Publications by authors named "Shaobin Zhong"

46 Publications

Function and evolution of allelic variation of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.).

Plant J 2021 Apr 7. Epub 2021 Apr 7.

USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, United States.

Resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2, and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed KASP marker KASPSr13 and four STARP markers, rwgsnp37 through rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2, and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1 although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the LRR region and differed from the other three R haplotypes by 1 - 2 additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic, and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation and the other three R alleles were likely derived from Sr13d through 1 - 2 additional point mutations.
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http://dx.doi.org/10.1111/tpj.15263DOI Listing
April 2021

Identification of fungal species associated with crown and root rots of wheat and evaluation of plant reactions to the pathogens in North Dakota.

Plant Dis 2021 Mar 1. Epub 2021 Mar 1.

North Dakota State University, Plant Pathology, Walster Hall 306, NDSU Dept. 7660, Fargo, North Dakota, United States, 58108-6050;

Common root rot (CRR) and crown rot (CR), caused by Bipolaris sorokiniana and Fusarium species, respectively, can cause significant yield losses in cereal crops. To assess the prevalence, incidence, and severity of these diseases in North Dakota, wheat samples were collected from spring wheat fields across the state in 2012, 2013, and 2014. Based on sub-crown internode symptoms, a greater incidence and severity of CRR was observed in 2012 (warm and dry year) than in 2013 and 2014. Also, the Northwestern Glaciated Plains and Northwestern Great Plains ecoregions showed greater CRR incidence and severity compared to the Northern Glaciated Plains and Lake Agassiz Plains ecoregions in the state. Bipolaris sorokiniana and Fusarium species including F. acuminatum, F. avenaceum, F. culmorum, F. graminearum, F. equiseti, F. pseudograminearum, F. oxysporum, F. redolens, F. sporotrichioides, and F. solani were isolated and identified from the root and crown tissues of the wheat samples. B. sorokiniana was isolated more frequently than other fungal species in all sampled years and ecoregions of North Dakota. F. acuminatum, F. avenaceum, F. culmorum, F. equiseti, F. graminearum, F. pseudograminearum, and F. redolens were pathogenic causing infections on seedlings of the two wheat genotypes (ND652 and Alsen), whereas isolates of F. oxysporum and F. solani were non-pathogenic and considered as secondary invaders associated with the root and crown rot diseases. Evaluation of some spring wheat genotypes for reactions to one B. sorokiniana isolate at seedling and adult plant stages, and one F. culmorum isolate at the seedling stage indicated that susceptibility to these pathogens varied among different wheat genotypes tested. This study provides useful information on fungal species associated with root and crown rots of wheat in North Dakota and on resistant/susceptible reactions of some spring wheat lines to the different fungal isolates evaluated.
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http://dx.doi.org/10.1094/PDIS-11-20-2412-REDOI Listing
March 2021

First Report of Causing Seedling Death on Sugar Beet in Minnesota, USA.

Plant Dis 2021 Feb 18. Epub 2021 Feb 18.

North Dakota State University, Plant Pathology, Walster Hall 306, NDSU Dept. 7660, Fargo, North Dakota, United States, 58108-6050;

In May 2019, sugar beet ( L.) seedlings with symptoms of wilting and root tip discoloration and necrosis were found in Moorhead (46.5507° N, 96.4208° W), Minnesota, USA. Roots of infected seedlings were surface sterilized with 10% bleach for 15 seconds, rinsed with sterile distilled water and cultured on water agar (MA Mooragar®, Inc, CA) for 3 days at 23 ± 2°C. Isolates were transferred to carnation leaf agar (CLA) and incubated at room temperature (22°C) under fluorescent light for 14 days. Abundant macroconidia were produced in sporodochia. Macroconidia were 5- to 7-septate, slightly curved at the apex, and ranged from 35 to 110 ×1.2 to 3.8 μm. No microconidia were produced. Chlamydospores with thick, roughened walls were observed in chains or in clumps, and were ellipsoidal or subglobose. Single spore was transferred from CLA to potato dextrose agar (HIMEDIA Laboratories, India) produced abundant white mycelium and was pale brown where the colony was in contact with the media. The morphological features of the isolates were consistent with (Corda) Sacc. (Leslie and Summerell 2006, Li et al. 2015). Genomic DNAs (NORGEN BIOTEK CORP, Fungi DNA Isolation Kit #26200) of two representative isolates were used for polymerase chain reaction (PCR). The second largest subunit of RNA polymerase (RPB2) was amplified by PCR with primers 5f2/7cr (O'Donnell et al. 2010). The amplified PCR product was sequenced and deposited in GenBank (accession number MW048778). A BLAST search in Genbank and the Fusarium MLST database showed 100% sequence alignment to with accession MK077037.1 and NRRL 25795, respectively. Pathogenicity testing was done using three sugar beet seedlings (Hilleshög proprietary material, Hilleshög Seed, LLC, Halsey, OR 97348) at cotyledonary stage grown in a pot (4˝×4˝×6˝) with six replicates. Seedlings were inoculated with conidial suspension (104 conidia ml-1 for 8 minutes) by the root dip method (Hanson, 2006). Mock inoculated plants were dipped in sterile water. Inoculated and control plants were placed in the greenhouse at 25 ± 2°C, and 75 to 85% relative humidity. One week later, inoculated seedlings showed root tip tissue discoloration similar to those observed in the field and non-inoculated seedlings were symptomless. This study was repeated. The fungus was re-isolated from diseased roots and confirmed to be based on morphological characters. was reported on freshly harvested and stored beet in Europe but was not found to be pathogenic (Christ et al. 2011). Strausbaugh and Gillen (2009) reported the association of and root rot of sugar beet but did not report pathogenicity. This pathogen is reported in several crops including edible beans that is grown in rotation with sugar beet in several production areas (Jacobs et al. 2018). The most important species reported to cause significant economic damage to sugar beet include and (Secor et al. 2014, Webb et. al. 2012). The presence of another pathogenic species in sugar beet will require monitoring to determine how widespread it is and whether current commercial cultivars are resistant. To our knowledge, this is the first report of causing disease on sugar beet seedlings in Minnesota, USA.
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http://dx.doi.org/10.1094/PDIS-10-20-2102-PDNDOI Listing
February 2021

A loss-of-function of the dirigent gene TaDIR-B1 improves resistance to Fusarium crown rot in wheat.

