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  1. Article ; Online: A geminivirus crosses the monocot-dicot boundary and acts as a viral vector for gene silencing and genome editing.

    Kumar, Jitendra / Alok, Anshu / Steffenson, Brian J / Kianian, Shahryar

    Journal of advanced research

    2023  

    Abstract: Introduction: Members of the family Geminiviridae have been reported to infect either a monocot plant or a dicot plant, but not both. This study reports a geminivirus, Wheat Dwarf India Virus (WDIV), first identified in wheat, that is capable of ... ...

    Abstract Introduction: Members of the family Geminiviridae have been reported to infect either a monocot plant or a dicot plant, but not both. This study reports a geminivirus, Wheat Dwarf India Virus (WDIV), first identified in wheat, that is capable of infecting both monocot and dicot plants and acting as a viral vector.
    Objectives: This study was aimed at developing a broad host range viral vector system for reverse genetics and genome editing.
    Methods: Here we used a wheat isolate of WDIV and Ageratum yellow leaf curl betasatellite (AYLCB) for infectivity assays and vector development. We performed Agrobacterium-mediated inoculation of WDIV and AYLCB in wheat, oat, barley, corn, soybean, and tobacco. To examine the potential of WDIV to act as a viral vector, we modified the WDIV genome and cloned DNA fragments of the phytoene desaturase (PDS) genes from wheat and tobacco, separately. For gene editing experiments, tobacco lines expressing Cas9 were infiltrated with a WDIV-based vector carrying gRNA targeting the PDS gene.
    Results: About 80 to 90% of plants inoculated with infectious clones of WDIV alone or WDIV together with AYLCB showed mild symptoms, whereas some plants showed more prominent symptoms. WDIV and AYLCB were detected in the systemically infected leaves of all the plant species. Furthermore, the inoculation of the WDIV vector carrying PDS fragments induced silencing of the PDS gene in both wheat and tobacco plants. We also observed high-efficiency genome editing in the Cas9-expressing tobacco plants that were inoculated with WDIV vector-carrying gRNA.
    Conclusion: Detection of WDIV in naturally infected wheat, barley, and sugarcane in the field and its ability to systemically infect wheat, oat, barley, corn, soybean, and tobacco under laboratory conditions, provides compelling evidence that WDIV is the first geminivirus identified with the capability of infecting both monocot and dicot plant species. The wide host range of WDIV can be exploited for developing a single vector system for high-throughput genome editing in many plant species.
    Language English
    Publishing date 2023-09-18
    Publishing country Egypt
    Document type Journal Article
    ZDB-ID 2541849-X
    ISSN 2090-1224 ; 2090-1224
    ISSN (online) 2090-1224
    ISSN 2090-1224
    DOI 10.1016/j.jare.2023.09.013
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  2. Article ; Online: Identification of a Small Translocation from 6R Possessing Stripe Rust Resistance to Wheat

    Ashraf, Rimsha / Johansson, Eva / Vallenback, Pernilla / Steffenson, Brian J. / Bajgain, Prabin / Rahmatov, Mahbubjon

    Plant Disease. 2023 Mar. 01, v. 107, no. 3 p.720-729

    2023  

    Abstract: Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici Eriks. & E. Henn, is the most devastating fungal disease of bread wheat. Here, a wheat-rye multiple disomic substitution line, SLU126 4R (4D), 5R (5D), and 6R (7D), possessing resistance ... ...

    Abstract Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici Eriks. & E. Henn, is the most devastating fungal disease of bread wheat. Here, a wheat-rye multiple disomic substitution line, SLU126 4R (4D), 5R (5D), and 6R (7D), possessing resistance against 25 races of P. striiformis f. sp. tritici, was used and crossed with Chinese Spring ph1b to induce homeologous recombination to produce introgressions with a reduced rye chromosome segment. Seedling assays confirmed that the stripe rust resistance from SLU126 was retained over multiple generations. Through genotyping-by-sequencing (GBS) platforms and aligning the putative GBS-single-nucleotide polymorphism (SNPs) to the full-length annotated rye nucleotide-binding leucine-rich repeat (NLR) genes in the parental lines (CS ph1b, SLU126, CSA, and SLU820), we identified the physical position of 26, 13, and 9 NLR genes on chromosomes 6R, 4R, and 5R, respectively. The physical positions of 25 NLR genes on chromosome 6R were identified from 568,460,437 bp to 879,958,268 bp in the 6RL chromosome segment. Based on these NLR positions on the 6RL chromosome segment, the three linked SNPs (868,123,650 to 873,285,112 bp) were validated through kompetitive allele-specific PCR (KASP) assays in SLU126 and resistance plants in the family 29-N3-5. Using these KASP markers, we identified a small piece of the rye translocation (i.e., as a possible 6DS.6DL.6RL.6DL) containing the stripe resistance gene, temporary designated YrSLU, within the 6RL segment. This new stripe rust resistance gene provides an additional asset for wheat improvement to mitigate yield losses caused by stripe rust.
    Keywords Puccinia striiformis f. tritici ; assets ; chromosomes ; fungi ; genotyping by sequencing ; resistance genes ; rye ; seedlings ; stripe rust of wheat ; substitution lines ; wheat ; genotyping-by-sequencing ; KASP markers ; NLR genes ; physical mapping ; translocation
    Language English
    Dates of publication 2023-0301
    Size p. 720-729.
    Publishing place The American Phytopathological Society
    Document type Article ; Online
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS-07-22-1666-RE
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Rating Scales for Assessing Infection Responses of Barley Infected with Cochliobolus sativus.

