Rust diseases are common in cereals, yet rice is not affected by the entire taxa of rust fungi. It is hypothesized that rice possesses non-host resistance (NHR) that confers complete resistance. Although NHR is the norm in plant-microbe interactions, the molecular basis of NHR is not well understood. Recent advances in Arabidopsis/powdery mildew interactions have demonstrated that NHR is not as genetically complex or intractable as initially thought, raising the possibility that NHR genes can be transferred between species. This component of the proposal aims to identify rice mutants and selected germplasm compromised in NHR to wheat rust fungi, so that rice rust resistance genes can be isolated and introduced into wheat.
Exploratory studies on the infection process of stem rust on rice show that development of rust infection structures does occur on rice, which is an essential pre-requisite for plant colonization. Rice is observed to respond by formation of callose and autofluorescent compounds, suggestive of an active defense response. Furthermore, in a preliminary screen of rice germplasm with stem rust, several rice lines exhibited distinct fleck reactions, suggesting that it is possible to detect stem rust infection macroscopically and to develop a high-throughput screening for a variety of mutant phenotypes. These observations together suggest that cereal rust can infect rice and implicate an active, genetically defined NHR response and that heritable changes can be identified to enable genetic dissection of rust immunity in rice. A research team has been assembled that has complementary expertise in plant genetics, rust pathology, and molecular biology. The team has a large collection of rice mutants and germplasm for systematic screening of rice-rust interaction at micro- and macro-levels. Over 20,000 mutant lines and 3,000 rice germplasm accessions will be screened for altered response to multiple rust and rice pathogens. The use of multiple pathogens in disease evaluation is important to ensure that the genes identified can eventually contribute to broad-spectrum resistance in wheat. Double or triple mutants will be constructed to identify the essential genes involved in NHR and determine their interactions. Once useful mutations are found, genes of interest will be isolated and validated for function. Efficient methodologies are in place for gene cloning using the T-DNA and deletion mutants.
Objective 9: Exploring Rice Immunity to Rust
| Activities |
Outputs |
Outcomes
(Short- and Long-Term) |
| Activity 9.1 Establish a panel of stem rust isolates for screening rice mutants. About 25-30 isolates of stem rust fungi (Puccinia graminis (P.g.) tritici, P.g. avenae, P.g. secalis, P.g. phleum, P.g. poae, P.g. festucae) will be propagated and increased for mass screening of rice lines. Collection will be actively maintained for duration of project. |
A reference collection representing diversity of P. graminis is actively maintained for screening at multiple stages of the project. |
Short term: A standardized collection of isolates for assessing rust interaction with wheat and rice |
| Activity 9.2 High throughput preliminary screening of rice mutants and rice collections (cultivated, landrace, and wild accessions) with a bulk of rust isolates. Establish proper conditions for inoculating rice plants with rust; develop a high-throughput scoring (visual) to differentiate altered response to rust; screen populations. |
Standardized and efficient screening procedures established for evaluating rust-rice interactions; rice mutants and selected lines with altered response to rust identified |
Short term: efficient screen for rust/rice interaction established; feasibility of detecting interaction phenotypes between rice mutants and rust fungi |
| Activity 9.3 Develop a HTP microscopic analysis technique for altered response to rust infection in relevant rice mutant populations. Apply microscopic screening of rice response to rust fungi; determine critical parameters for interactions, correlate micro- with macro-phenotypes to establish a HTP screen. |
Standardized microscopic protocols to evaluate rust-rice interactions; detailed description of rust fungal colonization on rice (wild type and mutants). |
Short term: Frequency of detecting rust-response mutations in rice known; decision point on whether additional screening is warranted |
| Activity 9.4 HTP screening for loss-of-resistance to rice pathogens. Combine multiple mutations to increase the likelihood of detecting rust response mutants. Screen 10,000 rice lines for enhanced susceptibility to blast infection; pre-select lines for detailed phenotyping with rust; create double or triple mutants; provide materials for detailed phenotyping with rust pathogens under 9.2 and 9.3. |
A sub-collection of rice mutants (>50) with altered defense mechanisms; series of double or multiple mutations created for elucidating genetic control of immunity. |
Short-term: mutants for genetic and pathological analyses |
| Activity 9.5 Detailed phenotypic evaluation of selected mutants with multiple rust fungi and races including Ug99. Characterize pathologically and physiologically the basis of enhanced infection in selected mutants and rice lines. |
Documented interaction between rust fungi and mutants or selected germplasm; phenotypic basis for immunity response understood. |
Short term: physiological understanding of rust immunity in rice |
| Activity 9.6 Genetically characterize populations of rice that segregate for stem rust reaction. Construct genetic crosses to determine the genetic control of rust immunity reaction in rice; map mutations conferring loss of resistance in mapping population |
Genetic loci controlling reaction to rust determined in rice; genetic basis of immunity established |
Short term: feasibility of finding rice genes for non-host resistance in wheat determined |
| Activity 9.7 Determine the spectrum of altered response to multiple pathogens (panel of rust fungi and rice pathogens). Assess rice mutants against an array of rust fungi and rice pathogens. |
A set of rice mutants/lines affecting broad-spectrum resistance available |
Short term: the relationship between non-host resistance and broad-spectrum resistance determined; indicator of potential effectiveness of non-host resistance for wheat rust |
| Activity 9.8 Chip-based mapping and positional cloning. Phenotypically confirmed mutants or genetic segregates will be scanned with whole-genome gene chips to determine the locations of genetic lesions responsible for the altered response to rust |
Genes and narrow chromosomal regions contributing to rust response identified |
Short term: panel of non-host resistance genes and genomic regions available for testing. Long term: genes for rust resistance proven useful in wheat |
| Activity 9.9 Isolate T-DNA tagged rust-susceptible mutants and gene identification by co-segregation analysis. Screen collection of T-DNA insertion lines with stripe rust in China; determine co-segregations between T-DNA insertions and rust response phenotypes; create double mutants as needed for detailed phenotypic characterization with multiple rust pathogens (in Activities 9.5 and 9.7). |
Tagged mutants available for detailed phenotypic characterization; known genes responsible for rust response |
Short term: non-host resistance genes available for testing |
