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Maize Genetics, Genomics, Bioinformatics workshop

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Maize Genetics, Genomics, Bioinformatics workshop. Doreen Ware ARS USDA Cold Spring Harbor Laboratory. The Plan. Acknowledgements Maize Sequences Massaging of data sets Maize FPC, MMP unigene alignments Comparative map views - PowerPoint PPT Presentation

Text of Maize Genetics, Genomics, Bioinformatics workshop

  • Maize Genetics, Genomics, Bioinformatics workshopDoreen Ware ARS USDACold Spring Harbor Laboratory

  • The PlanAcknowledgementsMaize 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?

  • CSHLWei ZhaoKiran RatnapuLincoln Stein

    ?LennyTeytelmanKenClark?

  • CornellNoel YapSusan McCouch

  • Maize sequencesRed genomic, Blue expressed, Green clustered, Black genetic map Pink FPC

  • ESTs (Expressed Sequence Tag)Clusters of ESTsTug- Plantgdb (www.plantgdb.org) GI-TIGR (www.tigr.org)Unigenes (Maizegdb) private sequences included deposited in GenbankNCBI has unigenes

  • Genomic Sequence Complete BACs Genomic Survey Sequences (GSS)BAC ends100 skim bacs Methyl filteredHi-Cot filtered

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

  • Leverage synteny of cereal genomes in the absences of complete sequence

    Rice sequenced based mapsCereal genetic and FPC maps Establish 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

  • Maize FPC mapIdentify 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

  • Finger Print Contig MapsFPC maps consist of contigs of clustered BACsThe BACs are represented by imaged bandsBands represent restriction enzyme digest fragments of the BAC clonescccG/ATATCcccggaccggatcaG/ATATCaccFeatures are anchored to BACs in the contigs

  • What is an overgo?~42 bp oligo sequence used for hybridizationDerived from the MMP unigenesGene specific?

  • MMP overgo positions on the maize FPC map

    contig

  • How many MMP overgo positions are on the maize FPC map?All MMP Unigene overgo positions 15,574contigovergos4 overgo positions on two contigs using 3 overgo probesContig AContig B

  • How many FPC contigs does an overgo hit?

  • Chart1

    3291

    2478

    1407

    704

    387

    257

    143

    80

    60

    58

    47

    36

    27

    16

    13

    12

    7

    6

    4

    3

    4

    # of MMP overgos

    # of BAC contigs

    # of contigs and MMP overgo hybridizes to in the maize FPC map

    Sheet1

    026

    13291

    22478

    31407

    4704

    5387

    6257

    7143

    880

    960

    1058

    1147

    1236

    1327

    1416

    1513

    1612

    177

    186

    194

    203

    214

    Sheet1

    # of BAC contigs

    # of MMP overgos

    # of contigs an MMP overgo hybridizes to in the Maize FPC

    Sheet2

    # of MMP overgos

    # of BAC contigs

    # of contigs and MMP overgo hybridizes to in the maize FPC map

    Sheet3

  • How many BACs does an overgo hit in a contig?

  • Chart1

    11649

    2232

    1780

    1633

    1547

    1400

    1147

    923

    740

    576

    469

    319

    185

    153

    97

    66

    32

    23

    15

    11

    # of BACS hybridized to in a contig

    # of MMP overgos

    # of BACs a MMP overgo hybridized to in a FPC contig

    Sheet1

    111649

    22232

    31780

    41633

    51547

    61400

    71147

    8923

    9740

    10576

    11469

    12319

    13185

    14153

    1597

    1666

    1732

    1823

    1915

    2011

    2110

    227

    233

    242

    252

    261

    271

    301

    381

    401

    412

    441

    Sheet1

    # of BACs in a contig

    instances of a cluster

    # of BACs a cluster hybridized to in a BAC contigs

    Sheet2

    # of BACS hybridized to in a contig

    # of MMP overgos

    # of BACs a MMP overgo hybridized to in a FPC contig

    Sheet3

  • 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

  • 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 BAC Minimum end position of a BACcontigBACsovergos

  • Align MMP clusters to the rice genomeSequenced based alignments of features to the rice genome using BLAT.Single best match in the rice genome6,771 maize unigenes (63%)

  • Filter based upon match-lengthMatches with less than 150bp match-length were removed leaving 7,770 hits.

    Chart1

    596

    776

    899

    930

    886

    815

    724

    541

    462

    362

    296

    270

    224

    188

    163

    1030

    hit length

    # of feature hits

    Distribution of maize unigene cluster hit length

    Sheet1

    0-100596

    100-150776

    150-200899

    200-250930

    250-300886

    300-350815

    350-400724

    400-450541

    450-500462

    500-550362

    550-600296

    600-650270

    650-700224

    700-750188

    750-800163

    >8001030

    Sheet1

    hit length

    # of feature hits

    Distribution of maize unigene cluster hit length

    Sheet2

    Sheet3

  • Distribution of percent identity of Maize Cornsensus unigenes mapped to riceThe hits represent 6,692 unique Clusters (62% of the total 10,678).