    Fetch, Thomas G / Steffenson, Brian J

    Plant disease

    2019  Volume 83, Issue 3, Page(s) 213–217

    Abstract: Spot blotch, caused by Cochliobolus sativus, is a common foliar disease of barley that is controlled primarily through the deployment of resistant cultivars. Resistance is often assessed at the seedling and adult plant stages, but currently no ... ...

    Abstract Spot blotch, caused by Cochliobolus sativus, is a common foliar disease of barley that is controlled primarily through the deployment of resistant cultivars. Resistance is often assessed at the seedling and adult plant stages, but currently no comprehensive visual scale exists that describes the full spectrum of infection responses (IRs) occurring on barley. From the evaluation of a diverse collection of barley germ plasm and C. sativus isolates, a 1 to 9 IR scale was developed based on the type (presence of necrosis and chlorosis) and relative size of spot blotch lesions observed on the second leaves of barley seedlings. The nine IRs were classified into three general categories of low (IRs 1 to 3), intermediate (IRs 4 and 5), and high (IRs 6 to 9) host-parasite compatibility. Low IRs consisted of minute to small necrotic lesions with no or very slight diffuse marginal chlorosis. Intermediate IRs consisted of medium-sized necrotic lesions with a distinct but restricted chlorotic margin, while high IRs consisted of large necrotic lesions with distinct chlorotic margins and varying degrees of expanding diffuse chlorosis. In addition to the seedling IR scale, a four-class adult plant IR scale (R = resistant, MR = moderately resistant, MS = moderately susceptible, and S = susceptible) was developed based again on the type and relative size of lesions present on the leaves. These rating scales should be useful for many types of studies on spot blotch of barley.
    Language English
    Publishing date 2019-03-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS.1999.83.3.213
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Identification of a Small Translocation from 6R Possessing Stripe Rust Resistance to Wheat.

    Ashraf, Rimsha / Johansson, Eva / Vallenback, Pernilla / Steffenson, Brian J / Bajgain, Prabin / Rahmatov, Mahbubjon

    Plant disease

    2023  Volume 107, Issue 3, Page(s) 720–729

    Abstract: Wheat stripe rust, caused ... ...

    Abstract Wheat stripe rust, caused by
    MeSH term(s) Triticum/genetics ; Triticum/microbiology ; Chromosomes, Plant/genetics ; Disease Resistance/genetics ; Basidiomycota/genetics ; Alleles ; Translocation, Genetic ; Puccinia
    Language English
    Publishing date 2023-03-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS-07-22-1666-RE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Virulence Dynamics of the Barley Leaf Rust Pathogen (

    Nazareno, Eric S / Matny, Oadi / Jin, Yue / Fetch, Thomas / Rouse, Matthew N / Steffenson, Brian J

    Plant disease

    2023  Volume 107, Issue 12, Page(s) 3952–3957

    Abstract: Barley leaf rust, caused ... ...

    Abstract Barley leaf rust, caused by
    MeSH term(s) United States ; Chromosome Mapping ; Hordeum/genetics ; Disease Resistance/genetics ; Virulence ; Basidiomycota/genetics ; Plant Diseases/genetics
    Language English
    Publishing date 2023-12-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS-03-23-0583-RE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Virulence Dynamics of the Barley Leaf Rust Pathogen (Puccinia hordei) in the United States from 1989 to 2020

    Nazareno, Eric S. / Matny, Oadi / Jin, Yue / Fetch, Thomas / Rouse, Matthew N. / Steffenson, Brian J.

    Plant Disease. 2023 Dec. 01, v. 107, no. 12 p.3952-3957

    2023  

    Abstract: Barley leaf rust, caused by Puccinia hordei, is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei ... ...

