Scholarly Work - Plant Sciences & Plant Pathology
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/8870
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Item Canopeo app as image-based phenotyping tool in controlled environment utilizing Arabidopsis mutants(Public Library of Science, 2024-03) Hale, Gabriella; Yuan, Ning; Mendu, Lavanya; Ritchie, Glen; Mendu, VenugopalCanopeo app was developed as a simple, accurate, rapid, and free tool to analyze ground cover fraction (GCF) from red-green-blue (RGB) images and videos captured in the field. With increasing interest in tools for plant phenotyping in controlled environments, the usefulness of Canopeo to identify differences in growth among Arabidopsis thaliana mutants in a controlled environment were explored. A simple imaging system was used to compare Arabidopsis mutants based on the FLAVIN-BINDING, KELCH REPEAT, F-BOX-1 (FKF1) mutation, which has been identified with increased biomass accumulation. Two FKF1 lines such as null expression (fkf1-t) and overexpression (FKF1-OE) lines were used along with wild type (Col-0). Canopeo was used to phenotype plants, based on biomass estimations. Under long-day photoperiod, fkf1-t had increased cellulose biosynthesis, and therefore biomass. Resource partitioning favored seedling vigor and delayed onset of senescence. In contrast, FKF1-OE illustrated a determinative growth habit where plant resources are primarily allocated for seed production. This study demonstrates the use of Canopeo for model plants and highlights its potential for phenotyping broadleaved crops in controlled environments. The value of adapting Canopeo for lab use is those with limited experience and resources have access to phenotyping methodology that is simple, accessible, accurate, and cost-efficient in a controlled environment setting.Item A “solid” solution for wheat stem sawfly (Hymenoptera: Cephidae) resistance: Genetics, breeding and development of solid stem wheat(Wiley, 2023-06) Bathini, Akshara; Mendu, Lavanya; Pratap Singh, Nagendra; Cook, Jason; Weaver, David; Sherman, Jamie; Hager, Megan; Mondal, Suchismita; Mendu, VenugopalWheat (Triticum spp. L) production needs to be improved to meet the needs of a global population of >9 billion people by 2050. Increasing the productivity of the crop under conditions of abiotic and biotic stress to achieve food security continues to be a challenging proposition. Wheat stem sawfly (WSS) (Cephus cinctus Norton) has been considered as a serious pest of wheat since the late 19th century, causing devastating losses of wheat productivity in the Northern Great Plains of United States and regions of Canada. Developing resistant varieties of wheat that show consistent agronomic performances in varying environments is an effective strategy to manage WSS infestations. To achieve this goal, it is necessary to understand the underlying mechanisms of WSS infestation, damage, subsequent response of the host plant, and resulting yield losses. The review focuses on genetics, breeding, and development of solid stem (SS)-mediated WSS resistance in wheat since it has been the most effective method of genetic resistance in reducing wheat yield losses. Furthermore, the knowledge gaps that need to be addressed to develop an effective resistant cultivar against WSS are also discussed.Item Characterization of chromatin accessibility and gene expression reveal the key genes involved in cotton fiber elongation(Wiley, 2023-07) Chen, Guoquan; Liu, Zhao; Li, Shengdong; Liu, Lili; Wang, Zhi; Mendu, Venugopal; Li, Fuguang; Yang, ZuorenCotton (Gossypium hirsutum L.) is an important economic crop, and cotton fiber is one of the longest plant cells, which provides an ideal model for the study of cell elongation and secondary cell wall synthesis. Cotton fiber length is regulated by a variety of transcription factors (TF) and their target genes; however, the mechanism of fiber elongation mediated by transcriptional regulatory networks is still unclear to a large extent. Here, we used a comparative assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) assay and RNA-seq analysis to identify fiber elongation transcription factors and genes using the short-fiber mutant ligon linless-2 (Li2) and wild type (WT). A total of 499 differential target genes were identified and GO analysis shows that differential genes are mainly involved in plant secondary wall synthesis and microtubule-binding processes. Analysis of the genomic regions preferentially accessible (Peak) has identified a number of overrepresented TF-binding motifs, highlighting sets of TFs that are important for cotton fiber development. Using ATAC-seq and RNA-seq data, we have constructed a functional regulatory network of each TF regulatory target gene and also the network pattern of TF regulating differential target genes. Further, to obtain the genes related to fiber length, the differential target genes were combined with FLGWAS data to identify the genes highly related to fiber length. Our work provides new insights into cotton fiber elongation.Item Two decades of association mapping: Insights on disease resistance in major crops(Frontiers Media SA, 2022-12) Gangurde, Sunil S.; Xavier, Alencar; Dashrath Naik, Yogesh; Chand Jha, Uday; Krushnaji Rangari, Sagar; Kumar, Raj; Sai Reddy, M. S.; Channale, Sonal; Elango, Dinakaran; Rouf Mir, Reyazul; Zwart, Rebecca; Laxuman, C.; Kishan Sudini, Hari; Pandey, Manish K.; Punnuri, Somashekhar; Mendu, Venugopal; Reddy, Umesh K.; Guo, Baozhu; Gangarao, N. V. P. R.; Sharma, Vinay