Genomic approaches to understanding resistance and virulence in the cereal-Striga interaction for targeted breeding of durable defence.

Rice plays a pivotal role in the national economies of sub-Saharan Africa and production is expanding faster than any other cereal; it is considered a key strategic crop for attaining food security and poverty alleviation. One of the reasons for the rapid expansion of rice in Africa has been the introduction of 18 upland rice cultivars known as NERICA. These interspecific cultivars, generated by crossing the African rice species (O. glaberrima) with the Asian rice species (O. sativa), are high yielding and have excellent drought tolerance and disease resistance. Thus, subsistence farmers working in these upland production environments are increasingly replacing maize, and even sorghum, with NERICA rice. However, the soils of these cereal growing areas are infested by the pernicious parasitic weeds S. asiatica or S. hermonthica, which increasingly limits rice production; the development of new management strategies is essential. The use of Striga-resistant cultivars, as part of an integrated control programme, is recognized as sustainable and cost effective yet we still do not know the identity of genes that make some cereal cultivars more resistant to these parasites than others, nor do we have enough different types or sources of resistance for breeding programmes. This is important because the Striga seed bank is so genetically diverse that the durability of resistant crop varieties is compromised by the potential for rapid evolution of parasite virulence. Thus, the long-term success of host cultivar resistance for the control of Striga requires the identification and exploitation of multiple sources of host resistance genes together with a greater understanding of the genetic variation for virulence within and among Striga populations from different locations. Such knowledge will allow us to combine appropriate resistance genes in cultivars that are suitable for different agro-ecological zones and to manage the use of cultivars more effectively such that virulence evolution is delayed. The aim of this project is to identify multiple Quantitative Trait Loci (QTL) and candidate resistance genes underlying resistance in rice to different Striga species and ecotypes and characterise, for the first time, Striga loci that enable parasites to overcome specific host resistances.
To achieve our aims, we will utilise molecular/genetic and population genomic approaches combined with extensive field testing of materials for resistance to Striga. We will identify multiple sources of resistance in rice to Striga species by phenotyping populations of rice plants in which small segments of the genomes of either O. glaberrima or O. rufipogon (wild ancestor of cultivated rice) have been introgressed into a tropical O. sativa background (Chromosome Segment Substitution Line populations) to determine the location of the resistance QTL/genes on these rice genomes. We will fine map an existing region of rice chromosome 12 (known to contain resistance genes) to identify those responsible and validate their function using a novel, high throughput, 'gene screen' based on Agrobacterium rhizogenes -induced 'hairy roots' in rice cultivars. We will use a population genomics approach to identify Striga loci that enable parasites to overcome host resistance(s) in specific cultivars and analyse their spatial variation within and amongst different parasite populations. A selection of our material will be screened at field sites in Kenya, Tanzania and Uganda to characterize their field expression of resistance as well as their levels of tolerance and yield across seasons and to expose our material to farmers and seed companies and get valuable feed-back from them. The project will generate resistant and adapted cultivars that can be used immediately by farmers working in Striga-infested areas and breeding material and valuable insights to enhance the work of rice breeders to further improve the resistance of farmer preferred cultivars.

