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Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato

Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato. Park et al. Genetics 176: 85-94 (May 2007). CENTROMERES. Important functional elements of eukaryotic chromosomes Ensure proper cell division Ensure stable transmission of genetic material

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Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato

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  1. Genetic Positioning of Centromeres Using Half-Tetrad Analysis in a 4x-2x Cross Population of Potato Park et al. Genetics 176: 85-94 (May 2007)

  2. CENTROMERES • Important functional elements of eukaryotic chromosomes • Ensure proper cell division • Ensure stable transmission of genetic material • Determining their composition and structure can provide insight into their functional roles • Identification of genetic position important for: • Distinguishing chromosome arms • Identifying proximal and distal markers or genes • Providing fixed positions in genetic maps

  3. RECENT CENTROMERE RESEARCH • Centromeres sequenced and studied extensively in: • Arabidopsis • Maize • Rice • Wheat • Little sequencing has been reported for potato.

  4. MAIN GOALS OF RESEARCH • Use half-tetrad analysis (HTA) to localize centromeres on 12 potato chromosomes • Compare results of HTA with UHD map proposing possible centromere positions based on marker density (van Os et al. 2006) • Determine whether there is truly a single crossover per chromosome arm Previous publications on these issues were theoretical proposals or were limited in loci/chromosome number.

  5. 4x – 2x Population • Male parent • Diploid • Produced numerically-unreduced 2n pollen by first-division restitution (FDR) • Female parent • Tetraploid Tetraploid mapping population

  6. FDR vs. SDR • FDR • Abnormal orientation of spindles before anaphase II • Non-sister chromatids end up in the same nucleus • Efficiently transmits heterozygosity of original genotype • SDR • Premature cytokinesis before second meiotic division • Sister chromatids end up in the same nucleus

  7. FDR vs. SDR: Probability of Heterozygosity

  8. FDR vs. SDR: Probability of Heterozygosity

  9. van Os et al. 2006 • Proposed centromere position • based on strong clustering of AFLP markers on UHD genetic map • AFLP markers tend to be clustered in centromeric regions in several other species Park et al. compared their HTA-based results with the proposed positions of van Os et al.

  10. aaaa x ab

  11. aaaa x ab CROSSING OVER OCCURRED. D = [ f(aaaa) + f(aabb)] x 100 cM

  12. AFLP Marker Patterns A1: Six nulliplex offspring genotypes More crossing over, farther from centromere A2: One nulliplex offspring genotype Less crossing over, closer to centromere

  13. Frequency of homozygosity • Based on location on UHD map (van Os et al. 2006), grouped linkage groups • Within linkage groups, arranged according to genetic position • Calculated frequencies of alleles • 233 genotypes • Map position: • [f(aa) + f(bb)] x 100 • [(# homozygous alleles)/233] x 100

  14. Combining results: HTA and UHD Marker-to-centromere distance (% homozygosity) Gray box marks bin containing centromere Zero distance to centromere

  15. Centromere Locations

  16. Centromere Locations Telocentric predominantly terminal location of the centromere

  17. Centromere Locations What about chromosomes 3 and 11?

  18. Chromosomes 3 and 11 • No markers with 100% heterozygosity Approaching zero

  19. Other funny stuff: Chromosomes 1 and 5 • 100% heterozygosity found in the wrong bin (chromosomes 1, 5) • 99.6% heterozygosity found in the “centromere” bin (chromosome 1)

  20. Cross-over frequency Only one crossover per chromosome arm? • Chromosome 2 (telocentric) • one arm analyzed • Chromosome 4 (metacentric) • one arm analyzed • Chromosome 6 (metacentric) • both arms analyzed

  21. Cross-over frequency Boldface: all markers are heterozygous (centromeric) Block a: no crossovers Block b: one crossover Block c: two crossovers

  22. Number crossovers per 233 genotypes

  23. Cross-over frequency • Confirms that 2n pollen originated through FDR • Since some markers were entirely heterozygous, cannot have involved an SDR mechanism • Fewer noncrossover events on telocentric chr2 • Telocentric chromosome shows more crossover? • No. X-squared not significant. • Second crossover per chromosome arm very rare • 5/233 for chr2, 8/233 for chr4, 5/233 for chr6 • Indicates strong interference

  24. Summary of Results • Used HTA to localize centromeres of most potato chromosomes • Confirmed centromere positions with those in UHD map (van Os et al. 2006) • Marker density approach w/ UHD can be used for positioning centromeres • HTA in potato is also powerful for positioning centromeres

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