Progress 03/28/16 to 02/23/21
Outputs
Target Audience:The primary audience iwll be plant patholggists and breeders intersted in developong disease resistant sorghum and cotton Changes/Problems:Wehave adopted whole genome sequ3ning and analysis as the primary tool for identification of resistance genes in the host and pathotype determinants in the pathogens. We are also hoping to use RNA-seq to verify activity of the genes identified at the appropriate time and tissue after inoculation. What opportunities for training and professional development has the project provided?Due primarily to the COVID epidemic, the student who completed a PhD working on the Johnsongrass project was able to stay on as a Post-doc and his research is or will be published in at least 3 additional publications. How have the results been disseminated to communities of interest?I believe all manuscripts publihed prio to the closing date of the project are listed in the proir reports. The project is renewed and 2021 papers will be listed in those reports. What do you plan to do during the next reporting period to accomplish the goals?We are focusing on identification of sorghum disease resistance in cultivars from countries where anthracnose and leaf blight are major constraints, We are also attempting to use sequencing to try to identify markers and genes in the anthracnose and head smut pathogens taht create new pathotypes.
Impacts
What was accomplished under these goals?
Wew were able to identify a molecular marker fo the FoV 4 strain that is a threat to cotton. We have several publications documenting differences in response of sorghum and johnsongrass to pathogenic fungi. We have identified a number of sorghum defense response genes based association with single nucleotide polymorphisms detectedon whole genome sequences of sorghum cultivars resistant or susceptible to several pathogens. We were able to use RNAi to create cotton that appeared to have resistance to nematodes, but were unable to secure funding for verification in whole plants.
Publications
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Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Researchers interested in disease resistance in sorghum and cotton, as well as those interested in pathogen population diversity as detected by DNA analysis. Changes/Problems:The main change that has occured is the use of whole genome sequencing to identify SNPS or indels that occurr throuout the genome of the host and the pathogen, a natural progression made possible due to reduced cost of sequencing. What opportunities for training and professional development has the project provided? Ezekiel Ahn completed his PhD in Plant Pathology and is currently working as a Post Doc on the project while seeking for a position or PostDoc to expand his science background. Part-time PostDoc Tany Wagner has developed the use of CRISPR technologyfor use in Fusarium. Undergraduate Ferris Fan has gained experience in laboratory reseach beyond making media and taking care of plant. How have the results been disseminated to communities of interest?Publications and 'virtual'participation in Cotton Conference Departmental seminar by Dr. Ahn. What do you plan to do during the next reporting period to accomplish the goals?We are taking advantage of the HPRC (supercomputer) to attempt to identify SNPs in the pathogen that show assocaition with pothogenic races. We are collaborating with Dr. Umesh Reddy, West Virginia State University to use RNA seq to identify genes involved in the interactions betwee resistant and susceptibe sorghum after inoculation with C. sublineola.
Impacts
What was accomplished under these goals?
1) SNPs idnetified from over 100 samples of C. sublineola and 44 samples of S. reiliana, via whole genome sequencing. 2) Phylogenetic analsis of S. reiliana does not reveal association with pathotype, but analyisis is not complete for SNP data. 3) Two papers; while some sorghum isolates can cause disease in johnsongrass and vice versa, levels of virulence on cross hosts is low. 4) Two papers identify genes via SNP alleles that appear to be associated with resistance/susceptibility. 5) Noprogress (not funded)
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Radwan, G.L., Prom, L.K., Odvody, G., Magill C.W. (2019). Mating type a locus alleles and genomic polymorphism in Sporisorium reilianum: comparison of sorghum isolates to those from maize. Australasian Plant Pathology 48:119-129
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wagner, T.A., Cai, Y., Bell, A.A., Puckhabe,r L.S., Magill, C., Duke, S.E., Liu, J. (2019). RNAi suppression of CYP82D P450 hydroxylase, an enzyme involved in gossypol biosynthesis, enhances resistance to Fusarium wilt in cotton. Journal of Phytopathology 168:103-112
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Ahn, E., Odvody, G., Prom, L.K., Magill, C. (2020). Late Growth Stages of Johnsongrass Can Act as an Alternate Host of Colletotrichum sublineola. Plant Health Progress 21:60-62