Rice production in Africa is expanding faster than any other cereal following the introduction of 18 upland rice cultivars known as NERICA. These interspecific cultivars (O. glaberrima x O. sativa) are high yielding with excellent drought tolerance and disease resistance. Subsistence farmers working in upland production environments are increasingly replacing other cereals with NERICA rice. However, the soils of these areas are infested by the parasitic weeds S. asiatica or S. hermonthica, which increasingly limits rice production. The use of Striga-resistant cultivars, as part of an integrated control programme, is recognized as sustainable and cost effective yet the identities of genes that make some cereal cultivars more resistant than others is unknown, nor do we have enough different types of resistance for breeding programmes. This is essential as the Striga seed bank is so genetically diverse that the durability of resistant crops is compromised by the potential for rapid evolution of parasite virulence. We will utilise molecular/genetic and population genomic approaches to: identify multiple QTL and genes for Striga resistance in rice using O. glaberrima X O. sativa and O. rufipogon X O. sativa Chromosome Segment Substitution Line (CSSL) populations; fine map an existing Striga resistance QTL(STR12.1) to identify candidate resistance genes and validate their function using a high throughput, 'gene screen' based on Agrobacterium rhizogenes -induced 'hairy roots' in rice; develop Near-Isogenic Lines (NILs) that will serve as direct candidates for variety release or as high breeding value progenitors in selection schemes; use a population genomics approach to identify Striga loci that enable parasites to overcome host resistance(s) in specific cultivars and analyse their spatial variation within and amongst different parasite populations and test the performance of resistant materials at field sites in Kenya, Tanzania and Uganda.

The research proposed in this project will be of direct benefit to African farmers, rice breeders, scientists and academic communities and will indirectly benefit seed companies and NGO's.

Farmers: A key output of this project will be the identification of multiple Striga resistance QTL/genes from the African the rice species O. glaberrima and wild rice species O. rufipogon resulting in the development of new upland rice cultivars with superior resistance and tolerance to Striga. Farmers working in rain-fed uplands in sub-Saharan Africa (SSA) where Striga infestation is endemic will be the prime beneficiaries of the project. In the short term our field trials will reveal how well our resistant cultivars (existing cultivars and new materials generated in the project) perform in different environments and identify the best Striga resistant/tolerant rice genotypes available. This, coupled with greater knowledge of the Striga population virulence loci in different areas, will lead to clear and useful recommendations for cultivar choice in Striga-infested areas. In collaboration with seed companies the project will be instrumental in the evaluation procedures required for release of some of the cultivars or advanced breeding lines. We anticipate the release and adoption of new improved rice cultivars in Uganda within the time scale of the project or soon afterwards.

Plant breeders: Plant breeders focusing on upland rice will clearly benefit from the proposed research efforts. The identification of multiple QTL for resistance to different ecotypes of Striga will be invaluable as sources of resistance for MAB programmes. The fine mapping of our existing Striga resistance QTL (STR12.1) and identification of the resistance gene(s) will be of immediate use to breeders for transfer to farmer preferred cultivars. Within the project we will produce fertile Near Isogenic Lines carrying the STR12.1 QTL/allele to serve as direct candidates for variety release or as high breeding value progenitors in selection schemes. We will also develop perfect markers for the STR 12.1 sequence, making the marker-based prediction of resistance levels in breeding programs 100% certain. In addition, iBridges lines (fertile interspecies O. sativa/O. glaberrima lines) developed at CIAT will allow breeders to rapidly transfer genes and QTL from the O. glaberrima genome (via MAS) into farmer preferred cultivars.

Seed companies and NGOs: The seed companies involved in this project will be able to conduct the compulsory cultivar evaluation of adapted material prior to release as part of our field trials. By linking up with our project and partners (CIAT, AfricaRice and NGO's) seed companies will receive new adapted rice lines that have a high potential for release and gain new avenues to disseminate seed and make profits. Our NGO project partners will benefit by the partnership with Ugandan and Kenyan universities, Africa Rice Center and the private seed companies as it will extend their reach within the countries where they operate as well as within the East African community.

Scientists and the Academic community: The project PIs and partners will benefit from the continuation of existing and new partnerships. Training workshops, and doctoral programmes in areas such as plant biotechnology and breeding, will contribute to building capacity in Africa. The academic community will benefit from the findings in this study as it will enhance understanding of the molecular genetic basis of resistance in rice to Striga and identify Striga genomic regions harbouring virulence loci allowing us to address questions about the evolution and spread of virulence within and amongst Striga populations. High quality research papers will benefit breeders, geneticists and those working in the field of plant parasite interactions.