Presentation on theme: "Maize Genetics, Genomics, Bioinformatics workshop"— Presentation transcript:
1 Maize Genetics, Genomics, Bioinformatics workshop Doreen Ware ARS USDACold Spring Harbor Laboratory
2 The Plan Acknowledgements Maize Sequences Massaging of data sets Maize FPC, MMP unigene alignmentsComparative map viewsPair wise alignments of maize genetic map t to the rice pseudomolecule, Gramene CMap viewsHow might this be useful?
3 CSHL Lincoln Stein Wei Zhao Kiran Ratnapu Ken Lenny ? ? Clark Teytelman?KenClark?
8 Rice and Maize Synteny Analysis public data sets Maize Mapping Project (MMP)AGI Maize FPC map Cone et al., 2002IBM 2 neighbors MapInternational Rice Sequencing Project (IRGSP)Rice Genome Sequencergp.dna.affrc.go.jp/IRGSP/TIGR rice assembly
9 Leverage synteny of cereal genomes in the absences of complete sequence Rice sequenced based mapsCereal genetic and FPC mapsEstablish common anchor points between the genetic and physical mapsExtend information available from the genetic maps of each species to the physical maps (leverage work of genetic systems)Quantitative Trait Loci (QTL) and Mutants
10 Maize FPC map Identify features to use Maize unigene overgos (MMP unigenes)Maize genetic markersIdentify high confidence features for correspondence to rice.Assign a position for the feature on a contig
11 Finger Print Contig Maps FPC maps consist of contigs of clustered BACsThe BACs are represented by imaged bandsBands represent restriction enzyme digest fragments of the BAC clonescccG/ATATCcccgga…ccggatcaG/ATATCaccFeatures are anchored to BACs in the contigs
12 What is an overgo? ~42 bp oligo sequence used for hybridization Derived from the MMP unigenesGene specific?
13 MMP overgo positions on the maize FPC map contigBACsovergos
14 How many MMP overgo positions are on the maize FPC map? All MMP Unigene overgo positions15,574contigContig BContig Aovergos4 overgo positions on two contigs using 3 overgo probes
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 rejected8864contigBACsovergos
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 contigMaximum start position of a BACMinimum end position of a BACcontigBACsovergos
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 genome6,771 maize unigenes (63%)
22 Filter based upon match-length Matches with less than 150bp match-length were removed leaving 7,770 hits.
23 Distribution of percent identity of Maize Cornsensus unigenes mapped to rice The hits represent 6,692 unique Clusters (62% of the total 10,678).
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 genomeMaizeRice
26 50Kb_1MBColinear gene pairs 400,000 bps or lower
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 genomeMaizeRice
29 Maize Contig 417 CTG 417 Anchored to the maize chromosome 8 by marker UMC1905
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?
31 Maize-Rice Colinear intervals with anchored maize genetic position
32 Genetic loci with sequence mapped to rice genome
33 Blue - Genetic markers Red -Common Green- Colinear FPC contigs
34 What can rice do for maize? Where colinear regions exist to riceProvide potential genetic neighborhood of unanchored maize contigsProvide link to other cereal genetic and physical mapsProvisional order of cereals features where no orientation is known. (Wheat deletion bin map, Maize filtered reads?)Candidate sequence for marker screening developmentWhere limited or no colinear regions exist to riceRethink candidate gene approach?
35 Provide potential genetic neighborhood of unanchored maize contigs chromosome 8 (red), 3 (blue) and unknown (black)
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 SummaryThe 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 genomesIn syntenic regions the rice sequence can provide a provisional order to cereal sequences