Facilitating smart crop breeding through understanding the genetics of resistance and virulence in the Striga-rice interaction

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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.