1 / 18

POTATO GENOME ANALYSIS

POTATO GENOME ANALYSIS. Christiane Gebhardt MPI for Plant Breeding Research Köln, Germany. Potatoes are like humans: Self-incompatible outbreeders. (A x B) x (C x D) crosses. All wild types. Large biodiversity. Differences: Ploidy level: 4n and 2n.

mahon
Download Presentation

POTATO GENOME ANALYSIS

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. POTATO GENOME ANALYSIS Christiane Gebhardt MPI for Plant Breeding Research Köln, Germany

  2. Potatoes are like humans: Self-incompatible outbreeders. (A x B) x (C x D) crosses. All wild types. Large biodiversity. Differences: Ploidy level: 4n and 2n. Large experimental F1 families possible Vegetative propagation. Genome size 1/3 of human genome: ~ 1000 Mbp.

  3. Long term goals • to elucidate the genetic basis of complex agronomic characters of potato at the molecular level; • to contribute to the understanding of structure, function and natural diversity of crop plant genomes; • to contribute to the genetic improvement of the cultivated potato by developing molecular diagnostic tools to assist the breeding of new cultivars.

  4. Applied science Haplotype-based plant breeding Markers for population-based MAS Engineering agronomic traits Markers for pedigree-based MAS Basic science Genome structure and evolution Molecular basis of QTL for agronomic traits Association studies Biodiversity, haplotypes Selective genomic sequencing Candidate genes R-gene cloning Function maps for pathogen resistance and tuber traits Comparative maps Molecular maps

  5. Ch. Gebhardt MPIZ Comparing the crop genome (genetic map) with the model genome (physical map) A a B b c C A. thaliana, 121 Mbp mb S. tuberosum, ca. 1000 Mbp cM

  6. COMPARATIVE MAPPING WITH ESTs and STS MARKERS CONSERVED BETWEEN POTATO AND ARABIDOPSIS (EuDicotMap): • Linkage maps of 12 potato chromosomes were constructed based on 445 RFLP loci. • Marker sequences were compared to the Arabidopsis genomic sequence (BLASTN: P < exp -10, BLASTX: P < exp - 15) • RESULTS • 321 RFLP loci in potato have multiple sequence similarity with the Arabidopsis genome sequence (1500 „hits“). • Ca. 41 % of the potato genetic map have syntenic relationships with ca. 50 % of the Arabidopsis physical map.

  7. Some potato chromosomes have more syntenic relationships with the Arabidopsis genome than others. Syntenic blocks are redundant. Potato map segments detect ancient duplications in the Arabidopsis genome. Gebhardt et al. 2003, TPJ 34: 529

  8. Synteny between different potato map segments and the same Arabidopsis genome segment reveals ‚hidden‘ intra- and interchromosomal duplications in the potato genome.

  9. Similar experiments, comparing sugar beet (Beta vulgaris), sunflower (Helianthus annuus) and Prunus spp with Arabidopsis thaliana, based on different sets of EST markers, give similar results.

  10. A.tha. 2 rDNA I-II B Sugar beet Sun flower Prunus Potato II-IV A I-II A I-II C II-III A mb 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Dominguez et al. 2003, PBJ 1: 91

  11. Ch. Gebhardt MPIZ Genome Archeology Comparing the genomes of contemporary, distantly related plant species ‚excavates‘ the remains of an ancestral plant genome.

  12. Applied science Haplotype-based plant breeding Markers for population-based MAS Engineering agronomic traits Markers for pedigree-based MAS Basic science Genome structure and evolution Molecular basis of QTL for agronomic traits Association studies Biodiversity, haplotypes Selective genomic sequencing Candidate genes R-gene cloning Function maps for pathogen resistance and tuber traits Comparative maps Molecular maps

  13. Potato function map for tuber traits

  14. RESPIRATION GLYCOLYSIS DEGRADATION Sucrose-P AMY STP S6P Ppa Glucose PPi Hexose-P Sucrose Starch PPi INV Fructose Sbe UGP SS UDP-Glc SUS SPS AGP GapC ADP-Glc Fructose SYNTHESIS Amyloplast Cytoplasm Vacuole Cell wall All genes functional in carbohydrate metabolism, regulation and transport are candidate genes. After Sowokinos 2001, Am. J. Pot. Res. 78

  15. Co-localization of a functional candidate gene (invertase) with QTL for tuber sugar content (Menendez et al. 2002, Genetics 162).

  16. The example of candidate gene association mapping of:CHIP COLOR The color of potato chips and French fries depends on the glucose and fructose content of raw tubers. High sugars, Low sugars Bad chips Good chips Li Li et al. (2005) Genetics 170: 813

  17. Chips quality depends on fructose and glucose content of tubers. Invertase allele d is associated with chips quality (P < 0.001) in a breeding pool of 179 tetraploid genotypes. Single strand conformation polymorphism (SSCP) of Invap in tetraploid breeding pools

  18. Thanks for your attention Funding: European Union (EuDicotMap) BMBF (German Federal Ministry for Education and Research), GABI-CHIPS. MPG (Max-Planck society).

More Related