Centre of Plant Structural and Functional Genomics

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Presentation transcript:

Centre of Plant Structural and Functional Genomics Jaroslav Doležel Institute of Experimental Botany Olomouc, Czech Republic, dolezel@ueb.cas.cz

Musa genotyping platform Flow cytometry and 19 SSR loci Fluorescent labels (5 dyes) Capillary electrophoresis ITC 0143 Chibulanana (AAB Plantain) SSR genotyping Precision scoring Reproducibility Comparability in time Multiplexing (4 markers) http://olomouc.ueb.cas.cz/ Christelová et al., AoB Plants 2011: plr024

Musa genotyping platform To date: 1058 accessions genotyped 450 SSR alleles Range 11 – 42 / marker 591 accessions form a core subset: No conflict between morphological and molecular characterization Materials genotyped: ITC Collection Collection missions Ad hoc samples Breeding populations http://olomouc.ueb.cas.cz/

Genetic diversity of Musa Diversity tree of the core subset accessions http://olomouc.ueb.cas.cz/

Genotyping a breeding population A weevil resistance breeding program population 190 accessions genotyped (SSR) Allele scores for mMaCIR01 locus in a subset of the population (incl. parents Kasaska and Borneo, and F1): http://olomouc.ueb.cas.cz/

Sequencing plantain genomes Two contrasting types: ITC0203 NIABANG – French type ITC1132 3 HANDS PLANTY – Horn type Illumina HiSeq 2x250bp paired-end reads (50x coverage) Dovetail Genomics Chicago and Hi-C scaffolding (HiRise) for 3 Hands Planty In progress (to improve genome assembly) BioNano optical map After the Dovetail assembly is finished DNA level polymorphism First 96 SNPs in genic regions identified Search for specific differences between the 2 types Flowering genes cascade (flower onset, regulation, etc.), in progress Epigenetic profiling http://olomouc.ueb.cas.cz/

Dovetail Genomics technology Improvement of illumina shotgun assemblies: Chicago library sequencing and HiRise scaffolder Dovetail Hi-C and HiRise scaffolder http://olomouc.ueb.cas.cz/

Optical mapping BioNano Genomics IRYS system Improvement of genome sequence assembly Structural and copy number variation http://olomouc.ueb.cas.cz/

Our team Eva Hřibová Pavla Christelová Jana Čížková Moses Nyine Alžběta Němečková Marie Seifertová http://olomouc.ueb.cas.cz/