    Chart1

    1

    2

    1

    1

    1

    1

    2

    1

    2

    2

    7

    5

    3

    7

    18

    18

    13

    21

    35

    33

    63

    64

    104

    119

    176

    195

    296

    354

    457

    586

    731

    820

    896

    870

    708

    485

    303

    168

    69

    54

    19

    13

    8

    Count

    Percent Identity

    Mapped Cornsensus Unigenes

    unigene_PERCENT_ID

    Count

    431

    532

    551

    581

    601

    611

    622

    631

    642

    652

    667

    675

    683

    697

    7018

    7118

    7213

    7321

    7435

    7533

    7663

    7764

    78104

    79119

    80176

    81195

    82296

    83354

    84457

    85586

    86731

    87820

    88896

    89870

    90708

    91485

    92303

    93168

    9469

    9554

    9619

    9713

    988

    unigene_PERCENT_ID

    Count

    Percent Identity

    Mapped Cornsensus Unigenes

  • What is the distribution of the maize unigenes across the rice genome?

    Chart1

    1295883140

    964666120

    997686170

    67044090

    548354100

    54937980

    643444100

    51535180

    35126190

    33423080

    20414860

    29120870

    MAPPED TO RICE

    ON MAIZE FPC

    UNIGENES PER 10MB

    Rice Chromosome

    Maize Cornsensus Unigenes

    Sheet1

    Sheet1

    1295883140

    964666120

    997686170

    67044090

    548354100

    54937980

    643444100

    51535180

    35126190

    33423080

    20414860

    29120870

    MAPPED TO RICE

    ON MAIZE FPC

    UNIGENES PER 10MB

    Rice Chromosome

    Maize Cornsensus Unigenes

    Sheet2

    Sheet3

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

    Rice Maize

  • 50Kb_1MBColinear gene pairs 400,000 bps or lower

    Chart2

    409

    148

    76

    31

    22

    10

    15

    8

    2

    1

    2

    2

    1

    1

    1

    1

    1

    1

    1

    1

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs and the distances within 50Kbp and 1Mbp on rice chromsome 1 ,4 and 10

    Sheet1

    10000175

    2000075

    3000060

    4000044

    5000055

    6000044

    7000030

    8000025

    9000021

    10000028

    11000013

    12000023

    13000017

    14000018

    1500005

    16000010

    1700007

    1800004

    1900003

    2000007

    50000409

    100000148

    15000076

    20000031

    25000022

    30000010

    35000015

    4000008

    4500002

    5000001

    5500002

    6000002

    6500001

    7000001

    7500001

    8000001

    8500001

    9000001

    9500001

    10000001

    1768

    1000000062

    10000000045

    Sheet1

    Sheet2

    Sheet3

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs and the distances within 50Kbp and 1Mbp on rice chromsome 1 ,4 and 10

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs found within 200kb on rice chromosome 1, 4, 10

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

    Chart3

    175

    75

    60

    44

    55

    44

    30

    25

    21

    28

    13

    23

    17

    18

    5

    10

    7

    4

    3

    7

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs found within 200kb on rice chromosome 1, 4, 10

    Sheet1

    10000175

    2000075

    3000060

    4000044

    5000055

    6000044

    7000030

    8000025

    9000021

    10000028

    11000013

    12000023

    13000017

    14000018

    1500005

    16000010

    1700007

    1800004

    1900003

    2000007

    50000409

    100000148

    15000076

    20000031

    25000022

    30000010

    35000015

    4000008

    4500002

    5000001

    5500002

    6000002

    6500001

    7000001

    7500001

    8000001

    8500001

    9000001

    9500001

    10000001

    1768

    1000000062

    10000000045

    Sheet1

    Sheet2

    Sheet3

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs and the distances within 50Kbp and 1Mbp on rice chromsome 1 ,4 and 10

    distance of pairs in bps on rice

    # of maize contig pairs

    Unigene clusters pairs found on maize contigs found within 200kb on rice chromosome 1, 4, 10

  • 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 genomeRice Maize

  • Maize Contig 417 CTG 417 Anchored to the maize chromosome 8 by marker UMC1905

  • 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?

  • Maize-Rice Colinear intervals with anchored maize genetic position

  • Genetic loci with sequence mapped to rice genome

  • Blue - Genetic markersRed -CommonGreen- Colinear FPC contigs

  • 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 development Where limited or no colinear regions exist to riceRethink candidate gene approach?

  • Provide potential genetic neighborhood of unanchored maize contigs chromosome 8 (red), 3 (blue) and unknown (black)

  • Comparative maps with other cerealsWheat EST deletion map (new)Sorghum RFLP map from Paterson (new)Rice TIGR assembly (new)Maize curated FPC

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

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

  • 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