ORCID Profile
0000-0001-7252-4397
Current Organisation
Colorado State University
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Publisher: Wiley
Date: 07-09-2022
DOI: 10.1002/SAE2.12029
Abstract: Citrus greening (aka Huanglongbing, HLB) caused primarily by the bacterial pathogen Candidatus Liberibacter asiaticus ( C Las) has devastating effects on the global citrus industry. Agricultural management‐induced changes in microbial communities are hypothesised to contribute toward HLB resistance by reducing pathogen titre and increasing root and soil health. However, we have a limited understanding of the impacts of management practices on the soil microbiome, making the extent of HLB management uncertain. Here we investigated the effect of agricultural management practices on reducing C Las titer via changes in rhizosphere‐associated bacterial communities. Rhizosphere and root s les were collected from two sites in Florida where different management practices (e.g., metalized reflective mulch ground covers, compost application and microbial inoculations) are currently being implemented to prevent HLB. Management‐induced changes in the rhizosphere bacterial community were assessed using licon sequencing. qPCR assays were used to quantify the titer of the pathogen C Las in roots. In addition, we measured soil properties and the activities of microbial enzymes involved in soil nutrient cycling. Our results indicated that certain management practices lead to shifts in the community structure of rhizosphere bacterial communities that negatively interact with the HLB pathogen. Management practices improved soil quality and reduced C Las titer. Additionally, we found that Actinobacteria were frequently enriched in the successful treatment sites, suggesting that Actinobacteria taxa could be indicators for HLB suppression properties in the soil. Our results suggest that microbiome manipulation, either through changes in the management practices or microbial amendment, can increase the suppressive potential of soils, resulting in the reduction in C Las titer and potentially leading to HLB suppression in citrus groves.
Publisher: Scientific Societies
Date: 2020
DOI: 10.1094/PDIS-05-19-1103-A
Abstract: Xanthomonas translucens pv. translucens causes bacterial leaf streak and bacterial blight diseases of barley. This pathogen limits barley production globally but remains understudied, with limited genomic resources. To better understand the biology of this X. translucens subgroup, we sequenced the complete genome of the X. translucens pv. translucens strain UPB886.
Publisher: Scientific Societies
Date: 11-2019
DOI: 10.1094/PDIS-10-18-1819-RE
Abstract: Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four lified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field s les from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 s les, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.
Publisher: Wiley
Date: 02-04-2021
DOI: 10.1111/NPH.17319
Abstract: Harnessing plant‐associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant‐associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high‐throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial‐based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant‐associated microbiome knowledge into real‐world scenarios will require concerted transdisciplinary research, cross‐training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.
Publisher: Springer Science and Business Media LLC
Date: 02-05-2023
Publisher: Oxford University Press (OUP)
Date: 05-2019
Publisher: Springer Science and Business Media LLC
Date: 07-02-2019
DOI: 10.1038/S41598-018-38195-X
Abstract: Plant disease resistance that is durable and effective against erse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens ( Magnaporthe oryzae , Rhizoctonia solani , and Xanthomonas oryzae pv. oryzae ) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis -Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis -elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.
Publisher: Cold Spring Harbor Laboratory
Date: 29-06-2018
DOI: 10.1101/358754
Abstract: Background Rice molecular genetics, breeding, genetic ersity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice ersity, improved varieties and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of s les, however, pose a challenge to non-computer savvy rice researchers. Findings We adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) assays, analyzing genome-wide association studies, population ersity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. Conclusions Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-11-2020
Abstract: A single gene with a dynamic evolutionary history allows plant pathogenic bacteria to spread systemically through their hosts.
No related grants have been discovered for Jan Leach.