- Fargo, North Dakota, United States
Gongjun Shi
North Dakota State University, Plant Pathlology, Graduate Student
Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address... more
Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host....
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The ascomycete fungus Pyrenophora tritici-repentis is the causal agent of tan spot of wheat. The disease can occur on both common wheat (Triticum aestivum) and durum wheat (T. turgidum ssp. durum) and has potential to cause significant... more
The ascomycete fungus Pyrenophora tritici-repentis is the causal agent of tan spot of wheat. The disease can occur on both common wheat (Triticum aestivum) and durum wheat (T. turgidum ssp. durum) and has potential to cause significant yield and quality losses. The fungal pathogen is known to produce necrotrophic effectors (NEs) that act as important virulence factors. Based on the NE production and virulence on a set of four differentials, P. tritici-repentis isolates have been classified into eight races. Race 4 produces no known NEs and is avirulent on the differentials. From a fungal collection in North Dakota, we identified several isolates that were classified as race 4. These isolates caused no or little disease on all common wheat lines including the differentials; however, they were virulent on some durum cultivars and tetraploid wheat accessions. Using two segregating tetraploid wheat populations and quantitative trait locus mapping, we identified several genomic regions s...
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Human selection during crop domestication alters numerous traits, including disease resistance. Studies of qualitative resistance to specialist pathogens typically find decreased resistance in domesticated crops in comparison to their... more
Human selection during crop domestication alters numerous traits, including disease resistance. Studies of qualitative resistance to specialist pathogens typically find decreased resistance in domesticated crops in comparison to their wild relatives. However, less is known about how crop domestication affects quantitative interactions with generalist pathogens. To study how crop domestication impacts plant resistance to generalist pathogens, and correspondingly how this interacts with the pathogen's genetics, we infected a collection of wild and domesticated tomato accessions with a genetically diverse population of the generalist pathogenBotrytis cinerea. We quantified variation in lesion size of 97B. cinereagenotypes (isolates) on 6 domesticatedSolanum lycopersicumand 6 wildS. pimpinellifoliumgenotypes. This showed that lesion size was significantly controlled by plant domestication, plant genetic variation, and the pathogen's genotype. Overall, resistance was slightly ele...
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Plant-pathogen interactions are largely modeled as co-evolutionary arms races based on specialist pathogens. Less is known about how generalist pathogens interact with diverse hosts. Here, we use a collection of 98 isolates of Botrytis... more
Plant-pathogen interactions are largely modeled as co-evolutionary arms races based on specialist pathogens. Less is known about how generalist pathogens interact with diverse hosts. Here, we use a collection of 98 isolates of Botrytis cinerea to address how this generalist necrotroph perceive plant evolution across 90 plant genotypes from eight Eudicot species. We show that interactions in this pathosystem are largely defined by the plant species with small and inconsistent effect of plant domestication. More surprisingly, plant susceptibility to Botrytis shows little association to evolutionary distances between the plant species. We also show that Botrytis virulence and host specificity is polygenic with GWA associated genes covering 12% of Botrytis gene transcript.
The fungus () causes tan spot of wheat crops, which is an important disease worldwide. Based on the production of the three known necrotrophic effectors (NEs), the fungal isolates are classified into eight races with race 4 producing no... more
The fungus () causes tan spot of wheat crops, which is an important disease worldwide. Based on the production of the three known necrotrophic effectors (NEs), the fungal isolates are classified into eight races with race 4 producing no known NEs. From a laboratory cross between 86⁻124 (race 2 carrying the gene for the production of Ptr ToxA) and DW5 (race 5 carrying the gene for the production of Ptr ToxB), we have obtained some isolates lacking both the and genes, which, by definition, should be classified as race 4. In this work, we characterized virulence of two of these isolates called B16 and B17 by inoculating them onto various common wheat ( L.) and durum (. L.) genotypes. It was found that the two isolates still caused disease on some genotypes of both common and durum wheat. Disease evaluations were also conducted in recombinant inbred line populations derived from two hard red winter wheat cultivars: Harry and Wesley. QTL mapping in this population revealed that three gen...
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Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of... more
Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9 Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets. Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported a...
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The ascomycete Pyrenophora tritici-repentis (Ptr) is an important fungal pathogen worldwide that causes tan spot of wheat. The fungus is self-fertile because each isolate contains both mating type (MAT) idiomorphs. In this work, we... more
The ascomycete Pyrenophora tritici-repentis (Ptr) is an important fungal pathogen worldwide that causes tan spot of wheat. The fungus is self-fertile because each isolate contains both mating type (MAT) idiomorphs. In this work, we developed knockouts of the MAT genes in Ptr and tested fertility of the knockout strains and outcrossing between the knockout strains carrying the opposite mating type. The fungal strains with deletions of either MAT1-1-1 or MAT1-2-1 did not form mature pseudothecia making them functionally heterothallic. The cross between the heterothallic strains of the same isolate (86-124) was fully fertile with the only difference compared to the homothallic wild type strain being the slightly lower percentage of pseudothecium formation. However, the cross between 86-124 (race 2, ToxA-containing isolate) and DW5 (race 5, ToxB-containing isolate) was partially fertile and had fewer mature pseudothecia. Furthermore, most mature asci produced only two or four instead of...