Plant Biotechnol J 2021 Feb 10. Epub 2021 Feb 10.

Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China (Henan) Joint Center of Wheat and Maize, Henan Agricultural University, Zhengzhou, China.

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http://dx.doi.org/10.1111/pbi.13554DOI Listing
February 2021

Thyroid nodule recognition using a joint convolutional neural network with information fusion of ultrasound images and radiofrequency data.

Eur Radiol 2021 Jan 6. Epub 2021 Jan 6.

State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Department of Ultrasound, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, Guangdong, People's Republic of China.

Objective: To develop a deep learning-based method with information fusion of US images and RF signals for better classification of thyroid nodules (TNs).

Methods: One hundred sixty-three pairs of US images and RF signals of TNs from a cohort of adult patients were used for analysis. We developed an information fusion-based joint convolutional neural network (IF-JCNN) for the differential diagnosis of malignant and benign TNs. The IF-JCNN contains two branched CNNs for deep feature extraction: one for US images and the other one for RF signals. The extracted features are fused at the backend of IF-JCNN for TN classification.

Results: Across 5-fold cross-validation, the accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve (AUROC) obtained by using the IF-JCNN with both US images and RF signals as inputs for TN classification were respectively 0.896 (95% CI 0.838-0.938), 0.885 (95% CI 0.804-0.941), 0.910 (95% CI 0.815-0.966), and 0.956 (95% CI 0.926-0.987), which were better than those obtained by using only US images: 0.822 (0.755-0.878; p = 0.0044), 0.792 (0.679-0.868, p = 0.0091), 0.866 (0.760-0.937, p = 0.197), and 0.901 (0.855-0.948, p = .0398), or RF signals: 0.767 (0.694-0.829, p < 0.001), 0.781 (0.685-0.859, p = 0.0037), 0.746 (0.625-0.845, p < 0.001), 0.845 (0.786-0.903, p < 0.001).

Conclusions: The proposed IF-JCNN model filled the gap of just using US images in CNNs to characterize TNs, and it may serve as a promising tool for assisting the diagnosis of thyroid cancer.

Key Points: • Raw radiofrequency signals before ultrasound imaging of thyroid nodules provide useful information that is not carried by ultrasound images. • The information carried by raw radiofrequency signals and ultrasound images for thyroid nodules is complementary. • The performance of deep convolutional neural network for diagnosing thyroid nodules can be significantly improved by fusing US images and RF signals in the model as compared with just using US images.
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http://dx.doi.org/10.1007/s00330-020-07585-zDOI Listing
January 2021

Genome Sequence Resources for the Maize Pathogen Isolated in Poland.

Mol Plant Microbe Interact 2021 Feb 4;34(2):214-217. Epub 2020 Dec 4.

Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A.

(Scaufl. & Munaut) is one of the most important fungal pathogens that cause ear and stalk rots in maize. In this study, we sequenced genomes of two isolates (KFI615 and KFI660) isolated from corn ears in Poland. A total of 110.3 and 116.3 million 100-nucleotide paired-end clean reads were obtained for KFI615 and KFI660, which were assembled into 20 and 18 scaffolds with an estimated genome size of 45.21 and 45.00 Mb, respectively. These genome sequences provide important resources for understanding pathogenicity and biology of the pathogens within the complex.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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http://dx.doi.org/10.1094/MPMI-09-20-0266-ADOI Listing
February 2021

Clove oil-in-water nanoemulsion: Mitigates growth of Fusarium graminearum and trichothecene mycotoxin production during the malting of Fusarium infected barley.

Food Chem 2020 May 26;312:126120. Epub 2019 Dec 26.

Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, United States. Electronic address:

Fusarium mycotoxin contamination in malting barley is of great concerns in malting industry. Our recent study found that clove oil nanoemulsions can act as highly efficient antifungal agents in vitro. Therefore, we explored the efficacy of clove oil nanoemulsions on Fusarium growth and mycotoxin during malting process. The impact of emulsifier types (Tween 80, BSA and quillaja saponins) on the formation of clove oil nanoemulsion, the mitigation effects on mycotoxin levels and fungal biomass, and the clove oil flavor residues on malts were measured. We observed that 1.5 mg clove oil/g nanoemulsion showed a negligible influence on germinative energy of barley, while still efficiently eliminated the DON levels and toxicogenic fungal biomass as quantified by Tri5 DNA content. Tween 80-stablized clove oil nanoemulsion displayed higher mycotoxin inhibitory activity and less flavor impact on the final malt. The results indicated the potential application of essential oil nanoemulsion during the malting process.
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http://dx.doi.org/10.1016/j.foodchem.2019.126120DOI Listing
May 2020

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

Phytopathology 2020 Feb 5;110(2):440-446. Epub 2020 Jan 5.

Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A.

Spot blotch (SB) caused by and powdery mildew (PM) caused by f. sp. 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 and one isolate (Race I) of f. sp. . Genetic analysis of the RILs revealed that one major gene () controls susceptibility to isolate ND90Pr, and another major gene () confers resistance to f. sp. isolate Race I, respectively. was mapped on chromosome 1H of Bowman, as previously reported. was also mapped to the short arm of 1H, which was tightly linked but not allelic to the locus. Quantitative trait locus (QTL) analysis identified two QTLs, and , responsible for susceptibility to spot blotch caused by isolate ND85F in ND5883, which are located on chromosome 1H and 7H, respectively. was mapped to the same region as , whereas 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.
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http://dx.doi.org/10.1094/PHYTO-08-19-0292-RDOI Listing
February 2020

Genetic Mapping and Prediction Analysis of FHB Resistance in a Hard Red Spring Wheat Breeding Population.

Front Plant Sci 2019 6;10:1007. Epub 2019 Aug 6.

Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.

head blight (FHB) is one of the most destructive diseases in wheat worldwide. Breeding for FHB resistance is hampered by its complex genetic architecture, large genotype by environment interaction, and high cost of phenotype screening. Genomic selection (GS) is a powerful tool to enhance improvement of complex traits such as FHB resistance. The objectives of this study were to (1) investigate the genetic architecture of FHB resistance in a North Dakota State University (NDSU) hard red spring wheat breeding population, (2) test if the major QTL and play an important role in this breeding population; and (3) assess the potential of GS to enhance breeding efficiency of FHB resistance. A total of 439 elite spring wheat breeding lines from six breeding cycles were genotyped using genotyping-by-sequencing (GBS) and 102,147 SNP markers were obtained. Evaluation of FHB severity was conducted in 10 unbalanced field trials across multiple years and locations. One QTL for FHB resistance was identified and located on chromosome arm 1AL, explaining 5.3% of total phenotypic variation. The major type II resistance QTL only explained 3.1% of total phenotypic variation and the QTL was not significantly associated with FHB resistance in this breeding population. Our results suggest that integration of many genes with medium/minor effects in this breeding population should provide stable FHB resistance. Genomic prediction accuracies of 0.22-0.44 were obtained when predicting over breeding cycles in this study, indicating the potential of GS to enhance the improvement of FHB resistance.
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http://dx.doi.org/10.3389/fpls.2019.01007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691880PMC
August 2019

Influence of nonionic and ionic surfactants on the antifungal and mycotoxin inhibitory efficacy of cinnamon oil nanoemulsions.

Food Funct 2019 May;10(5):2817-2827

Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.

The influence of ionic surfactants (cationic surfactant lauric arginate and anionic surfactant lysolecithin) on the physical properties, antifungal and mycotoxin inhibitory efficacy of Tween 80 stabilized cinnamon oil-in-water nanoemulsions was investigated. Nanoemulsion droplets of similar particle diameter (∼100 nm), but variable electrical characteristics, were formed by mixing 0.1 wt% ionic surfactant with 0.9 wt% Tween 80 before homogenization. The nanoemulsions were physically stable over 28 days at 23 °C. The antifungal activity (against mycelial growth and spore germination) and mycotoxin inhibitory activity of cinnamon oil nanoemulsions bearing positive, neutral, and negative charge surface was then evaluated against two chemotypes of Fusarium graminearum. In general, the cinnamon oil played a decisive role in the resulting antifungal and mycotoxin inhibitory activities. The surfactant charge had a limited impact on the antifungal mycotoxin inhibitory activities of cinnamon oil in the nanoemulsions. Both ionic surfactant-based cinnamon oil nanoemulsions showed greater activity in inhibiting mycelial growth and mycotoxin production of F. graminearum than those based on Tween 80. Treatment of mycelium with cinnamon oil nanoemulsions resulted in the loss of cytoplasm from fungal hyphae, and accounted for the antifungal action. These results have important implications for the design of essential oil based nanoemulsions as effective antifungal delivery systems in foods.
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http://dx.doi.org/10.1039/c9fo00470jDOI Listing
May 2019

Physical properties, antifungal and mycotoxin inhibitory activities of five essential oil nanoemulsions: Impact of oil compositions and processing parameters.

Food Chem 2019 Sep 8;291:199-206. Epub 2019 Apr 8.

Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, United States. Electronic address:

The influence of homogenization conditions on selected essential oil (thyme, lemongrass, cinnamon, peppermint, and clove)-in-water nanoemulsion formation and stability was investigated. Physically stable essential oil nanoemulsions could be fabricated by a microfludizer under optimized processing conditions (10,000 psi and 2 passes). The chemical compositions of EOs was characterized using GC-MS. The antifungal activity and mycotoxin inhibitory activity of essential oils in both bulk and nanoemulsion forms were determined using two isolates of Fusarium graminearum. The major chemical components of essential oil had a remarkable impact on long term physical stability, antifungal activity, and inhibition of mycotoxin production. With regard to inhibition of mycotoxin production, the mycotoxin inhibitory activity of essential oils was enhanced considerably in nanoemulsion form, which was attributed to greater solubility of the essential oils. It was also noted that the same essential oils exhibited significant differences in inhibition of mycotoxin production in the two isolates of F. graminearum.
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http://dx.doi.org/10.1016/j.foodchem.2019.04.032DOI Listing
September 2019

Genetic Diversity and Resistance to Fusarium Head Blight in Synthetic Hexaploid Wheat Derived From and Diverse Subspecies.

Front Plant Sci 2018 11;9:1829. Epub 2018 Dec 11.

Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States.

Synthetic hexaploid wheat (SHW) can serve as a bridge for the transfer of useful genes from and tetraploid wheat () into common wheat (). The objective of this study was to evaluate 149 SHW lines and their 74 tetraploid parents for their genetic diversity, breeding values and inter-genomic interactions for resistance to Fusarium head blight (FHB). The genetic diversity analysis was performed based on the population structure established using 4,674 and 3,330 polymorphic SNP markers among the SHW lines and tetraploid parents, respectively. The results showed that all and most accessions formed different clusters and subpopulations, respectively, whereas all the , , , and accessions were clustered together, suggesting that was more closely related to , , and than to . The genetic diversity of the SHW lines mainly reflected that of the tetraploid parents. The SHW lines and their tetraploid parents were evaluated for reactions to FHB in two greenhouse seasons and at two field nurseries for 2 years. As expected, most of the SHW lines were more resistant than their tetraploid parents in all environments. The FHB severities of the SHW lines varied greatly depending on the and tetraploid genotypes involved. Most of the SHW lines with a high level of FHB resistance were generally derived from the tetraploid accessions with a high level of FHB resistance. Among the 149 SHW lines, 140 were developed by using three accessions CIae 26, PI 268210, and RL 5286. These SHW lines showed FHB severities reduced by 21.7%, 17.3%, and 11.5%, respectively, with an average reduction of 18.3%, as compared to the tetraploid parents, suggesting that the D genome may play a major role in reducing disease severity in the SHW lines. Thirteen SHW lines consistently showed a high level of FHB resistance compared to the resistant check, Sumai 3, in each environment. These SHW lines will be useful for the development of FHB-resistant wheat germplasm and populations for discovery of novel FHB resistance genes.
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http://dx.doi.org/10.3389/fpls.2018.01829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298526PMC
December 2018

Fine mapping of a dominant gene conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in barley.