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Prom, L.K., Cuevas, H.E., Ahn, E., Isakeit, T., Rooney, W.L., Magill. C. (2020). Genome-wide association study of grain mold resistance in sorghum association panel as affected by inoculation with Alternaria alternata alone and Alternaria alternata, Fusarium thapsinum, and Curvularia lunata combined. European Journal of Plant Pathology 157:783-798
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Prom, L.K., Cuevas, H., Isakeit. T., Magill, C. (2020). Screening Sorghum Accessions for Resistance against Anthracnose and Grain Mold through Inoculating with Pathogens. Journal of Experimental Agriculture International:73-83
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Prom, L.K., Adamou I, Haougui, A., Abdoulkadri ,A., Karimou, I., Al,i O., Magill, C. (2020). Response of the Set of Anthracnose Differentials to other Foliar and Panicle Diseases in Niger. Journal of Agriculture and Crops 6:1-4
- Type:
Theses/Dissertations
Status:
Other
Year Published:
2020
Citation:
Ahn, E. 2020 Host defense responses of sorghum and johnsongrass to Colletotrichum sublineolum and identification of candidate defense related genes in sorghum. Dissertation,TAMU
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Plant Pathologists and breeders interested in incorpoarating genetic resistance into culativars of sorghum for use by growers. Changes/Problems:We had a major problem with contamination when trying to grow S. reilianum in liquid culture for DNA extraction and sequencing. We are repurifying the cultures and will extract DNA directly from colonies growing on plates. Due to the loss of almost a year between the award of funds and actually receiveing funds, we have asked for a one year extension on our CAP grant. What opportunities for training and professional development has the project provided?An undergraduate student learned the techonolgy involved with DNA extraction A graduate student has become proficient in the use of DNA comparative analysis and gene identification. How have the results been disseminated to communities of interest?Three publications in scientific journals with more on the way. What do you plan to do during the next reporting period to accomplish the goals? 1. Verify that identified genes show differential expression in resistant vs susceptible cultivars. 2. Compare isolates of Colletotrichum sublineola from sorghum and johnson grass for their effects on the other species. 3. Compare the effects of mixing compatible and incompatible strains ofColletotrichum sublineola to determine if induction of defense response genes alters the disease outcome.
Impacts
What was accomplished under these goals?
We were able to identify a number of genes via internal or nearby SNP DNA-based markers that appear to play a role in disease resistance in sorghum. These ase based on genome-wide assocaition study results using disease ratings and publicly available geneome sequences for a large number of inbred sorghum accessions.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Ahn E, Hu Z, Perumal R, Prom LK, Odvody G, Upadhyaya HD, Magill C (2019) Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut. PLOS ONE 14:e0216671
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Ahn E, Prom LK, Odvody G, Magill C (2019) Defense responses against the sorghum anthracnose pathogen in leaf blade and midrib tissue of johnsongrass and sorghum. Physiological and Molecular Plant Pathology 106:81-86
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Prom LK, Ahn E, Isakeit T, Magill C (2019) GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola. Theoretical and Applied Genetics 132:1389-1396
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:During this reporting period, publications we authored will provide information for other scientist working with sorghum diseases. The results will also provideinformation usefulto private companies engagedin sorghum breeding by identifyingsources of disease resistance, especially to anthracnose and headsmut. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate student Ezekiel Ahn has gained expretise in methods of plant pathology and the use of software for genomic analysis. Undergraduates Tiffany gunnels and Deepthi Perumal were trained toextractDNA from fungal isolates. The half time Post-doc continued analysis of defense response product in a USDA cooperative project involving cotton wilt. How have the results been disseminated to communities of interest?Only via publications in academic journals over this period. What do you plan to do during the next reporting period to accomplish the goals?1. Complete and publish identifiation of genes identified by SNPs associated withresistanceto anthranose, to head smut and to downy mildewin the cultivars in the sorghum minicore collection. 2. Determine the pathotype of as many of our C. sublineola isolates as possible and test for pathotype-associated DNA-based polymorphisms. 3. Examine johnsongrass cultivars for disease and defense response after inoculation with sorghum downy mildew and head smut isolates.
Impacts
What was accomplished under these goals?