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A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around... more
A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around the world. Although resistance to BLS is limited in wheat, several triticale accessions have high levels of resistance. To characterize the genetic basis of this resistance, we developed triticale mapping populations using a resistant accession (Siskiyou) and two susceptible accessions (UC38 and Villax St. Jose). Bulked segregant analysis in an F2 population derived from the cross of Siskiyou × UC38 led to the identification of a simple sequence repeat (SSR) marker (XSCM138) on chromosome 5R that co-segregated with the resistance gene. The cross of Siskiyou × Villax St. Jose was advanced into an F2:5 recombinant inbred line population and evaluated for BLS reaction. Genetic linkage maps on this population were assembled with markers generated using...
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Tan spot susceptibility is conferred by multiple interactions of necrotrophic effector and host sensitivity genes. Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the... more
Tan spot susceptibility is conferred by multiple interactions of necrotrophic effector and host sensitivity genes. Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the world. The disease system is known to involve at least three fungal-produced necrotrophic effectors (NEs) that interact with the corresponding host sensitivity (S) genes in an inverse gene-for-gene manner to induce disease. However, it is unknown if the effects of these NE-S gene interactions contribute additively to the development of tan spot. In this work, we conducted disease evaluations using different races and quantitative trait loci (QTL) analysis in a wheat recombinant inbred line (RIL) population derived from a cross between two susceptible genotypes, LMPG-6 and PI 626573. The two parental lines each harbored a single known NE sensitivity gene with LMPG-6 having the Ptr ToxC sensitivity gene Tsc1 and PI 626573 having the Ptr ToxA sensitiv...
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Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is... more
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is SnTox3, which evokes programmed cell death and leads to disease when recognized by the wheat Snn3-B1 gene. Here, we developed saturated genetic linkage maps of the Snn3-B1 region using two F2 populations derived from the SnTox3-sensitive line Sumai 3 crossed with different SnTox3-insensitive lines. Markers were identified and/or developed from various resources including previously mapped simple sequence repeats, bin-mapped expressed sequence tags, single nucleotide polymorphisms, and whole genome survey sequences. Subsequent high-resolution mapping of the Snn3-B1 locus in 5600 gametes delineated the gene to a 1.5 cM interval. Analysis of micro-colinearity of the Snn3-B1 region indicated that it was highly disrupted compared to rice and Brachypodiu...
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The necrotrophic fungal pathogen Stagonospora nodorum produces multiple necrotrophic effectors (NEs), also known as host-selective toxins, which interact with corresponding wheat genes in an inverse gene-for-gene manner to cause the... more
The necrotrophic fungal pathogen Stagonospora nodorum produces multiple necrotrophic effectors (NEs), also known as host-selective toxins, which interact with corresponding wheat genes in an inverse gene-for-gene manner to cause the disease Stagonospora nodorum blotch (SNB). In previous research, we showed that the homoeologous wheat genes Snn3-B1 and Snn3-D1, located on wheat chromosome arms 5BS and 5DS, respectively, both recognize the NE SnTox3 to confer effector-triggered susceptibility. Here, we describe genome analysis and mapping results from ongoing efforts to clone the two Snn3 genes. Saturation mapping of the genes in relatively small F2 populations using SSRs and EST-derived markers followed by comparative analysis with the rice and Brachypodium genomes revealed that both the Snn3-B1 and Snn3-D1 regions were highly conserved with regions of rice chromosome 12 and Brachypodium chromosome 4. This colinearity allowed us to develop numerous additional markers to further satur...
The Tsn1 gene confers sensitivity to the necrotrophic effector (NE) ToxA, which is produced by the pathogens that cause tan spot and Stagonospora nodorum blotch on wheat. Although Tsn1 is a susceptibility gene, it contains resistance... more
The Tsn1 gene confers sensitivity to the necrotrophic effector (NE) ToxA, which is produced by the pathogens that cause tan spot and Stagonospora nodorum blotch on wheat. Although Tsn1 is a susceptibility gene, it contains resistance gene-like features such as protein kinase, nucleotide binding (NB) and leucine-rich repeat (LRR) domains. Previous research indicated that Tsn1 arose in the diploid B-genome progenitor of polyploid wheat. However, nucleotide variation in Tsn1 is nearly non-existent among polyploids. Here, accessions of Aegilops speltoides (SS genome), a close relative of the B-genome progenitor, were studied to further characterize the structure, function, evolution, and diversity of Tsn1. Multiple plants from each of 123 accessions were evaluated for reaction to ToxA and genotyped for presence of Tsn1. A total of 95 accessions were insensitive to ToxA and null for Tsn1, whereas the remaining 28 harbored Tsn1 alleles and were either sensitive or insensitive to ToxA. Com...