Theor Appl Genet 2019 Jan 21;132(1):41-51. Epub 2018 Sep 21.

Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.

Key Message: We fine-mapped and physically anchored a dominant gene (Rbs7) conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in a genomic interval of 304 kb on barley chromosome 6H. Spot blotch, caused by Bipolaris sorokiniana, is an economically important disease on barley in the Upper Midwest region of the USA and Prairie Provinces of Canada. A new pathotype (pathotype 7, represented by isolate ND4008) of B. sorokiniana has been identified, which is highly virulent on barley cultivars with resistance to other pathotypes of the fungus. In this study, we fine-mapped a dominant gene conferring resistance to pathotype 7 in the barley line PI 235186. Genetic analysis of the F and F plants from a cross between PI 356741 (highly susceptible to ND4008) and PI 235186 (highly resistant to ND4008) indicated that a single dominant gene (Rbs7) controls the resistance in PI 235186. This result was confirmed by genetic analysis of the F families and a recombinant inbred line (RIL) population derived from the same cross. Bulked segregant analysis using simple sequence repeat markers localized Rbs7 on the short arm of chromosome 6H. Additional DNA markers were developed from the 6H pseudomolecule sequence of barley cv. Morex and mapped to the genomic region carrying Rbs7 using the RIL population and F recombinants derived from the PI 356741 × PI 235186 cross. Rbs7 was fine-mapped between two markers (M13.06 and M13.37), which spans a physical distance of 304 kb on Morex chromosome 6H. These results provide a foundation for future cloning of the resistance gene and development of user-friendly molecular markers that can be used for development of spot-blotch-resistant cultivars in barley breeding programs.
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http://dx.doi.org/10.1007/s00122-018-3192-5DOI Listing
January 2019

Molecular mapping of QTL for Fusarium head blight resistance introgressed into durum wheat.

Theor Appl Genet 2018 Sep 4;131(9):1939-1951. Epub 2018 Jun 4.

Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.

Key Message: The major QTL for FHB resistance from hexaploid wheat line PI 277012 was successfully introgressed into durum wheat and minor FHB resistance QTL were detected in local durum wheat cultivars. A combination of these QTL will enhance FHB resistance of durum wheat. Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease of durum wheat. To combat the disease, great efforts have been devoted to introgress FHB resistance from its related tetraploid and hexaploid wheat species into adapted durum cultivars. However, most of the quantitative trait loci (QTL) for FHB resistance existing in the introgression lines are not well characterized or validated. In this study, we aimed to identify and map FHB resistance QTL in a population consisting of 205 recombinant inbred lines from the cross between Joppa (a durum wheat cultivar) and 10Ae564 (a durum wheat introgression line with FHB resistance derived from the hexaploid wheat line PI 277012). One QTL (Qfhb.ndwp-2A) from Joppa and two QTL (Qfhb.ndwp-5A and Qfhb.ndwp-7A) from 10Ae564 were identified through phenotyping of the mapping population for FHB severity and DON content in greenhouse and field and genotyping with 90K wheat Infinium iSelect SNP arrays. Qfhb.ndwp-2A explained 14, 15, and 9% of the phenotypic variation, respectively, for FHB severity in two greenhouse experiments and for mean DON content across the two greenhouse environments. Qfhb.ndwp-5A explained 19, 10, and 7% of phenotypic variation, respectively, for FHB severity in one greenhouse experiment, mean FHB severity across two field experiments, and mean DON content across the two greenhouse experiments. Qfhb.ndwp-7A was only detected for FHB severity in the two greenhouse experiments, explaining 9 and 11% of the phenotypic variation, respectively. This study confirms the existence of minor QTL in North Dakota durum cultivars and the successful transfer of the major QTL from PI 277012 into durum wheat.
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http://dx.doi.org/10.1007/s00122-018-3124-4DOI Listing
September 2018

Influence of oil phase composition on the antifungal and mycotoxin inhibitory activity of clove oil nanoemulsions.

Food Funct 2018 May;9(5):2872-2882

Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.

The influence of oil composition on the physical properties and antifungal and mycotoxin inhibitory activity of clove oil-in-water nanoemulsions was investigated. Physically stable clove oil-in-water nanoemulsions could be fabricated by incorporating either ≥75 wt% of corn oil or ≥50 wt% of medium chain triacylglycerol (MCT) into clove oil before homogenization to prevent Ostwald ripening. The clove oil-in-water nanoemulsions with mean diameters of <150 nm showed high physical stability over 30 days storage. The antifungal activity of physically stable clove oil nanoemulsions was further evaluated using effective concentration (EC) and inhibitory activity towards mycotoxin production in two chemotypes of Fusarium graminearum isolates. The composition of the oil phase, i.e., ripening inhibitor type and concentration, in clove oil-in-water nanoemulsions had a remarkable impact on antifungal activity as well as inhibition of mycotoxin production. In general, under the same clove oil concentration in oil phase, the addition of MCT decreased the antifungal and mycotoxin inhibitory activity of clove oil more than corn oil. Compared with the bulk clove oil, this study also indicated that the mycotoxin inhibitory activity of clove was significantly enhanced when encapsulated in nanoemulsions. These results have important implications for the design of essential oil based nanoemulsions as effective antifungal and detoxification delivery systems in the food or other industries.
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http://dx.doi.org/10.1039/c7fo02073bDOI Listing
May 2018

The gene conferring susceptibility to spot blotch caused by Cochliobolus sativus is located at the Mla locus in barley cultivar Bowman.

Theor Appl Genet 2018 Jul 16;131(7):1531-1539. Epub 2018 Apr 16.

Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.

