Facilitating smart crop breeding through understanding the genetics of resistance and virulence in the Striga-rice interaction
Principal Investigator / Supervisor
Professor Julie Scholes
Professor Roger Butlin
University of Sheffield
Animal and Plant Sciences
Striga hermonthica (Sh) and S. asiatica (Sa) are obligate root parasitic weeds that parasitize rainfed rice in Africa causing devastating yield losses. To enable effective breeding of durable defence to multiple ecotypes of Striga, we need to stack resistance genes with different modes of action in rice varieties. To prolong the longevity of resistance, knowledge of the evolutionary potential and population genetics of parasite virulence is crucial. We have identified the first cluster of Receptor-Like-Protein resistance genes that provide resistance against several ecotypes of Sh and Sa and shown that by down-regulating many of these genes simultaneously in the resistant variety Nipponbare, that full susceptibility is restored. To identify exactly which gene or genes are responsible we will utilize CRISPR/Cas9 gene editing to knock out specific genes, singly and in combination and test their effect on susceptibility to different ecotypes of Striga. We will characterise the variation of recently identified candidate Sh virulence loci (from a single Sh ecotype from Kibos, Kenya) in other Sh ecotypes from different regions of Africa. For each ecotype, we will infect the same resistant and susceptible varieties used originally, collect 50 individual Sh plants that attach and grow and genotype them for 100 SNPs, including 50 virulence candidates and 50 control SNPs. This will reveal the population structure of Sh ecotypes, essential for understanding the evolution of virulence alleles and determine how our candidate Sh virulence loci are distributed in different ecotypes. We will also identify, for the first time, candidate virulence loci from Sa ecotypes using both population genomic and quantitative genetic approaches. Finally, we will phenotype a novel, Nested Association Mapping population of rice for resistance to Sa and Sh ecotypes to discover multiple new resistance genes with different modes of action for breeding elite varieties with durable resistance.
Summary (4000 characters) Rice is one of the most important crops worldwide and plays a pivotal role in the national economies of sub-Saharan Africa (SSA) yet yields are constrained by species of obligate root parasitic weeds called Striga that cause yield losses of 20-100%. Striga is extremely difficult to control as individuals produce millions of small, long-lived, genetically diverse seeds that only germinate in response to germination stimulants present in host root exudates. As Striga severely damages the development of the crop immediately after attaching to the host root, control measures must act early in the life cycle to prevent losses in yield. Resistant varieties should play a key role in control strategies yet there is no published information about the identity or mechanism of action of Striga-resistance genes. Striga evolves rapidly to overcome host resistance, strongly influencing the sustainability of crop improvement strategies based on breeding for resistance. Stacking many resistance genes in a variety is essential to reduce the likelihood of resistance being overcome by the evolution of the parasite but this requires knowledge about the identity of host resistance and parasite virulence genes. This project aims to discover new resistance genes and to link this with an understanding the molecular genetic basis of parasite virulence genes for breeding of durable defence. We have recently identified the first cluster of resistance genes (Receptor-Like-Proteins (RLP)) on chromosome 12 of rice that provide resistance against several ecotypes (genetic variants) of S. hermonthica and S. asiatica and shown that simultaneous down-regulation of many of these genes in a resistant cultivar (by RNAi) restores susceptibility. However, for effective breeding of varieties, we need to know whether one, or more of the genes, acts to provide resistance, or whether different combinations of genes act against different genetic ecotypes of the parasite. We will investigate this by inactivating RLP genes, singly and in combination using CRISPR/Cas9 in resistant varieties, infecting with different ecotypes of Striga, and determining the effect on susceptibility. Recently we have compared Striga growing on susceptible and resistant hosts and taken a population genomics approach to identify a set of candidate virulence genes. To determine whether they interact with the RLP resistance genes we will collect Striga ecotypes from multiple host species/varieties across SSA. These will be genotyped with 'neutral' markers (SNPs) to look at the structure of the populations, (critical for interpretation and management of virulence) and then with SNPs in candidate virulence genes to test for specific associations with known forms of resistance. This will provide a foundation for future studies on the functional interaction between resistance and virulence genes and for association analyses to detect virulence genes relevance to other sets of resistance genes. To discover new resistance genes we will use a rice (Nested Association Mapping (NAM)) population derived from crossing one common O. sativa ssp indica parent (cv. IR64) with ten diverse parents. Two thousand NAM lines have been genotyped to produce highly detailed genetic maps for each of the 10 populations, facilitating the rapid discovery of new Striga resistance genes. We will first phenotype the 10 parents with existing and new Striga ecotypes to form a matrix of virulence/resistance to allow us to select interesting ecotypes and NAM populations to phenotype during the 2-year project whilst providing data for more extensive phenotyping in the field and laboratory in the future.
Our goal is to undertake research that will facilitate the production of rice varieties that are resistant to Striga and produce high yields. We will take a multi-disciplinary approach involving molecular, quantitative and population genetics that both builds on and advances previous work to identify resistance genes in rice and candidate virulence loci in Striga to elucidate the molecular genetic basis of host-parasite specificity. This knowledge will facilitate the future development of a rice-Striga interaction model for predictive breeding of resistance in elite varieties and a rice variety 'decision tool' to advise farmers which varieties to grow in different areas. The expected impacts of this project consist of academic knowledge, applied tools, techniques and methodologies of immediate use to plant breeders and capacity building activities to disseminate information and establish new contacts in Africa. This project will provide new insights into biology of the plant-plant interaction and will advance our understanding of the interaction between virulence genes and resistance alleles. The discovery of new resistance genes and QTL, together with high-resolution marker data, will enhance the effectiveness of the genetics and the breeding pipeline through the use of marker-assisted selection. Such information will be made available to plant breeders via our established relationship with Africa Rice. The project will provide the basis for CRISPR-(Cas9) strategies to quickly develop resistant varieties from elite lines already highly performing but susceptible to Striga, a potential breakthrough for breeding. Identification of new resistance genes will allow us to explore the O. sativa genetic diversity of the genes through allelic analysis of the publically available 3,000 genomes data potentially allowing the discovery of new or rare alleles for breeding resistance. The long-term impact is to facilitate 'smart' breeding and effective use of varieties with appropriate combinations of resistance genes to protect crops against different genetic variants of the parasite, ultimately improving rice yields and food security for resource for poor farmers. This will be achieved through follow-on projects and field-testing of elite varieties. Prof Scholes and Dr Rodenburg already have established field sites for testing varieties for resistance to Striga in Uganda, Tanzania and Uganda. By partnering with African-based organizations, like the Africa Rice Center (AfricaRice), the knowledge and products derived from the project will be readably available to African rice breeding programs. They have already shown a keen interest for implementation. AfricaRice has an impressive track record in breeding and delivering improved rice varieties in the region. The path from gene-discovery to variety adoption and increased food security and/or income generation is rather long but the Africa-based partner in this project, AfricaRice, has extensive experience with this and a clear strategy. Africa Rice is coordinating an effective African-wide Rice Breeding Task Force (RBTF) of more than twenty African countries, involving national agricultural research systems (NARS), most of which effectively reach out to national extension and seed systems.
Not funded via Committee
Crop Science, Microbiology, Plant Science
X – Research Priority information not available
GCRF Foundation Awards for Global Agricultural and Food Systems Research (GCRF FA GAFSR) 
X – not Funded via a specific Funding Scheme
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