Genome organisation, evolution and biodiversity in Musa : application to stress-related gene discovery and plant breeding

This thesis shows how anonymous markers are used to assay genetic polymorphisms, and then describes the analysis of major biotic-stress related genomic motifs from diverse Musa accessions, before identifying Bacterial Artificial Chromosome (BAC) clones carrying biotic and abiotic stress-related DN MOTIFS. Microsatellite (SSR) and retroelement-related sequences are abundant and can be exploited as anonymous genetic markers in Musa. SSR primers designed within sequenced BAC clones identified polymorphisms in Musa. LTR-retrotransposon fragments, including Pseudoviridae (Tyl-copia-like) and Metaviridae (Ty3-gypsy-like) families were present as different families in BACs with no correspondence to particular Musa genomes, but are useful for understanding genome evolution. Primers designed from genomic and EST databases were exploited to characterize sequences containing Nucleotide Binding Sites (NBS) and Leucine-Rich Repeat (LRR) motifs (associated with disease resistance genes), and genes associated with tolerance to heat (HSP, 70HSP), salinity (STP) and drought (DRFP) stress. Neither NBS nor LRR sequences are conserved with respect to genome, indicating that R-genes are specific and exist independently. BAC libraries allow tagging of conserved domains of NBS, LRR, retroelement and SSR motifs, giving understanding of the genomic context and control of R-genes. Reliable characterisation of these domains in Musa is possible via PCR-based screening. The thesis gives abroad insight into genome organisation, evolution and diversity of major classes of R-genes, enabling progress towards gene discovery and exploitation for plant breeding.