Key Message: We identified, fine mapped, and physically anchored a dominant spot blotch susceptibility gene Scs6 to a 125 kb genomic region containing the Mla locus on barley chromosome 1H. Spot blotch caused by Cochliobolus sativus is an important disease of barley, but the molecular mechanisms underlying resistance and susceptibility to the disease are not well understood. In this study, we identified and mapped a gene conferring susceptibility to spot blotch caused by the pathotype 2 isolate (ND90Pr) of C. sativus in barley cultivar Bowman. Genetic analysis of F and F progeny as well as F families from a cross between Bowman and ND 5883 indicated that a single dominant gene (designated as Scs6) conferred spot blotch susceptibility in Bowman. Using a doubled haploid (DH) population derived from a cross between Calicuchima-sib (resistant) and Bowman-BC (susceptible), we confirmed that Scs6, contributed by Bowman-BC, was localized at the same locus as the previously identified spot blotch resistance allele Rcs6, which was contributed by Calicuchima-sib and mapped on the short arm of chromosome 1H. Using a genome-wide putative linear gene index of barley (Genome Zipper), 13 cleaved amplified polymorphism markers were developed from 11 flcDNA and two EST sequences and mapped to the Scs6/Rcs6 region on a linkage map constructed with the DH population. Further fine mapping with markers developed from barley genome sequences and F recombinants derived from Bowman × ND 5883 and Bowman × ND B112 crosses delimited Scs6 in a 125 kb genomic interval harboring the Mla locus on the reference genome of barley cv. Morex. This study provides a foundational step for further cloning of Scs6 using a map-based approach.
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http://dx.doi.org/10.1007/s00122-018-3095-5DOI Listing
July 2018

Molecular Mapping of Fusarium Head Blight Resistance in the Spring Wheat Line ND2710.

Phytopathology 2018 08 29;108(8):972-979. Epub 2018 Jun 29.

First, third, fifth, and eighth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; second, fourth, and sixth authors: Monsanto Company, St. Louis 63104; and seventh author: Department of Crop and Soil Sciences, University of Georgia, Griffin 30223.

ND2710 is a hard red spring wheat line with a very high level of resistance to Fusarium head blight (FHB). It was selected from the progeny of a cross between ND2603 (an advanced breeding line derived from the Sumai 3/Wheaton cross) and Grandin (a spring wheat cultivar). The FHB resistance of ND2710 is presumably derived from Sumai 3 because the other parents (Grandin and Wheaton) are very susceptible to FHB. To identify and map the quantitative trait loci (QTL) for FHB resistance in ND2710, we developed a mapping population consisting of 233 recombinant inbred lines (RILs) from the cross between ND2710 and the spring wheat cultivar Bobwhite. These RILs along with their parents and checks were evaluated for reactions to FHB in three greenhouse experiments and one field experiment during 2013 to 2014. The population was also genotyped with the wheat 90K iSelect single-nucleotide polymorphism (SNP) assay, and a genetic linkage map was developed with 1,373 non-cosegregating SNP markers, which were distributed on all 21 wheat chromosomes spanning 914.98 centimorgans of genetic distance. Genetic analyses using both phenotypic and genotypic data identified one major QTL (Qfhb.ndwp-3B) on the short arm of chromosome 3B, and three minor QTL (Qfhb.ndwp-6B, Qfhb.ndwp-2A, and Qfhb.ndwp-6A) on 6B, 2A, and 6A, respectively. The major QTL on 3B was detected in all experiments and explained 5 to 20% of the phenotypic variation, while the three minor QTL on 6B, 2A, and 6A explained 5 to 12% phenotypic variation in at least two experiments, except for Qfhb.ndwp-2A, which was only detected in the field experiment. Qfhb.ndwp-3B and Qfhb.ndwp-6B were mapped to the genomic regions containing Fhb1 and Fhb2, respectively, confirming that they originated from Sumai 3. The additive effect of the major and minor QTL may contribute to the high level of FHB resistance in ND2710. The SNP markers closely linked to the FHB resistance QTL will be useful for marker-assisted selection of FHB resistance in wheat breeding programs.
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http://dx.doi.org/10.1094/PHYTO-12-17-0392-RDOI Listing
August 2018

RNA-Seq Revealed Differences in Transcriptomes between 3ADON and 15ADON Populations of Fusarium graminearum In Vitro and In Planta.

PLoS One 2016 27;11(10):e0163803. Epub 2016 Oct 27.

Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America.

Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) in barley and wheat in North America. The fungus not only causes yield loss of the crops but also produces harmful trichothecene mycotoxins [Deoxynivalenol (DON) and its derivatives-3-acetyldeoxynivalenol (3ADON) and 15-acetyldeoxynivalenol (15ADON), and nivalenol (NIV)] that contaminate grains. Previous studies showed a dramatic increase of 3ADON-producing isolates with higher aggressiveness and DON production than the 15ADON-producing isolates in North America. However, the genetic and molecular basis of differences between the two types of isolates is unclear. In this study, we compared transcriptomes of the 3ADON and 15ADON isolates in vitro (in culture media) and in planta (during infection on the susceptible wheat cultivar 'Briggs') using RNA-sequencing. The in vitro gene expression comparison identified 479 up-regulated and 801 down-regulated genes in the 3ADON isolates; the up-regulated genes were mainly involved in C-compound and carbohydrate metabolism (18.6%), polysaccharide metabolism (7.7%) or were of unknown functions (57.6%). The in planta gene expression analysis revealed that 185, 89, and 62 genes were up-regulated in the 3ADON population at 48, 96, and 144 hours after inoculation (HAI), respectively. The up-regulated genes were significantly enriched in functions for cellular import, C-compound and carbohydrate metabolism, allantoin and allantoate transport at 48 HAI, for detoxification and virulence at 96 HAI, and for metabolism of acetic acid derivatives, detoxification, and cellular import at 144 HAI. Comparative analyses of in planta versus in vitro gene expression further revealed 2,159, 1,981 and 2,095 genes up-regulated in the 3ADON isolates, and 2,415, 2,059 and 1,777 genes up-regulated in the 15ADON isolates at the three time points after inoculation. Collectively, our data provides a foundation for further understanding of molecular mechanisms involved in aggressiveness and DON production of the two chemotype isolates of F. graminearum.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082872PMC
June 2017

Sources and Genetics of Spot Blotch Resistance to a New Pathotype of Cochliobolus sativus in the USDA National Small Grains Collection.

Plant Dis 2016 Oct 1;100(10):1988-1993. Epub 2016 Aug 1.

