Tutorial for the Genome Browser for Soybean: by David A. Lightfoot Center for Excellence in Soybean Research, Teaching and Outreach Genomics - PowerPoint PPT Presentation

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Tutorial for the Genome Browser for Soybean: by David A. Lightfoot Center for Excellence in Soybean Research, Teaching and Outreach Genomics

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Title: Tutorial for the Genome Browser for Soybean: by David A. Lightfoot Center for Excellence in Soybean Research, Teaching and Outreach Genomics


1
Tutorial for the Genome Browser for Soybean by
David A. LightfootCenter for Excellence in
Soybean Research, Teaching and Outreach Genomics
Proteomics Core Facility, Southern Illinois
University at Carbondale, Carbondale, IL
62901-4415 USA ga4082_at_siu.edu. Supported by NSF,
USB and ISPOB
2
Overview of the site contents
3
The Homepage
Click here for build 3 or build 4
4
Click here to choose build 3 or build 4
5
Click here to choose examples of regions
6
Input marker clone or contig name here to find a
region
7
Select what sorts of data you want to see here
8
An Example of some data
9
3. Gene Distribution islands, swamps and oceans
Ideotype of MLG G Chromosome 18
6.66 microns euchromatin
10
Linkage group
C2
And E
Queue
11
(No Transcript)
12
Gene
13
(No Transcript)
14
Queue Contigs are being placed by BES-SSR on
Genetic MAP
BES SSRs Map Single Paralogs
SSRs from the Genetic Map
GATCATTATTATTATTGCAT
736bp
736bp
BAC3
Contig8001
Contig9001
736bp
736bp
736bp
736bp
BAC2
BAC1
Contig8001
Contig9001
15
SIUC-Microsatellites from the 13,747 MTP BES
Sufficient Marker Density for Elite x Elite Maps
Eliminate Physical Map Gaps
Table Numbers of Microsatellite Repeats and
Polymorphism ratios in Soybean. Mapped SSRs
compared to BES Derived SSRs. TA TT CT CA TAA
Others Total AT AA GA GT ATT tri-N penta- S
IUC-BES 290 192 34 58 81 109 289 1,053 BARC-SSR 3
86 0 24 0 598 11 2 1,021
BES derived SNPs and SLPs are being developed
from diploid contigs, avoiding polyploid contigs
16
2. Genome Architecture linkage disequilibrium
BES Derived SIUC-SatB16A10 Population parents E
F P D M
New QTL for SCN and Yield, Plt 0.01
17
(No Transcript)
18
STATUS OF SOYBEAN PHYSICAL MAP AFTER FIVE
ASSEMBLIES. Automated Manual
Manual Manual
Build 2 Build3
Build 4 Judged by BACs/ Build 5
Sept. 2001
Oct 2002 Oct 2003 unique band to be July
2005 Total (pploid) unique BAC
clones in FPC database 81,024 83,026
78,001 78,001 BACs used in contig
assembly 75,568 78,001 72,942
72,837 Number of singletons
5,884 4,954 27,812 17,942 Marker
anchored singletons 0
0 120 63 Clones in contigs
(fold genome) 69,684 73,069
45,135 58,765 Fold genome in contigs
8.7 9.1 5.6
6.2 Number of contigs
5,488 2,907 2,854 (646)
2208 521 Anchoring Markers
0 385
404 (280) 124 1,523 Anchored Contigs
0 781
742 (181) 223 455 Contigs contain
gt 25 clones 220 921
477 (268) 209 335 10 25 clones
3,038 920 1,458 (433)
1025 110 3 9 clones 1,845
850 820 (0) 820 43
2 clones 385
216 99 (0) 99
33 Unique bands in the contigs 396,843
345,457 258,240 (64,560)
257,356 Length of the contigs (Mb) 1,667
1,451 1.037 (0.258) 0.769 1.034  
Based on 4.00 kbp per unique band. Based on
4.05 kbp per unique band, for 2, 854 contigs
containing 68 unique bands in 15 clones, 264
duplicated region contigs containing 68 unique
bands in 30 clones 15,840 unique bands and 406
highly repeated region contigs containing 68
unique bands in 60 clones, 48,720 unique bands.
19
Summary of Site
  • 78001 high quality fingerprints and 404 unique
    BARC- microsatellite positives identified
  • 1,053 new SIUC-microsatellites developed
  • New Ontology Developed for Tetraploids
  • GBrowse Representation Improved
  • Sequence and gene model representation from
    22,747 BES.
  • Homeologous and syntenic regions are catalogued
  • Editing problem/solutions presented
  • Minimum Tile Paths are available.
  • Positional cloning rates increased 10-20 fold.
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