIUrl":"https://doi.org/10.1111/ppa.13877","url":null,"abstract":"<jats:italic>Xylella fastidiosa</jats:italic> is a plant‐pathogenic bacterium that poses a serious threat to the production of economically important plant species including grapes, almonds, olives and a broad range of amenity plants, causing significant economic losses worldwide. While multiple molecular detection assays have been developed for <jats:italic>X</jats:italic>. <jats:italic>fastidiosa</jats:italic>, there is a lack of molecular tools available for detection and differentiation of the closely related pear pathogen, <jats:italic>Xylella taiwanensis</jats:italic>. In this study, we present a novel conventional PCR assay with primers that can amplify both <jats:italic>Xylella</jats:italic> species. The amplified product could be sequenced and used for discrimination between the two species and the subspecies within the <jats:italic>fastidiosa</jats:italic> species. This PCR assay was designed using a genome‐informed approach to target the <jats:italic>ComEC/Rec2</jats:italic> gene of both <jats:italic>Xylella</jats:italic> species, ensuring a higher specificity than other previously developed PCR assays. A test performance study across five national plant diagnostic laboratories in Australia and New Zealand demonstrated this assay's high sensitivity and specificity to all known species and subspecies within the <jats:italic>Xylella</jats:italic> genus. This PCR assay can be used for <jats:italic>Xylella</jats:italic> identification at the species and subspecies level and is compatible with Sanger sequencing and nanopore sequencing for rapid turnaround time. The newly developed conventional PCR assay presented here offers rapid detection and accurate identification of both <jats:italic>Xylella</jats:italic> species from plant, insect vector or bacterial samples, enabling timely implementation of biosecurity measures or disease management responses.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"23 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frédéric Suffert, Stéphanie Le Prieur, Sandrine Gélisse, Emmie Dzialo, Cyrille Saintenac, Thierry C. Marcel
Monitoring virulent strains within pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in pathogen genomes based on high‐throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms, and in planta phenotyping remains necessary. We developed a method for ‘bulk phenotyping on checkerboard microcanopies of wheat near‐isogenic lines’ (BPC) for estimating the frequency of virulence against a resistance gene in mixed populations of the fungal pathogen Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB) in wheat, without the need for strain‐by‐strain pathogen phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines—one with the target resistance gene and the other without it—with a multistrain mixture of isolates representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using Stb16q, a wheat resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, as well as synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with molecular methods.
{"title":"Estimating the frequency of virulence against an Stb gene in Zymoseptoria tritici populations by bulk phenotyping on checkerboard microcanopies of wheat near‐isogenic lines","authors":"Frédéric Suffert, Stéphanie Le Prieur, Sandrine Gélisse, Emmie Dzialo, Cyrille Saintenac, Thierry C. Marcel","doi":"10.1111/ppa.13894","DOIUrl":"https://doi.org/10.1111/ppa.13894","url":null,"abstract":"Monitoring virulent strains within pathogen populations is crucial to improve host resistance deployment strategies. Such monitoring increasingly involves field pathogenomics studies of molecular polymorphisms in pathogen genomes based on high‐throughput screening technologies. However, it is not always straightforward to predict virulence phenotypes from these polymorphisms, and in planta phenotyping remains necessary. We developed a method for ‘bulk phenotyping on checkerboard microcanopies of wheat near‐isogenic lines’ (BPC) for estimating the frequency of virulence against a resistance gene in mixed populations of the fungal pathogen <jats:italic>Zymoseptoria tritici</jats:italic>, the causal agent of Septoria tritici blotch (STB) in wheat, without the need for strain‐by‐strain pathogen phenotyping. Our method involves the uniform inoculation of a microcanopy of two wheat lines—one with the target resistance gene and the other without it—with a multistrain mixture of isolates representative of the population to be characterized, followed by the differential quantification of infection points (lesions). Using <jats:italic>Stb16q</jats:italic>, a wheat resistance gene that has recently broken down in Europe, we found a robust correlation between the ratio of the mean number of lesions on each wheat line and the frequency of virulent strains in the inoculum. Using pairs of virulent and avirulent strains, as well as synthetic populations consisting of 10 virulent strains and 10 avirulent strains mixed in different proportions, we validated the principle of the method and established standard curves at virulence frequencies close to those observed in natural conditions. We discuss the potential of this method for virulence monitoring in combination with molecular methods.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"1 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Virus diseases represent important economic threats to seed potato production worldwide, yet relatively little is known of their epidemiology at the landscape‐scale. In this study, data was compiled from the Scottish national seed potato classification scheme on the incidence of 10 different potato viruses for the years 2009–2022. A co‐occurrence analysis identified that 12 virus species pairs occurred together more often than expected by chance, and potato blackleg was positively associated with eight potato viruses. ArcGIS was used to investigate spatial and spatiotemporal variation in incidence rates of the three most prevalent viruses (potato virus Y, potato leaf roll virus and potato virus A), and this revealed prominent geographic differences in long‐term disease outcomes. Focusing on potato virus Y as the most commonly occurring single infection, interpretable machine‐learning techniques were used to investigate the influence of key crop, management and environmental factors on patterns of incidence in space and time. The results showed that health characteristics of seed stocks were among the most important predictors of incidence, along with blackleg infection, several management features, cultivar resistance, distance to the nearest seed and ware crop, temperature variables and several soil features. This approach provides a comprehensive overview of potato viruses in Scotland, a deeper understanding of epidemiological risk factors at the landscape‐scale and a forecast model that could serve as the basis of a decision support tool for improved management of potato virus Y.