Department of Plant Pathology, North Dakota State University, Fargo, ND 58108.

Spot blotch, caused by Cochliobolus sativus, is one of the important barley diseases in the northern Great Plains of the United States and the Prairie Provinces of Canada. The disease has been under control for almost five decades due to the use of durable spot blotch resistance derived from the barley line ND B112. However, the emergence of isolate ND4008 with virulence on ND B112 prompted us to identify new sources of resistance to this new pathotype. In this study, we screened 2,062 barley accessions from the United States Department of Agriculture National Small Grains Collection for spot blotch resistance, and identified 40 barley accessions exhibiting a high level of resistance to isolate ND4008 at the seedling stage. In all, 24 of the barley accessions with seedling resistance also exhibited moderate to high adult plant resistance to ND4008 in greenhouse tests. Seven of the ND4008-resistant barley accessions showed seedling resistance to two other pathotypes (1 and 2) of the pathogen. Genetic study of resistant barley accessions PI 235186, PI 592275, and PI 643242 indicated that a single major dominant gene controls spot blotch resistance to ND4008 in each of these three accessions. These resistant sources are useful for developing barley cultivars with spot blotch resistance to all pathotypes of C. sativus.
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http://dx.doi.org/10.1094/PDIS-02-16-0152-REDOI Listing
October 2016

Coordinated and independent functions of velvet-complex genes in fungal development and virulence of the fungal cereal pathogen Cochliobolus sativus.

Fungal Biol 2016 08 20;120(8):948-960. Epub 2016 May 20.

Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA. Electronic address:

LaeA and velvet proteins regulate fungal development and secondary metabolism through formation of multimeric complexes in many fungal species, but their functions in the cereal fungal pathogen Cochliobolus sativus are not well understood. In this study, four velvet complex genes (CsLaeA, CsVeA, CsVelB, and CsVelC) in C. sativus were identified and characterized using knockout mutants generated for each of the genes. Both ΔCsVeA and ΔCsVelB showed significant reduction in aerial mycelia growth. ΔCsVelB also exhibited a hypermorphic conidiation phenotype with indeterminate growth of the conidial tip cells and premature germination of conidia. ΔCsLaeA, ΔCsVeA, and ΔCsVelB produced more conidia under constant dark conditions than under constant light conditions whereas no differences were observed under the two conditions for the wild type. These three mutants also showed significantly reduced conidiation under constant light conditions, but produced more small sized conidia under constant dark conditions compared to the wild type. All knockout mutants (ΔCsLaeA, ΔCsVeA, ΔCsVelB and ΔCsVelC) showed some extent of reduction in virulence on susceptible barley plants compared to the wild type strain. The results revealed the conserved and unique roles of velvet-complex proteins as regulators in mediating fungal development and secondary metabolism in C. sativus.
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http://dx.doi.org/10.1016/j.funbio.2016.05.004DOI Listing
August 2016

The regulatory gene VosA affects conidiogenesis and is involved in virulence of the fungal cereal pathogen Cochliobolus sativus.

Fungal Biol 2015 Oct 3;119(10):884-900. Epub 2015 Jul 3.

Department of Plant Pathology, North Dakota State University, Fargo, ND 58108-6050, USA. Electronic address:

VosA is one of the four components in the velvet complex shown to be involved in regulation of fungal development and secondary metabolism in filamentous fungi. However, the function of VosA has only been studied in a few plant pathogenic fungi. In this study, we identified the ortholog (CsVosA) of VosA in the cereal spot blotch pathogen Cochliobolus sativus and generated gene knockout mutants for functional characterization of the gene. Conidia of the CsVosA knockout mutants (ΔCsVosA) lacked trehalose, were significantly reduced in viability, had less pigmentation, and showed a dramatic reduction in tolerance to heat, oxidative, and ion stresses. However, ΔCsVosA produced more conidia than the wild type under both constant dark, and constant light conditions, suggesting that CsVosA is a negative-feedback regulator in conidiation. Interestingly, the ΔCsVosA mutants exhibited a hypermorphic conidiation phenotype with indeterminate growth of the conidial tip cells resulting in head-to-tail (acropetal) arrays of conidiogenesis, indicating that some genes involved in conidiation are also regulated by CsVosA. The ΔCsVosA mutants showed significant reduction in virulence on susceptible barley plants and the two genes for nonribosomal peptide synthetases (NRPSs) involved in virulence during host infection were down-regulated in ΔCsVosA, suggesting that CsVosA may affect virulence of the fungus by regulating the expression of the genes for NRPSs, as well as other genes directly or indirectly involved in virulence.
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http://dx.doi.org/10.1016/j.funbio.2015.06.009DOI Listing
October 2015

Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat.

Theor Appl Genet 2016 Jan 18;129(1):31-43. Epub 2015 Sep 18.

Departments of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.

Key Message: New molecular markers were developed and mapped to the FHB resistance QTL region in high resolution. Micro-collinearity of the QTL region with rice and Brachypodium was revealed for a better understanding of the genomic region. The wild emmer wheat (Triticum dicoccoides)-derived Fusarium head blight (FHB) resistance quantitative trait locus (QTL) Qfhs.ndsu-3AS previously mapped to the short arm of chromosome 3A (3AS) in a population of recombinant inbred chromosome lines (RICLs). This study aimed to attain a better understanding of the genomic region harboring Qfhs.ndsu-3AS and to improve the utility of the QTL in wheat breeding. Micro-collinearity of the QTL region with rice chromosome 1 and Brachypodium chromosome 2 was identified and used for marker development in saturation mapping. A total of 42 new EST-derived sequence tagged site (STS) and simple sequence repeat (SSR) markers were developed and mapped to the QTL and nearby regions on 3AS. Further comparative analysis revealed a complex collinearity of the 3AS genomic region with their collinear counterparts of rice and Brachypodium. Fine mapping of the QTL region resolved five co-segregating markers (Xwgc1186/Xwgc716/Xwgc1143/Xwgc501/Xwgc1204) into three distinct loci proximal to Xgwm2, a marker previously reported to be closely linked to the QTL. Four other markers (Xwgc1226, Xwgc510, Xwgc1296, and Xwgc1301) mapped farther proximal to the above markers in the QTL region with a higher resolution. Five homozygous recombinants with shortened T. dicoccoides chromosomal segments in the QTL region were recovered by molecular marker analysis and evaluated for FHB resistance. Qfhs.ndsu-3AS was positioned to a 5.2 cM interval flanked by the marker Xwgc501 and Xwgc510. The recombinants containing Qfhs.ndsu-3AS and new markers defining the QTL will facilitate utilization of this resistance source in wheat breeding.
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http://dx.doi.org/10.1007/s00122-015-2606-xDOI Listing
January 2016

Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat.