    Abstract Barley leaf rust, caused by Puccinia hordei, is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei isolates collected in the United States from the 1989 to 2000 and 2010 to 2020 survey periods on 15 Rph (Reaction to Puccinia hordei) genes. We analyzed linearized infection type data to detect virulence patterns across the United States and in five geographical regions: Pacific/West (PW), Southwest (SW), Midwest (MW), Northeast (NE), and Southeast (SE). Over 32 years, we observed high mean infection scores for Rph1.a, Rph4.d, and Rph8.h; intermediate scores for Rph2.b, Rph9.i, Rph10.o, Rph11.p, and Rph13.x; and low scores for Rph3.c, Rph5.e, Rph5.f, Rph7.g, Rph9.z, Rph14.ab, and Rph15.ad. Virulence for Rph2.b, Rph3.c, Rph5.e, Rph9.z, Rph10.o, Rph11.p, and Rph13.x significantly differed between the two survey periods. From 1989 to 2020, regional patterns of virulence were found for Rph5.e, Rph5.f, Rph7.g, and Rph14.ab, while regionalities of virulence for Rph3.c, Rph9.i, Rph9.z were only observed in the 2010 to 2020 survey period. Virulence associations were also detected in the P. hordei population. Notably, isolates that were virulent to Rph5.e and Rph6.f were more likely to be avirulent to Rph7.g and Rph13.x, and vice versa. In decreasing order of effectiveness, Rph15.ad, Rph5.e, Rph3.c, Rph9.z, Rph7.g, Rph5.f, and Rph14.ab were the most effective Rph genes in the United States from 1989 to 2020. Pyramiding Rph15.ad with other widely effective Rph and adult plant resistance genes may provide long-lasting resistance against P. hordei.
    Keywords Puccinia hordei ; barley ; leaf rust ; mature plants ; pathogens ; surveys ; virulence ; pathotyping ; regional variation ; rust resistance ; virulence survey
    Language English
    Dates of publication 2023-1201
    Size p. 3952-3957.
    Publishing place The American Phytopathological Society
    Document type Article ; Online
    ZDB-ID 754182-x
    ISSN 0191-2917
    ISSN 0191-2917
    DOI 10.1094/PDIS-03-23-0583-RE
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  7. Article ; Online: The genetic basis of transpiration sensitivity to vapor pressure deficit in wheat

    Tamang, Bishal G. / Monnens, Daniel / Anderson, James A. / Steffenson, Brian J. / Sadok, Walid

    Physiologia Plantarum. 2022 Sept., v. 174, no. 5 p.e13752-

    2022  

    Abstract: Genetic manipulation of whole‐plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non‐ ... ...

    Abstract Genetic manipulation of whole‐plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non‐linear TR response to VPD are expected to achieve yield gains under terminal drought, thanks to a water conservation strategy, while those with a linear response exhibit a consumptive strategy that is more adequate for well‐watered or transient‐drought environments. In wheat, previous efforts indicated that TR has a genetic basis under naturally fluctuating conditions, but because TR is responsive to variation in temperature, photosynthetically active radiation, and evaporative demand, the genetic basis of its response VPD per se has never been isolated. To address this, we developed a controlled‐environment gravimetric phenotyping approach where we imposed VPD regimes independent from other confounding environmental variables. We screened three nested association mapping populations totaling 150 lines, three times over a 3‐year period. The resulting dataset, based on phenotyping nearly 1400 plants, enabled constructing 63‐point response curves for each genotype, which were subjected to a genome‐wide association study. The analysis revealed a hotspot for TR response to VPD on chromosome 5A, with SNPs explaining up to 17% of the phenotypic variance. The key SNPs were found in haploblocks that are enriched in membrane‐associated genes, consistent with the hypothesized physiological determinants of the trait. These results indicate a promising potential for identifying new alleles and designing next‐gen wheat cultivars that are better adapted to current and future drought regimes.
    Keywords chromosomes ; cultivars ; data collection ; drought ; evaporative demand ; genetic engineering ; genome-wide association study ; genotype ; phenotype ; phenotypic variation ; photosynthetically active radiation ; temperature ; transpiration ; vapor pressure deficit ; water conservation ; wheat
    Language English
    Dates of publication 2022-09
    Publishing place Blackwell Publishing Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2020837-6
    ISSN 1399-3054 ; 0031-9317
    ISSN (online) 1399-3054
    ISSN 0031-9317
    DOI 10.1111/ppl.13752
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  8. Article: Improving winter barley adaptation to freezing and heat stresses in the U.S. Midwest: bottlenecks and opportunities

    Sadok, Walid / Wiersma, Jochum J. / Steffenson, Brian J. / Snapp, Sigelinde S. / Smith, Kevin P.

    Field crops research. 2022 Oct. 01, v. 286

    2022  

    Abstract: Continental cropping systems are increasingly exposed to extreme and opposing trends of temperatures over the same growing season. This situation is epitomized by winter barley grown in the Upper Midwest, which is subject to temperatures that can be as ... ...

