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

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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.