Theor Appl Genet 2015 Dec 11;128(12):2367-74. Epub 2015 Aug 11.

Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.

Key Message: A robust and diagnostic STS marker for stem rust resistance gene Sr47 was developed and validated for marker-assisted selection. Stem rust (caused by Puccinia graminis f. sp. tritici, Pgt) resistance gene Sr47, originally transferred from Aegilops speltoides to durum wheat (Triticum turgidum subsp. durum) line DAS15, confers a high level of resistance to Pgt race TTKSK (Ug99). Recently, the durum Rusty 5D(5B) substitution line was used to reduce the Ae. speltoides segment, and the resulting lines had Sr47 on small Ae. speltoides segments on wheat chromosome arm 2BL. The objective of this study was to develop a robust marker for marker-assisted selection of Sr47. A 200-kb segment of the Brachypodium distachyon genome syntenic with the Sr47 region was used to identify wheat expressed sequence tags (ESTs) homologous to the B. distachyon genes. The wheat EST sequences were then used to develop sequence-tagged site (STS) markers. By analyzing the markers for polymorphism between Rusty and DAS15, we identified a co-dominant STS marker, designated as Xrwgs38, which amplified 175 and 187 bp fragments from wheat chromosome 2B and Ae. speltoides chromosome 2S segments, respectively. The marker co-segregated with the Ae. speltoides segments carrying Sr47 in the families from four BC2F1 plants, including the parent plants for durum lines RWG35 and RWG36 with the pedigree of Rusty/3/Rusty 5D(5B)/DAS15//47-1 5D(5B). Analysis of 62 durum and common wheat cultivars/lines lacking the Sr47 segment indicated that they all possessed the 175-bp allele of Xrwgs38, indicating that it was diagnostic for the small Ae. speltoides segment carrying Sr47. This study demonstrated that Xrwgs38 will facilitate the selection of Sr47 in durum and common wheat breeding.
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http://dx.doi.org/10.1007/s00122-015-2590-1DOI Listing
December 2015

The Role of Mitogen-Activated Protein (MAP) Kinase Signaling Components in the Fungal Development, Stress Response and Virulence of the Fungal Cereal Pathogen Bipolaris sorokiniana.

PLoS One 2015 26;10(5):e0128291. Epub 2015 May 26.

Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America.

Mitogen-activated protein kinases (MAPKs) have been demonstrated to be involved in fungal development, sexual reproduction, pathogenicity and/or virulence in many filamentous plant pathogenic fungi, but genes for MAPKs in the fungal cereal pathogen Bipolaris sorokiniana have not been characterized. In this study, orthologues of three MAPK genes (CsSLT2, CsHOG1 and CsFUS3) and one MAPK kinase kinase (MAPKKK) gene (CsSTE11) were identified in the whole genome sequence of the B. sorokiniana isolate ND90Pr, and knockout mutants were generated for each of them. The ∆Csfus3 and ∆Csste11 mutants were defective in conidiation and formation of appressoria-like structures, showed hypersensitivity to oxidative stress and lost pathogenicity on non-wounded leaves of barley cv. Bowman. When inoculated on wounded leaves of Bowman, the ∆Csfus3 and ∆Csste11 mutants were reduced in virulence compared to the wild type. No morphological changes were observed in the ∆Cshog1 mutants in comparison with the wild type; however, they were slightly reduced in growth under oxidative stress and were hypersensitive to hyperosmotic stress. The ∆Cshog1 mutants formed normal appressoria-like structures but were reduced in virulence when inoculated on Bowman leaves. The ∆Csslt2 mutants produced more vegetative hyphae, had lighter pigmentation, were more sensitive to cell wall degrading enzymes, and were reduced in virulence on Bowman leaves, although they formed normal appressoria like the wild type. Root infection assays indicated that the ∆Cshog1 and ∆Csslt2 mutants were able to infect barley roots while the ∆Csfus3 and ∆Csste11 failed to cause any symptoms. However, no significant difference in virulence was observed for ∆Cshog1 mutants while ∆Csslt2 mutants showed significantly reduced virulence on barley roots in comparison with the wild type. Our results indicated that all of these MAPK and MAPKKK genes are involved in the regulation of fungal development under normal and stress conditions and required for full virulence on barley plants.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128291PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443973PMC
April 2016

Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen.

Theor Appl Genet 2015 Mar 19;128(3):431-43. Epub 2014 Dec 19.

Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.

Key Message: Mapping studies confirm that resistance to Ug99 race of stem rust pathogen in Aegilops tauschii accession Clae 25 is conditioned by Sr46 and markers linked to the gene were developed for marker-assisted selection. The race TTKSK (Ug99) of Puccinia graminis f. sp. tritici, the causal pathogen for wheat stem rust, is considered as a major threat to global wheat production. To address this threat, researchers across the world have been devoted to identifying TTKSK-resistant genes. Here, we report the identification and mapping of a stem rust resistance gene in Aegilops tauschii accession CIae 25 that confers resistance to TTKSK and the development of molecular markers for the gene. An F2 population of 710 plants from an Ae. tauschii cross CIae 25 × AL8/78 were first evaluated against race TPMKC. A set of 14 resistant and 116 susceptible F2:3 families from the F2 plants were then evaluated for their reactions to TTKSK. Based on the tests, 179 homozygous susceptible F2 plants were selected as the mapping population to identify the simple sequence repeat (SSR) and sequence tagged site (STS) markers linked to the gene by bulk segregant analysis. A dominant stem rust resistance gene was identified and mapped with 16 SSR and five new STS markers to the deletion bin 2DS5-0.47-1.00 of chromosome arm 2DS in which Sr46 was located. Molecular marker and stem rust tests on CIae 25 and two Ae. tauschii accessions carrying Sr46 confirmed that the gene in CIae 25 is Sr46. This study also demonstrated that Sr46 is temperature-sensitive being less effective at low temperatures. The marker validation indicated that two closely linked markers Xgwm210 and Xwmc111 can be used for marker-assisted selection of Sr46 in wheat breeding programs.
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http://dx.doi.org/10.1007/s00122-014-2442-4DOI Listing
March 2015

Brachypodium distachyon-Cochliobolus sativus Pathosystem is a New Model for Studying Plant-Fungal Interactions in Cereal Crops.