    Abstract Continental cropping systems are increasingly exposed to extreme and opposing trends of temperatures over the same growing season. This situation is epitomized by winter barley grown in the Upper Midwest, which is subject to temperatures that can be as low as −30 °C during the winter and over 30 °C during summer. This interaction severely limits the potential of this emerging crop, by threatening the winter survival of the crown which is often exposed to lethal freezing stress and by exposing reproductive organs to high temperature (HT) stress, to which this cool-season grass is highly sensitive. This poses a unique challenge that requires the discovery and capture of well-defined sets of traits enabling adaptation to extreme tail ends of a stressor, with limited trade-offs, while minimizing costs. Here, based on a critical literature review, we propose a framework integrating i) environmental characterization (envirotyping), ii) envirotype-relevant scouting of genetic resources, iii) ecophysiology-informed trait identification and phenotyping and iv) breeding pipelines. We outline propositions and guidelines for implementing these steps and discuss their feasibility, with an emphasis on i) identifying novel genetic resources and eco-physiological traits relevant to this problem, ii) navigating their physiological trade-offs and iii) leveraging this information to develop ad hoc phenotyping methods for deployment in breeding programs. Our review indicates that the eco-physiological and genetic bases for improving tolerance to both stresses in the same organism likely exists based on evidence from crop relatives and extremophile species, with smaller vasculature (freezing tolerance) and transpirational cooling (HT tolerance) being prime examples. Our findings indicate that such traits could be captured with minimal trade-offs, and that is possible to use similar phenotyping concepts (thermal imaging) and infrastructure (cold/heat tents) to screen for these traits and accelerate breeding to enhance adaptation to temperature extremes.
    Keywords cold ; cool season grasses ; cooling ; ecophysiology ; extremophiles ; heat ; infrastructure ; overwintering ; phenotype ; research ; summer ; temperature ; winter ; winter barley ; Midwestern United States
    Language English
    Dates of publication 2022-1001
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 435684-6
    ISSN 1872-6852 ; 0378-4290
    ISSN (online) 1872-6852
    ISSN 0378-4290
    DOI 10.1016/j.fcr.2022.108635
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  9. Article ; Online: The genetic basis of transpiration sensitivity to vapor pressure deficit in wheat.

    Tamang, Bishal G / Monnens, Daniel / Anderson, James A / Steffenson, Brian J / Sadok, Walid

    Physiologia plantarum

    2022  Volume 174, Issue 5, Page(s) e13752

    Abstract: Genetic manipulation of whole-plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non- ... ...

    Abstract Genetic manipulation of whole-plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non-linear TR response to VPD are expected to achieve yield gains under terminal drought, thanks to a water conservation strategy, while those with a linear response exhibit a consumptive strategy that is more adequate for well-watered or transient-drought environments. In wheat, previous efforts indicated that TR has a genetic basis under naturally fluctuating conditions, but because TR is responsive to variation in temperature, photosynthetically active radiation, and evaporative demand, the genetic basis of its response VPD per se has never been isolated. To address this, we developed a controlled-environment gravimetric phenotyping approach where we imposed VPD regimes independent from other confounding environmental variables. We screened three nested association mapping populations totaling 150 lines, three times over a 3-year period. The resulting dataset, based on phenotyping nearly 1400 plants, enabled constructing 63-point response curves for each genotype, which were subjected to a genome-wide association study. The analysis revealed a hotspot for TR response to VPD on chromosome 5A, with SNPs explaining up to 17% of the phenotypic variance. The key SNPs were found in haploblocks that are enriched in membrane-associated genes, consistent with the hypothesized physiological determinants of the trait. These results indicate a promising potential for identifying new alleles and designing next-gen wheat cultivars that are better adapted to current and future drought regimes.
    MeSH term(s) Vapor Pressure ; Triticum/genetics ; Genome-Wide Association Study ; Plant Leaves/physiology ; Plant Transpiration/genetics
    Language English
    Publishing date 2022-10-25
    Publishing country Denmark
    Document type Journal Article
    ZDB-ID 2020837-6
    ISSN 1399-3054 ; 0031-9317
    ISSN (online) 1399-3054
    ISSN 0031-9317
    DOI 10.1111/ppl.13752
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  10. Article ; Online: Developing adapted wheat lines with broad-spectrum resistance to stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing data.

    Yazdani, Mahboobeh / Rouse, Matthew N / Steffenson, Brian J / Bajgain, Prabin / Patpour, Mehran / Johansson, Eva / Rahmatov, Mahbubjon

    PloS one

    2023  Volume 18, Issue 10, Page(s) e0292724

    Abstract: Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum ... ...

    Abstract Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses.
    MeSH term(s) Triticum/genetics ; Triticum/microbiology ; Genotype ; Chromosome Mapping ; Disease Resistance/genetics ; Alleles ; Basidiomycota/genetics ; Plant Diseases/genetics ; Plant Diseases/microbiology
    Language English
    Publishing date 2023-10-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0292724
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