1. & 2. Data from Rad-Sequencing of a number of isolates of Colletotrichum sublineola fromdiffernt locations is now available, and a large number of single nucleotide polymorphisms (SNPs) have been identified. Although the dataallowcomparisons among isolates from different regions, we do not yet have sufficient pathotypesto identify SNPs associated with pathotypespecificity. DNA from 180 Sporisorium reilianum isolates has beenextracted and iseady for sequencing. 3.Two isolates of Colletotrichum sublineola isolated from johnsongrassdescribed inpart 1 were phylogenetically separated fromthe sorghum isolates. Inoculation of host differential sorghum cultivars with C. sublineola isolates from johnsongrass resulted in high levels of defense response pigmentation and stunting in most cultivars, but did not lead to sporulation in the fungus. Response of johnsongrass to sorghum isolates was varied, as described in the first pulication listed. 4. We have used publicly available sorghum genomic sequencing reads to identify SNPS that are associated with response to anthracnose in the accessions fromboth the sorghum association panel and minicore collection. One publication has been submitted (after the term of this report) and another is in preparation. 5. No progress to report (no funding attained).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Prom,Louis, Cuevas, Hugo, , Perumal, Ramasamy, Isakeit , Thomas and Magill, Clint. 2017. Inheritance of reisitance of three sorghum lines to pathotypes of Colletotrichum sublineola, causal agent of anthrracnosee. Plant Pathology Journal (online) DOI: 10.3923/ppj.2018.75.79
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Prom, L.K., Magill, C.W. and Drosleskey,R. (2017) Aggressiveness of loose kernel smut isolate from Johnson grass on sorghum line BTx643. Journal of Agriculture and Crops, 3:94-96.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Prom, L.K., Radwan, R., Perumal, R. H., Cuevas, H. Katile, S.O., Isakeit, T. and Magill, C. 2017. Grain Biodeterioration of Sorghum Converted Lines Inoculated with a Mixture of Fusarium thapsinum and Curvularia lunata. Plant Pathology Journal, 16: 19-24.
- Type:
Book Chapters
Status:
Published
Year Published:
2018
Citation:
Perumal, R. Magill,. C . Prom. LK, Bashir, E. Peterson., G , Tesso, T. 2018
"Sorghum breeding for biotic stress tolerance" Ch 7 in Volume I, Achieving Sustainable Cultivation of Sorghum Taylor & Francis. Editor. Rooney, W
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Other scientists working with diseases of sorghum and cotton. Changes/Problems:We have found the use retached leaf assays for analysis of Johnsongrass susceptibility to anthracnose is more reliablethan the use of live plant infections, primarily due to temperature regulationproblems with our greenhouse and frequent infestations with sugar-cane aphids. What opportunities for training and professional development has the project provided?Ezekiel Ahn, the graduate student workingon the sorghum/Jonsongrass project has developed skills in microscopy, DNA sequence analysis and quantitative PCR. Dheepthi Perumal, the undergraduate worker is competent in sterileculture transfers and media preparation. Carlos Ortiz' work of FoV race 4 enhanced his skills in creating gene knockouts before acceptaing a position with USDA-NIFA. How have the results been disseminated to communities of interest?The information on FoV race4 presence in Texas was disseminated via Texas Agrilife Extension. Information on loose smut infecting sorghum was published. Ezekiel Ahn presented a 'progress report' as a Departmental seminar. What do you plan to do during the next reporting period to accomplish the goals?All ongoing projects will be continued. We are also collecting isolates of Sporisorium reiliana (sorghum head smut) for diversity analysis based on RAD-Sequencing.
Impacts
What was accomplished under these goals?
1) The PCR protocol developed in 2016 was used to demonstrate the race 4 of Fusarium oxysporum is present in cotton in west Texas. 2) RAD-DNAsequences of 140 samples of the sorghum anthracnose pathogen collected from the southern US were compared. Some geogaphical groupings are apparent in phylogenetic analsysis, but race information based on 13 host differentialsis so far only available for a small number of the isolates, so no comparsions are possible at this time. Although only two isolates werefrom Johnsongrass, they were quite similar and did not clusternot closely to the isolates from sorghum. 3) Loose smut collected from Johnson grass caused disease on the sorghum cultivars tested. However, while Johnsongrass cultivars differed in the level of visible host response to a mixture of sorghum isolates of C. sublineolum, essentially no sign of disease,as defined byability of the pathogen to sporulate,was observed. 4) Detached leaf assays have been used to observe responses of 5 defense-response genes in 24 Johnsongrass cultivars inoculated with Colletotrichum isolates from sorghum. While variation is present, data to date are inconclusive as to a role in resistance. 5) Plants in advanced generations continue to be resistant.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Prom, L.K., Radwan, G., Perumal, R., Cuevas, H., Katile, S., Isakeit, T., Magill, C., (2016) Grain biodeterioration of sorghum converted lines inoculated with a mixture of Fusarium thapsinum and Curvularia lunata Plant Pathology Journal, 16: 19-24.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Prom, L.K., Magill, C.W. and Drosleskey,R. (2017) Aggressiveness of loose kernel smut isolate from Johnson grass on sorghum line BTx643. Journal of Agriculture and Crops, 3:94-96.