病毒病是全球马铃薯种薯生产的重要经济威胁，但人们对其在景观尺度上的流行病学却知之甚少。在这项研究中，我们从苏格兰国家马铃薯种薯分类计划中汇编了 2009-2022 年 10 种不同马铃薯病毒的发病率数据。通过共现分析发现，有 12 种病毒同时出现的频率高于偶然出现的频率，马铃薯黑腿病与 8 种马铃薯病毒呈正相关。利用 ArcGIS 调查了三种最流行病毒（马铃薯病毒 Y、马铃薯卷叶病毒和马铃薯病毒 A）发病率的空间和时空变化，发现了长期病害结果的显著地理差异。马铃薯病毒 Y 是最常发生的单一感染病害，研究人员利用可解释的机器学习技术研究了作物、管理和环境等关键因素对发病率时空模式的影响。结果表明，除黑胫病感染、几种管理特征、栽培品种抗性、与最近的种子和器皿作物的距离、温度变量和几种土壤特性外，种群的健康特征也是预测发病率的最重要因素之一。这种方法提供了苏格兰马铃薯病毒的全面概况，加深了对景观尺度上流行病风险因素的理解，并提供了一个预测模型，可作为改进马铃薯病毒 Y 管理的决策支持工具的基础。
{"title":"Landscape‐scale patterns and predictors of potato viruses in Scotland","authors":"Peter Skelsey","doi":"10.1111/ppa.13891","DOIUrl":"https://doi.org/10.1111/ppa.13891","url":null,"abstract":"Virus diseases represent important economic threats to seed potato production worldwide, yet relatively little is known of their epidemiology at the landscape‐scale. In this study, data was compiled from the Scottish national seed potato classification scheme on the incidence of 10 different potato viruses for the years 2009–2022. A co‐occurrence analysis identified that 12 virus species pairs occurred together more often than expected by chance, and potato blackleg was positively associated with eight potato viruses. ArcGIS was used to investigate spatial and spatiotemporal variation in incidence rates of the three most prevalent viruses (potato virus Y, potato leaf roll virus and potato virus A), and this revealed prominent geographic differences in long‐term disease outcomes. Focusing on potato virus Y as the most commonly occurring single infection, interpretable machine‐learning techniques were used to investigate the influence of key crop, management and environmental factors on patterns of incidence in space and time. The results showed that health characteristics of seed stocks were among the most important predictors of incidence, along with blackleg infection, several management features, cultivar resistance, distance to the nearest seed and ware crop, temperature variables and several soil features. This approach provides a comprehensive overview of potato viruses in Scotland, a deeper understanding of epidemiological risk factors at the landscape‐scale and a forecast model that could serve as the basis of a decision support tool for improved management of potato virus Y.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"499 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant host tolerance is a key plant defence response to parasites, including viruses. This complex genetic trait involves multiple molecular mechanisms and, in particular, selective autophagy. Experimental data on the role of various selective autophagy factors and, in particular, cargo receptors in plant tolerance to viral infection are extremely limited. In this communication, I present the results of in silico identification of sequences in the shallot transcriptome encoding homologues of several selective autophagy receptors (SARs) related to the immune response and their expression patterns in response to asymptomatic infection of shallot virus X, a member of the genus Allexivirus, subgenus Acarallexivirus, within the family Alphaflexiviridae. The results obtained, together with the relevant literature data, suggest that some SARs likely to be involved in the regulation of the unfolded protein response and programmed cell death may play an active role in the formation of the state of tolerance of the host plant to allexivirus infection.
{"title":"Selective autophagy receptor‐encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection","authors":"Valeriy K. Vishnichenko","doi":"10.1111/ppa.13887","DOIUrl":"https://doi.org/10.1111/ppa.13887","url":null,"abstract":"Plant host tolerance is a key plant defence response to parasites, including viruses. This complex genetic trait involves multiple molecular mechanisms and, in particular, selective autophagy. Experimental data on the role of various selective autophagy factors and, in particular, cargo receptors in plant tolerance to viral infection are extremely limited. In this communication, I present the results of in silico identification of sequences in the shallot transcriptome encoding homologues of several selective autophagy receptors (SARs) related to the immune response and their expression patterns in response to asymptomatic infection of shallot virus X, a member of the genus <jats:italic>Allexivirus</jats:italic>, subgenus <jats:italic>Acarallexivirus</jats:italic>, within the family <jats:italic>Alphaflexiviridae</jats:italic>. The results obtained, together with the relevant literature data, suggest that some SARs likely to be involved in the regulation of the unfolded protein response and programmed cell death may play an active role in the formation of the state of tolerance of the host plant to allexivirus infection.","PeriodicalId":20075,"journal":{"name":"Plant Pathology","volume":"33 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140053969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：