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Diversity Arrays Technology (DArT) combines the ability to identify various types of DNA polymorphism with the low cost and high throughput platforms DArT offers several-fold gain over other technologies in terms of marker throughput and assay cost and was successfully deployed in over 50 organisms including those with complex, polyploid genomes (www.DiversityArrays.com). We will report the current status of technology development of DArT for sugarcane, one of the most genetically complex crops. Several effective methods of genome complexity reduction were established leading to creation of genotyping array containing 7.680 probes. All markers on the array were sequenced. The analysis of sequence data shows that similarly to other crops sugarcane DArT markers are highly enriched for the genic, low copy number, sequences, enabling effective comparison against sorghum genome assembly. The genotyping array was successfully used for diversity analysis of cultivated materials and ancestral lines as well as for genetic mapping in several populations. The good genome coverage afforded by DArT array enabled efficient discovery of significant marker-trait associations and informed decisions on initiating molecular breeding of sugarcane in Australia. Several challenges identified in the course of technology development and application as well as some novel approaches to dealing with molecular marker and phenotypic data will be presented. (Texte intégral)

The genetic improvement of ¿orphan¿ crops is going to benefit from modern breeding methods underpinned by molecular marker technologies. Establishing reliable associations between complex traits and genomic regions requires both accurate and comprehensive phenotypic characterization of the germplasm and cost-effective, high-density genotyping methods. Whole-genome, molecular profiles also enable breeders and scientists to better manage and utilize the available genetic diversity. Since many marker systems such as SSR and SNP depend on sequence information, marker discovery is still expensive and limits the development of whole-genome profiling tools for ¿orphan¿ crops. Diversity Arrays Technology (DArT) circumvents the need for sequence information and accelerates marker discovery and typing, both at a very low cost. We have established DArT for the Musa genus. Two arrays of 6,000 clones each are now available. On each array, 700 to 800 polymorphic markers were discovered in a broad survey of Musa genotypes. The majority of the markers separate the A and the B genomes, but subsets of markers resolve the diversity within each genome. A few markers also identify genetic heterogeneity within clones of cultivated banana. The low cost of DArT assays opens new opportunities for germplasm characterization and trait mapping in banana and plantain. In addition, the phenotypic effects of DNA methylation polymorphisms can now be identified and studied. The density of DArT molecular profiles will also benefit applications in Musa genomics. (Texte intégral)