K.; Wang, Xingjun; Zhao, Chuanzhi; Thudi, MahendarClimate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.Item Seed coat mediated resistance against Aspergillus flavus infection in peanut(Seed coat mediated resistance against Aspergillus flavus infection in peanut, 2022-12) Mendu, Lavanya; Cobos, Christopher J.; Tengey, Theophilus K.; Commey, Leslie; Balasubramanian, Vimal K.; Williams, Lindsay D.; Dhillon, Kamalpreet K.; Sharma, Dimple; Pandey, Manish K.; Falalou, Hamidou; Varshney, Rajeev K.; Burow, Mark D.; Sudini, Hari Kishan; Mendu, VenugopalToxic metabolites known as aflatoxins are produced via certain species of the Aspergillus genus, specifically A. flavus, A. parasiticus, A. nomius, and A. tamarie. Although various pre- and post-harvest strategies have been employed, aflatoxin contamination remains a major problem within peanut crop, especially in subtropical environments. Aflatoxins are the most well-known and researched mycotoxins produced within the Aspergillus genus (namely Aspergillus flavus) and are classified as group 1 carcinogens. Their effects and etiology have been extensively researched and aflatoxins are commonly linked to growth defects and liver diseases in humans and livestock. Despite the known importance of seed coats in plant defense against pathogens, peanut seed coat mediated defenses against Aspergillus flavus resistance, have not received considerable attention. The peanut seed coat (testa) is primarily composed of a complex cell wall matrix consisting of cellulose, lignin, hemicellulose, phenolic compounds, and structural proteins. Due to cell wall desiccation during seed coat maturation, postharvest A. flavus infection occurs without the pathogen encountering any active genetic resistance from the live cell(s) and the testa acts as a physical and biochemical barrier only against infection. The structure of peanut seed coat cell walls and the presence of polyphenolic compounds have been reported to inhibit the growth of A. flavus and aflatoxin contamination; however, there is no comprehensive information available on peanut seed coat mediated resistance. We have recently reviewed various plant breeding, genomic, and molecular mechanisms, and management practices for reducing A. flavus infection and aflatoxin contamination. Further, we have also proved that seed coat acts as a physical and biochemical barrier against A. flavus infection. The current review focuses specifically on the peanut seed coat cell wall-mediated disease resistance, which will enable researchers to understand the mechanism and design efficient strategies for seed coat cell wall-mediated resistance against A. flavus infection and aflatoxin contamination.Item Insight into the Roles of Proline-Rich Extensin-like Receptor Protein Kinases of Bread Wheat (Triticum aestivum L.)(MDPI AG, 2022-06) Shumayla; Mendu, Venugopal; Singh, Kashmir; Kumar Upadhyay, SantoshProline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their gene and protein structures, various cis-regulatory elements, expression profiling, and interacting miRNAs. The TaPERK genes formed 12 homeologous groups and clustered into four phylogenetic clades. All the proteins exhibited a typical domain organization of PERK and consisted of conserved proline residue repeats and serine-proline and proline-serine repeats. Further, the tyrosine-x-tyrosine (YXY) motif was also found conserved in thirteen TaPERKs. The cis-regulatory elements and expression profiling under tissue developmental stages suggested their role in plant growth processes. Further, the differential expression of certain TaPERK genes under biotic and abiotic stress conditions suggested their involvement in defense responses as well. The interaction of TaPERK genes with different miRNAs further strengthened evidence for their diverse biological roles. In this study, a comprehensive analysis of obtained TaPERK genes was performed, enriching our knowledge of TaPERK genes and providing a foundation for further possible functional analyses in future studies.Item Lignin and cellulose content differences in roots of different cotton cultivars associated with different levels of Fusarium wilt race 4 (FOV4) resistance-response(Elsevier BV, 2022-12) Mendu, Lavanya; Ulloa, Mauricio; Payton, Paxton; Monclova-Santana, Cecilia; Chagoya, Jennifer; Mendu, VenugopalFusarium wilt disease is caused by fungal pathogen Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4), which enters the plant through the root system for its successful colonization of xylem. Plant cell wall forms the primary barrier against pathogen infection in addition to providing the mechanical support. However, the role of cell walls for developing FOV4 resistance has not been explored. The present study focused on examining the variation in lignin and cellulose contents in root tissue of Pima (Gossypium barbadense L.) and Upland (G. hirsutum L.) cotton with different levels of FOV4 wilt resistance-response. Traditional cultivar-checks susceptible Pima S-7, resistant Pima S-6, susceptible Upland Stoneville 474, and resistant Upland PSSJ-FRU14 (U77B) were used in the present study. Biochemical differences in root cell walls were investigated first by a rapid visual staining method for both lignin (phloroglucinol-HCL) and cellulose (Congo red) contents of root cross sections at three stages of cotton plant development followed by biochemical estimation of root lignin and cellulose contents. These studies revealed differences between susceptible and resistant cultivars at specific stages visually by rapid staining