Phytopathology 2015 Apr;105(4):482-9

First, second, third, and fourth authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and fifth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, University of Minnesota, St. Paul 55108.

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) causes spot blotch, common root rot, and kernel blight or black point in barley and wheat. However, little is known about the molecular mechanisms underlying the pathogenicity of C. sativus or the molecular basis of resistance and susceptibility in the hosts. This study aims to establish the model grass Brachypodium distachyon as a new model for studying plant-fungus interactions in cereal crops. Six B. distachyon lines were inoculated with five C. sativus isolates. The results indicated that all six B. distachyon lines were infected by the C. sativus isolates, with their levels of resistance varying depending on the fungal isolates used. Responses ranging from hypersensitive response-mediated resistance to complete susceptibility were observed in a large collection of B. distachyon (2n=2x=10) and B. hybridum (2n=4x=30) accessions inoculated with four of the C. sativus isolates. Evaluation of an F2 population derived from the cross between two of the B. distachyon lines, Bd1-1 and Bd3-1, with isolate Cs07-47-1 showed quantitative and transgressive segregation for resistance to C. sativus, suggesting that the resistance may be governed by quantitative trait loci from both parents. The availability of whole-genome sequences of both the host (B. distachyon) and the pathogen (C. sativus) makes this pathosystem an attractive model for studying this important disease of cereal crops.
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http://dx.doi.org/10.1094/PHYTO-08-14-0214-RDOI Listing
April 2015

Functional characterization of the gene FoOCH1 encoding a putative α-1,6-mannosyltransferase in Fusarium oxysporum f. sp. cubense.

Fungal Genet Biol 2014 Apr 4;65:1-13. Epub 2014 Feb 4.

Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China. Electronic address:

Fusarium oxysporum f. sp. cubense (FOC) is the causal agent of banana Fusarium wilt and has become one of the most destructive pathogens threatening the banana production worldwide. However, few genes related to morphogenesis and pathogenicity of this fungal pathogen have been functionally characterized. In this study, we identified and characterized the disrupted gene in a T-DNA insertional mutant (L953) of FOC with significantly reduced virulence on banana plants. The gene disrupted by T-DNA insertion in L953 harbors an open reading frame, which encodes a protein with homology to α-1,6-mannosyltransferase (OCH1) in fungi. The deletion mutants (ΔFoOCH1) of the OCH1 orthologue (FoOCH1) in FOC were impaired in fungal growth, exhibited brighter staining with fluorescein isothiocyanate (FITC)-Concanavalin A, had less cell wall proteins and secreted more proteins into liquid media than the wild type. Furthermore, the mutation or deletion of FoOCH1 led to loss of ability to penetrate cellophane membrane and decline in hyphal attachment and colonization as well as virulence to the banana host. The mutant phenotypes were fully restored by complementation with the wild type FoOCH1 gene. Our data provide a first evidence for the critical role of FoOCH1 in maintenance of cell wall integrity and virulence of F. oxysporum f. sp. cubense.
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http://dx.doi.org/10.1016/j.fgb.2014.01.005DOI Listing
April 2014

Genetic analysis and molecular mapping of crown rust resistance in common wheat.

Theor Appl Genet 2014 Mar 4;127(3):609-19. Epub 2013 Dec 4.

USDA-ARS, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND, 58102, USA.

This is the first report on genetic analysis and genome mapping of major dominant genes for near non-host resistance to barley crown rust ( Puccinia coronata var. hordei ) in common wheat. Barley crown rust, caused by Puccinia coronata var. hordei, primarily occurs on barley (Hordeum vulgare L.) in the Great Plain regions of the United States. However, a few genotypes of common wheat (Triticum aestivum L.) were susceptible to this pathogen among 750 wheat accessions evaluated. To investigate the genetics of crown rust resistance in wheat, a susceptible winter wheat accession PI 350005 was used in crosses with two resistant wheat varieties, Chinese Spring and Chris. Analysis of F1 plants and F2 populations from these two crosses indicated that crown rust resistance is controlled by one and two dominant genes in Chris and Chinese Spring, respectively. To determine the chromosome location of the resistance gene Cr1 in Chris, a set of 21 monosomic lines derived from Chris was used as female parents to cross with a susceptible spring type selection (SSTS35) derived from the PI 350005/Chris cross. Monosomic analysis indicated that Cr1 is located on chromosome 5D in Chris and one of the crown rust resistance genes is located on chromosome 2D in Chinese Spring. The other gene in Chinese Spring is not on 5D and thus is different from Cr1. Molecular linkage analysis and QTL mapping using a population of 136 doubled haploid lines derived from Chris/PI 350005 further positioned Cr1 between SSR markers Xwmc41-2 and Xgdm63 located on the long arm of chromosome 5D. Our study suggests that near non-host resistance to crown rust in these different common wheat genotypes is simply inherited.
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http://dx.doi.org/10.1007/s00122-013-2245-zDOI Listing
March 2014

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

PLoS Genet 2013 24;9(1):e1003233. Epub 2013 Jan 24.

Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA.

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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http://dx.doi.org/10.1371/journal.pgen.1003233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554632PMC
May 2013

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.

PLoS Pathog 2012 6;8(12):e1003037. Epub 2012 Dec 6.

United States Department of Energy DOE Joint Genome Institute JGI, Walnut Creek, California, United States of America.

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
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http://dx.doi.org/10.1371/journal.ppat.1003037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516569PMC
May 2013