ABSTRACT Stagonospora nodorum is a necrotrophic fungal pathogen of wheat that causes the disease Stagonospora nodorum blotch (SNB). The wheat-S. nodorum pathosystem involves pathogen-produced necrotrophic effectors (NEs) (formerly known... more
ABSTRACT Stagonospora nodorum is a necrotrophic fungal pathogen of wheat that causes the disease Stagonospora nodorum blotch (SNB). The wheat-S. nodorum pathosystem involves pathogen-produced necrotrophic effectors (NEs) (formerly known as host-selective toxins) that are recognized by corresponding host genes to confer disease susceptibility. To date, five host gene-NE interactions have been reported in the wheat-S. nodorum system, all of which play significant roles in the development of SNB. Here, we present the identification and mapping of three additional wheat genes that confer sensitivity to different NEs produced by S. nodorum. One NE sensitivity gene (temporarily designated Snn4B) was identified in the durum wheat variety Lebsock and mapped to the long arm of chromosome 4B in a population of doubled haploids. Evaluation of SNB in this population indicated that the Snn4B locus explained as much as 53% of the variation demonstrating that Snn4B is a major SNB susceptibility gene. The second NE sensitivity gene (Snn6A) was identified in the hexaploid variety Opata 85 and mapped to the long arm of chromosome 6A in the ITMI population. This gene accounted for 20% of the variation in SNB development. Finally, a third NE sensitivity gene (Snn5D) was discovered in the hexaploid landrace Chinese Spring and mapped to the long arm of chromosome 5D using chromosome deletion lines. Further characterization, analysis, and marker development for these susceptibility genes is underway. This research broadens our knowledge of the wheat-S. nodorum pathosystem and will lead to the efficient development of SNB resistant wheat varieties.
Necrotrophic pathogens live and feed on dying tissue, but their interactions with plants are not well understood compared to biotrophic pathogens. The wheat Snn1 gene confers susceptibility to strains of the necrotrophic pathogen... more
Necrotrophic pathogens live and feed on dying tissue, but their interactions with plants are not well understood compared to biotrophic pathogens. The wheat Snn1 gene confers susceptibility to strains of the necrotrophic pathogen Parastagonospora nodorum that produce the SnTox1 protein. We report the positional cloning of Snn1, a member of the wall-associated kinase class of receptors, which are known to drive pathways for biotrophic pathogen resistance. Recognition of SnTox1 by Snn1 activates programmed cell death, which allows this necrotroph to gain nutrients and sporulate. These results demonstrate that necrotrophic pathogens such as P. nodorum hijack host molecular pathways that are typically involved in resistance to biotrophic pathogens, revealing the complex nature of susceptibility and resistance in necrotrophic and biotrophic pathogen interactions with plants.