as well as biochemically in their cellulose and lignin contents within Pima and Upland cultivars. This is the first report in lignin and cellulose content estimation of Pima and Upland resistant and susceptible FOV4 cotton cultivars and paves the way for developing cell wall mediated FOV resistance.Item Mutation in the Endo-β-1,4-glucanase (KORRIGAN) Is Responsible for Thick Leaf Phenotype in Sorghum(MDPI AG, 2023-12) Mendu, Lavanya; Jalathge, Gayani; Kaur Dhillon, Kamalpreet; Pratap Singh, Nagendra; Kumar Balasubramanian, Vimal; Fewou, Rebecca; Gitz, Dennis C.; Chen, Junping; Xin, Zhanguo; Mendu, VenugopalSorghum [Sorghum bicolor (L.) Moench] is an important crop for food, feed, and fuel production. Particularly, sorghum is targeted for cellulosic ethanol production. Extraction of cellulose from cell walls is a key process in cellulosic ethanol production, and understanding the components involved in cellulose synthesis is important for both fundamental and applied research. Despite the significance in the biofuel industry, the genes involved in sorghum cell wall biosynthesis, modification, and degradation have not been characterized. In this study, we have identified and characterized three allelic thick leaf mutants (thl1, thl2, and thl3). Bulked Segregant Analysis sequencing (BSAseq) showed that the causal mutation for the thl phenotype is in endo-1,4-β-glucanase gene (SbKOR1). Consistent with the causal gene function, the thl mutants showed decreased crystalline cellulose content in the stem tissues. The SbKOR1 function was characterized using Arabidopsis endo-1,4-β-glucanase gene mutant (rsw2-1). Complementation of Arabidopsis with SbKOR1 (native Arabidopsis promoter and overexpression by 35S promoter) restored the radial swelling phenotype of rsw2-1 mutant, proving that SbKOR1 functions as endo-1,4-β-glucanase. Overall, the present study has identified and characterized sorghum endo-1,4-β-glucanase gene function, laying the foundation for future research on cell wall biosynthesis and engineering of sorghum for biofuel production.Item Lignin and cellulose content differences in roots of different cotton cultivars associated with different levels of Fusarium wilt race 4 (FOV4) resistance-response(Elsevier, 2022-12) Mendu, Lavanya; Ulloa, Mauricio; Payton, Paxton; Monclova-Santana, Cecilia; Chagoya, Jennifer; Mendu, VenugopalFusarium wilt disease is caused by fungal pathogen Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4), which enters the plant through the root system for its successful colonization of xylem. Plant cell wall forms the primary barrier against pathogen infection in addition to providing the mechanical support. However, the role of cell walls for developing FOV4 resistance has not been explored. The present study focused on examining the variation in lignin and cellulose contents in root tissue of Pima (Gossypium barbadense L.) and Upland (G. hirsutum L.) cotton with different levels of FOV4 wilt resistance-response. Traditional cultivar-checks susceptible Pima S-7, resistant Pima S-6, susceptible Upland Stoneville 474, and resistant Upland PSSJ-FRU14 (U77B) were used in the present study. Biochemical differences in root cell walls were investigated first by a rapid visual staining method for both lignin (phloroglucinol-HCL) and cellulose (Congo red) contents of root cross sections at three stages of cotton plant development followed by biochemical estimation of root lignin and cellulose contents. These studies revealed differences between susceptible and resistant cultivars at specific stages visually by rapid staining as well as biochemically in their cellulose and lignin contents within Pima and Upland cultivars. This is the first report in lignin and cellulose content estimation of Pima and Upland resistant and susceptible FOV4 cotton cultivars and paves the way for developing cell wall mediated FOV resistance.Item Peanut Seed Coat Acts as a Physical and Biochemical Barrier against Aspergillus flavus Infection(MDPI AG, 2021-11) Commey, Leslie; Tengey, Theophilus K.; Cobos, Christopher J.; Dampanaboina, Lavanya; Dhillon, Kamalpreet K.; Pandey, Manish K.; Sudini, Hari Kishan; Falalou, Hamidou; Varshney, Rajeev K.; Burow, Mark D.; Mendu, VenugopalAflatoxin contamination is a global menace that adversely affects food crops and human health. Peanut seed coat is the outer layer protecting the cotyledon both at pre- and post-harvest stages from biotic and abiotic stresses. The aim of the present study is to investigate the role of seed coat against A. flavus infection. In-vitro seed colonization (IVSC) with and without seed coat showed that the seed coat acts as a physical barrier, and the developmental series of peanut seed coat showed the formation of a robust multilayered protective seed coat. Radial growth bioassay revealed that both insoluble and soluble seed coat extracts from 55-437 line (resistant) showed higher A. flavus inhibition compared to TMV-2 line (susceptible). Further analysis of seed coat biochemicals showed that hydroxycinnamic and hydroxybenzoic acid derivatives are the predominant phenolic compounds, and addition of these compounds to the media inhibited A. flavus growth. Gene expression analysis showed that genes involved in lignin monomer, proanthocyanidin, and flavonoid biosynthesis are highly abundant in 55-437 compared to TMV-2 seed coats. Overall, the present study showed that the seed coat acts as a physical and biochemical barrier against A. flavus infection and its potential use in mitigating the aflatoxin contamination.