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Maize Genetics, Genomics, Bioinformatics workshop

The Plan. AcknowledgementsMaize Sequences Massaging of data setsMaize FPC, MMP unigene alignmentsComparative map viewsPair wise alignments of maize genetic map t to the rice pseudomolecule, Gramene CMap views How might this be useful?. CSHL. Wei Zhao. Kiran Ratnapu. . . . Lincoln Stein. . . ?.

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Maize Genetics, Genomics, Bioinformatics workshop

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    1. Maize Genetics, Genomics, Bioinformatics workshop Doreen Ware ARS USDA Cold Spring Harbor Laboratory

    2. The Plan Acknowledgements Maize Sequences Massaging of data sets Maize FPC, MMP unigene alignments Comparative map views Pair wise alignments of maize genetic map t to the rice pseudomolecule, Gramene CMap views How might this be useful?

    3. CSHL

    4. Cornell

    5. Maize sequences

    6. ESTs (Expressed Sequence Tag) Clusters of ESTs Tug- Plantgdb (www.plantgdb.org) GI-TIGR (www.tigr.org) Unigenes (Maizegdb) private sequences included deposited in Genbank NCBI has unigenes

    7. Genomic Sequence Complete BACs Genomic Survey Sequences (GSS) BAC ends 100 skim bacs Methyl filtered Hi-Cot filtered

    8. Rice and Maize Synteny Analysis public data sets Maize Mapping Project (MMP) AGI Maize FPC map Cone et al., 2002 www.maizemap.org, www.genome.arizona.edu/FPC/maize/ IBM 2 neighbors Map www.maizegdb.org International Rice Sequencing Project (IRGSP) Rice Genome Sequence rgp.dna.affrc.go.jp/IRGSP/ TIGR rice assembly www.tigr.org

    9. Leverage synteny of cereal genomes in the absences of complete sequence

    10. Maize FPC map Identify features to use Maize unigene overgos (MMP unigenes) Maize genetic markers Identify high confidence features for correspondence to rice. Assign a position for the feature on a contig

    11. Finger Print Contig Maps

    12. What is an overgo? ~42 bp oligo sequence used for hybridization Derived from the MMP unigenes Gene specific?

    13. MMP overgo positions on the maize FPC map

    14. How many MMP overgo positions are on the maize FPC map? All MMP Unigene overgo positions 15,574

    15. How many FPC contigs does an overgo hit?

    17. How many BACs does an overgo hit in a contig?

    19. Select overgos with at least two BACs hybridized in an FPC contig. To remove potential false positives, require an overgo be found on more than one BAC in a Maize FPC contigs. Red and pink are accepted blue is rejected 8864

    20. Generate a position for the overgo on the FPC contig To establish a rough order of the overgo on the contig the position of the BACs the overgo hit in the FPC contig is used. This establishes a relative order of the overgos within the contig Maximum start position of a BAC Minimum end position of a BAC

    21. Align MMP clusters to the rice genome Sequenced based alignments of features to the rice genome using BLAT. Single best match in the rice genome 6,771 maize unigenes (63%)

    22. Filter based upon match-length

    23. Distribution of percent identity of Maize Cornsensus unigenes mapped to rice

    24. What is the distribution of the maize unigenes across the rice genome?

    25. Calculate adjacent distances between pairs of unigenes on maize contigs and their distance of the rice genome

    27. 90% of colinear maize overgos contig-pairs fall under 400,000 bps are found within 165,000 bps on rice

    28. A maize contig span will be defined as syntenic if it contains a unigenes pair that is less than 400 kb apart on the rice genome

    29. Maize Contig 417

    30. Plot the colinear rice and maize spans that contain genetic marker information What regions of the rice genome are syntenic with maize? What regions of the rice genome have no synteny with maize? What regions of the maize genome have no synteny to rice?

    34. What can rice do for maize? Where colinear regions exist to rice Provide potential genetic neighborhood of unanchored maize contigs Provide link to other cereal genetic and physical maps Provisional order of cereals features where no orientation is known. (Wheat deletion bin map, Maize filtered reads?) Candidate sequence for marker screening development Where limited or no colinear regions exist to rice Rethink candidate gene approach?

    36. Comparative maps with other cereals Wheat EST deletion map (new) Sorghum RFLP map from Paterson (new) Rice TIGR assembly (new) Maize curated FPC

    37. Rice chromosome 1 to Wheat deletion map, Sorghum genetic map, and Maize FPC map

    38. Provisional order of cereals features where no orientation is known.

    39. Summary The maize physical map can provide a provisional order for the maize sequences that have been anchored. In syntenic regions the rice sequence can serve as an anchor to define contact points between cereal genomes In syntenic regions the rice sequence can provide a provisional order to cereal sequences

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