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BACKGROUND: Microtubules are prominent components of the cytoskeleton in every eukaryotic cell. Plant microtubules are essential for a wide variety of cellular functions, including generation of cell polarity, intracellular transport,... more
BACKGROUND: Microtubules are prominent components of the cytoskeleton in every eukaryotic cell. Plant microtubules are essential for a wide variety of cellular functions, including generation of cell polarity, intracellular transport, positioning of organelles, cell wall deposition and cell division. The major component of microtubules is tubulin, an α,β heterodimer protein with a molecular mass of each subunit of around 50 kDa. Tubulin exists in cells as a mixture of polypeptides differing in their isoelectric points. Some post-translational modifications of tubulins are thought to modulate the functions and localization of microtubules within the cell.RESULTS: The complete sequence of a single-copy α-tubulin gene Tuba1, belonging to a multiple gene family of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino), was obtained. The gene was expressed in high levels in young leaves and stamens, and it was also highly expressed during all stages of microsporogenesis in the maintainer. However, there was a distinct difference in α-tubulin expression between the sterile stage and the normal stages of pollen in a cytoplasmic male sterility line and its maintainer.CONCLUSION:Tuba1 was significantly related to the cell division and elongation of non-heading Chinese cabbage, demonstrating that this gene played an important role in the development of pollen and may be closely related to male sterility. Copyright © 2008 Society of Chemical Industry
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Changes in ascorbic acid content and antioxidant enzyme activities were investigated in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) leaves of ‘Wutacai’ and ‘Erqing’ exposed to excess copper (Cu). Cu treatment... more
Changes in ascorbic acid content and antioxidant enzyme activities were investigated in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) leaves of ‘Wutacai’ and ‘Erqing’ exposed to excess copper (Cu). Cu treatment reduced the fresh weight of shoot and root by 57% and 46% in ‘Wutacai’, and 60 and 54% in ‘Erqing’, respectively. The accumulation of copper in leaves was higher in ‘Wutacai’ than that in ‘Erqing’. Compared to the control, ascorbic acid (AsA) contents were significantly decreased after copper treatment in both cultivars, while they were higher in ‘Wutacai’ than in ‘Erqing’, which may explain the higher copper-tolerance of ‘Wutacai’ with higher copper accumulation. The higher AsA contents of ‘Wutacai’ resulted from their lower activities of degrading enzymes, such as ascorbate oxydase (AAO) and ascorbate peroxidase (APX), as well as the increasing activity of dehydroascorbate reductase (DHAR) after copper treatment compared with ‘Erqing’. Copper stimulated superoxide dismutase (SOD) activity in both cultivars, but for catalase (CAT), there was little difference between both cultivars. Peroxidases (POD) activity was decreased after copper treatment in ‘Erqing’, while in ‘Wutacai’, it was significantly increased at 14 days, and POD activity was higher in ‘Wutacai’ than that in ‘Erqing’ at 21 and 28 days. Therefore, the induced increasing activity of POD in ‘Wutacai’ also played an important role in its copper tolerance.
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Many plants increase in freezing tolerance upon exposure to low non-freezing temperatures, a phenomenon known as cold acclimation. Cold acclimation in Arabidopsis involves rapid cold-induced expression of the inducer of... more
Many plants increase in freezing tolerance upon exposure to low non-freezing temperatures, a phenomenon known as cold acclimation. Cold acclimation in Arabidopsis involves rapid cold-induced expression of the inducer of C-repeat/dehydration-responsive element-binding factor (CBF) expression (ICE) transcriptional activators followed by expression of the CBF; subsequently, CBF-targeted genes that increase freezing tolerance. Here, we present evidence for a CBF cold-response pathway in non-heading Chinese cabbage (Brassica campestris ssp. chinensis L. Makino). We show that non-heading Chinese cabbage encodes ICE1-like gene BrICE1 that bracket an open reading frame of 1,491 bp encoding a protein with a potential bHLH domain, which accumulates rapidly in response to low temperature followed closely by expression of the BrCBF gene, an ortholog of the Arabidopsis CBF3-like gene, and then BrCOR14 gene, an ortholog of the Arabidopsis CBF-targeted COR15b gene. An alignment of the later two genes from Arabidopsis, Brassica napus revealed the presence of conserved CANNTG core element and AP2 domain in BrCBF and a CCG core element in BrCOR14. In addition, BrCBF and BrCOR14 showed increased expression induced by low temperature as well as salt and drought, but not by ABA stress which are similar to those of Arabidopsis. We conclude that components of the CBF cold-response pathway are highly conserved in non-heading Chinese cabbage.
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CMS is induced by the coordinated expression of certain mitochondrial and nuclear genes in flower development. Mitochondrial genes regulate manifestation of CMS, whereas nuclear genes regulate fertility phenotype and thus affect... more
CMS is induced by the coordinated expression of certain mitochondrial and nuclear genes in flower development. Mitochondrial genes regulate manifestation of CMS, whereas nuclear genes regulate fertility phenotype and thus affect negatively. In this article, the buds of newly bred Ogura CMS of non-heading Chinese cabbage and its maintainer line as plant materials, genes differentially expressed transcripts were analyzed by cDNA-AFLP. Seventeen differently expressed genes were found in new Ogura CMS and nine genes in maintainer line. These genes were involved in energy metabolism, signal transduction, flower development, stress-related metabolism, transcription, etc. Expression patterns of three genes encoding BrCAM6, BrANK, BrTUB3 were verified by qRT-PCR in different organs and various stage flower buds of CMS and its maintainer line. The results revealed that two genes related to signal transduction, BrCAM6 and BrANK, were highly expressed in stamens and microspores of CMS than in maintainer line. As believed, these two genes involved in signal transduction of male sterile in CMS line. In comparison, BrTUB3 gene was accumulated in stamens and was expressed in significantly lower level in CMS line than in maintainer line. It expressed significantly lower in CMS than maintainer line after tetrad stage. This expression profile suggests that BrTUB3 played an important role in the development of the pollen, and may be closely related to male sterility.