Discovery and analysis of effector genes in th eparasitic weed striga asiatica: a multifaceted genomics approach
Lead Research Organisation:
University of Sheffield
Department Name: Animal and Plant Sciences
Abstract
Parasitic plants are plants that rely entirely or partly on another plant in order to survive and reproduce [1]. In Africa, two parasitic plants causing particularly high levels of damage to cereal crops are Striga hermonthica and Striga asiatica. Both of which attach to the roots of their host plant and cause massive reductions in yield [2]. The development of resistant cultivars is seen as an important part of the strategy to tackle these parasites, but progress has been hampered, in part, by a lack of understanding of the molecular genetic basis of the interaction between the host and parasite [3]. To this end, it is important to better understand the molecular basis of resistance in the host and of virulence in the parasite. The latter is the broad aim of this project.
I aim to use a combination of genomics, transcriptomics and bioinformatics to compare and analyze different isolates of the root parasitic plant Striga asiatica at the molecular level, with the goal of selecting candidate genes that may function as effectors for parasite virulence. Effectors are proteins secreted by parasites, which are predicted to modify the function and/or structure of the host in order to facilitate parasite fitness [4]. The discovery of such proteins from parasitic pants would open new avenues of research that would likely lead to the identification of novel resistance genes in host plants that could be invaluable to crop breeders.
Initially, the genomes of virulent and avirulent isolates of S. asiatica will be compared for the presence/absence of genes, when growing on particular rice cultivars. This initial analysis will be followed up with a bioinformatics pipeline that will annotate the genomes according to known effector-properties from other pathosystems, in order to generate a list of potential candidate effectors. This list will be refined by integrating transcriptomics data, which will provide information on genes differentially regulated in the infection organ of the parasite (called the haustorium).
A selection of the most promising candidates will be functionally analyzed in order to determine; (i) whether the gene plays a role in virulence and (ii) if a role in virulence is detected then further analysis will aim to characterize precisely how it functions.
I aim to use a combination of genomics, transcriptomics and bioinformatics to compare and analyze different isolates of the root parasitic plant Striga asiatica at the molecular level, with the goal of selecting candidate genes that may function as effectors for parasite virulence. Effectors are proteins secreted by parasites, which are predicted to modify the function and/or structure of the host in order to facilitate parasite fitness [4]. The discovery of such proteins from parasitic pants would open new avenues of research that would likely lead to the identification of novel resistance genes in host plants that could be invaluable to crop breeders.
Initially, the genomes of virulent and avirulent isolates of S. asiatica will be compared for the presence/absence of genes, when growing on particular rice cultivars. This initial analysis will be followed up with a bioinformatics pipeline that will annotate the genomes according to known effector-properties from other pathosystems, in order to generate a list of potential candidate effectors. This list will be refined by integrating transcriptomics data, which will provide information on genes differentially regulated in the infection organ of the parasite (called the haustorium).
A selection of the most promising candidates will be functionally analyzed in order to determine; (i) whether the gene plays a role in virulence and (ii) if a role in virulence is detected then further analysis will aim to characterize precisely how it functions.
Organisations
Publications
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011151/1 | 01/10/2015 | 30/09/2023 | |||
| 1657393 | Studentship | BB/M011151/1 | 01/10/2015 | 30/09/2019 |
| Description | This PhD project has focussed on understanding the pathogenicity of two weedy parasitic plants, Striga hermonthica and Striga asiatica, which cause substantial damage to a range of cereal crops grown by subsistence farmers throughout Sub-Saharan Africa. The recent availability of a whole genome sequence for S. hermonthica has allowed the development of a bioinformatics pipeline that identified suites of candidate genes that encode secreted proteins potentially involved in pathogenicity of S. hermonthica. Amongst these, were a range of genes encoding proteins predicted to function in cell wall modification and/or have proteinase activity, which are biologically interesting in the context of Striga spp., which must penetrate multiple layers of host root cells in order to reach the xylem vessels from which they abstract water and minerals. A key output of this pipeline was the generation of 4 sets of genes (ranging in size from 25 to 375 genes) that are a high priority to investigate further. In order to study the function of some of the aforementioned candidate pathogenicity-related genes, an attempt was made to generate stable knockout S. hermonthica plants, in which the candidate genes had been rendered inactive. However, due to the fact that Striga is an obligate parasitic plant, that requires a host plant in order to survive, a number of attempts proved unsuccessful. Therefore, alternative approaches to functionally investigate some of these genes were developed. For example, a selection of the most promising candidate genes were cloned and are being used to develop a transient expression system. In addition, an RNAseq analysis was conducted in which gene expression levels for all the genes in the S. hermonthica genome were compared for individuals infecting either a susceptible or resistant rice line. Using this data set, the set of candidate pathogenicity-related genes encoding secreted proteins (mentioned above) was reduced even further. During this analysis, groups of co-expressed genes were identified that highlighted key functional changes in the biology of Striga hermonthica during the infection process. For example, genes associated with cell wall modification were upregulated 2 days post infection and those associated with xylem biogenesis at 4 days post infection. The identification and characterisation of genes involved in the pathogenicity of S. hermonthica described above, is helping to understand the molecular mechanisms utilised by this devastating parasitic plant in order to successfully parasitize its host plant. |
| Exploitation Route | There is now a clear list of candidate genes encoding secreted proteins, which can be investigated further in order to better understand how Striga hermonthica might utilise these proteins as part of its infection process. Indeed, a number of candidate genes have already been cloned and will be available for future work. Moreover, the RNA sequencing dataset generated here will be a very useful resource for increasing our understanding pathogenicity in Striga hermonthica and for generating hypothesise that can be investigated further in the future. |
| Sectors | Agriculture, Food and Drink |