Cis-acting regulatory elements in the rice genome: a novel source of alleles for rice breeding

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Striga species are angiosperm parasites that cause devastating losses in crop yield throughout sub Saharan Africa. The use of Striga-resistant cultivars would represent a cost effective control measure, however, such a strategy is limited by a lack of resistant germplasm and by a lack of understanding of the molecular genetic basis of host resistance to Striga. Over the last 5 years we have carried out an extensive screening programme in rice and have identified cultivars that show good post-attachment resistance to S. hermonthica. Using a mapping population of rice we have identified some Quantitative Trait Loci (QTL) underlying the resistance. In this project we propose to take an integrative approach to identify and investigate the molecular genetic basis of resistance to Striga in rice by combining our extensive knowledge of Striga-host interactions, our novel plant growth systems and modern genomic and comparative genomic techniques for the improvement of both the rice and sorghum crop in Africa. Our specific objectives are: (1) To screen selected African rice cultivars for resistance to different ecotypes of S. hermonthica, S. asiatica and S. aspera and to determine the phenotype of the resistance. (2) To identify QTL underlying resistance in rice to these different ecotypes and species of Striga using two different mapping populations of rice in order to select the most genetically stable QTL for use in Marker Assisted Breeding Programmes (MAB). (3) To identify genes that are up and down regulated in rice roots undergoing a resistance reaction and, by integrating the results with the QTL data, to identify candidate resistance genes and (4) to utilize our knowledge of the molecular genetic basis of resistance in rice to Striga species to take a comparative genomic approach to identify and confirm the existence of homologous QTL and resistance genes in sorghum.