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Progress 03/28/16 to 09/30/16
Outputs
Target Audience:Scientists, seed companies and famersinterested in managing fungal diseases of sorghum and cotton. Changes/Problems:We have had to reduce the number of Johnson Grass cultivars being tested for disease response to sorghum pathogens due to problems in getting sufficient seed. A subset of 20 cultivars has been assembled based on the ability to grow the plants directly from rhizomes, which actually provided the benefit that each of the researchers will be working with identical genotypes. What opportunities for training and professional development has the project provided?A new graduate student is bing funded from the Johnson Grass USDA sonsoredproject. How have the results been disseminated to communities of interest?Results have been reported through the published articles and by poster at the Beltwide Cotton Meetings which are attended by growers as well as scientists. What do you plan to do during the next reporting period to accomplish the goals?We expect to continue progress on each of the original goalslisted. Dr. Keerti Rathore and I are seeking funding for the nematode resistance project.
Impacts
What was accomplished under these goals?
1) In collaboration with Dr. Jinggao Liu, USDA, our Postdoctoral researcher discovered that the presence of a transposon in the PHO gene of Fusarium oxysporum f. sp. Vasinfectum, a pathogen that causes wilt in cotton is specifically associated with the most virulent race (Race 4) and used that information to develop a PCR diagnistic test. 2) Rad -equencing of over 150 isolates of Colletotrichum sublineolum, the causative agent of anthracnose in sorghum has been completed. Limited initial analysis has identified a large number of single nucleotide polymorphisms when the reads from each isolate are first matched to a published genomic sequence. Dr. Shichen Wang, a Bioinformatics Scientist with the Texas A&M Agrilife Research Genomics and Bioinformatics unit is providing assistance with analysis. 3) Thus far, none of the five Johnson grass cultivars tested has shown more than the red coloration associated with host defense responses when inoculated with a mixture of spores from five pathotypes that cause disease on susceptible sorghum cultivars. The tests are being repeated with the aid of Dr. Louis Prom (USDA) in his greenhpuse that is equipped with a misting system which allows much better assessment of resistant versus susceptible responses. 4) Initial tests using RT-rt-PCR have examined expression of genes previously shown to be induced in sorghum after inoculation with Colletotrichum sublineolum in Johnson grass. While the control levels of b-tubulin mRNA are nearly identical, variation in the levels of expression of these defense-response genes among these five Johnson grass cultivars two and three days post inoculation has been shown. However, since none of these Johnson grass cultivars developed anthracnose symptoms, it has not been able to associate activation of any specific gene with resistance. 5. The nematode work, although very promising has been set aside due to lack of funding for the project.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Ortiz, C.S., Bell, A.A., Magill, C.W., Liu, J. (2016) Specific PCR Detection of Fusarium oxysporum f. sp. vasinfectum California Race 4 Based on a Unique Tfo1 Insertion Event in the PHO Gene. Plant Disease:PDIS-03-16-0332-RE
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Prom, L.K., Perumal, R., Cuevas, H.E., Radwan, G., Katile, S., Isakeit, T., Magill, C. (2016) Assessing the vulnerability of sorghum converted lines to anthracnose and downy mildew infection. Journal of Agriculture and Crops. 2(10):101-106.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2017
Citation:
Prom, L.K., Radwan, G., Perumal, R., Cuevas, H., Katile, S., Isakeit, T., Magill, C., (2016) Grain biodeterioration of sorghum converted lines inoculated with a mixture of Fusarium thapsinum and Curvularia lunata Plant Pathology Journal
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
Ortiz, C.S., Liu, J., Magill, C.W., Bell,A.A. (2016) A PCR-Based Method for the Identification of Highly Pathogenic California Race 4 Isolates of Fusarium oxysporum f. Sp. Vasinfectum Presented at the Beltwide Cotton Meetings, New Orleans
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