CHALLENGE

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Overall Goal

• To understand the genetic basis of plant
  adaptation to adverse drought prone environments.
• To identify and characterize genes and gene
  regulatory networks that contribute to
  adaptation.
• To identify, map and utilize beneficial alleles
  for traits that contribute to improved crop
  productivity in adverse environments.

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Focus on Sorghum

• 5th most important cereal grain world wide
• Excellent biomass feedstock for bioenergy
• Reference C4 grass for maize, millet, sugarcane
• 800Mbp genome, 2n 20 (S. bicolor)
• High colinearity with the rice genome (C3 grass)
• Africa center of origin, diverse germplasm
• Excellent drought tolerance
• C4 photosynthesis, thick cuticle, deep roots
• Inducible tolerance, flexible phenology (escape)
• Special avoidance adaptations such as the stay
  green trait

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Recent Progress in Sorghum Genome Research

• Integrated genetic/physical maps TAMU-ARS,
  AGI/UGA
• Chromosome numbering and cytogenetic architecture
  determined Kim et al., 2005
• 22,000 EST/gene clusters Pratt et al., 2005,
  2006
• Microarray profiling Buchanan et al., 2005
  Salzman et al., 2005
• Map-based cloning validated Klein et al., 2005
• TILLING populations Xin et al., Henry et al.,
  2006
• Transformation technology Howe et al., 2006
• 500,000 methyl filtered sequences Bedell et
  al., 2005
• 8X whole genome sequence DOE/JGI, 2007

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TAMU-ARS Integrated Sorghum Genome Platforms

• RIL population (BTx623 X IS3620C) - gt 3,000 DNA
  markers
• HICF fingerprinting of BAC libraries - 2,200
  contigs (6X) 1,200 BAC contigs genetically
  mapped using 6D BAC pools
• Chromosome architecture analyzed by BAC FISH
• Sorghum/cereal comparative maps aligned by BAC
  sequencing
• EST/microarray analysis identify genes and
  regulons
• Germplasm diversity, graphical genotypes,
  haplotypes

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Integrated Sorghum Genome Map Construction
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Cytogenetic Analysis of Sorghum Chr. 3

• 800Mbp
• 10 Chromosomes
• 50 Euchromatin
• 40,000 genes
• 75 of the genes in euchromatin
• Heterochromatin- low recombination

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Map-based Cloning Projects

• Fertility restorer (Rf1)
• Klein et al., 2005
• Aluminum tolerance
• Kochian et al., 2005/6
• Maturity, flowering time
• Childs et al., 1998 Brady et al., 2006
• Midge resistance
• Hardy et al., in progress
• Stay green QTL
• Borrell, Jordan et al., in progress

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Sorghum Gene Expression
Comparison of sorghum, maize and rice
Biochemical pathways
Microarrays
Regulons
Regulatory elements
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The Effect of Osmotic Stress on Gene Expression
as determined by qRT-PCR
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Functional Classification of Osmotically Induced
Genes
Kinase/Phosphatase, Signaling
Transcription, RNA stability
Stress Responsive
Regulatory
Translation
Protein degradation
Growth/ Metabolism
Unknown
Ubiquitous
General plant
Monocot-including rice
Monocot-excluding rice
Sorghum-specific
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Kinetic and Amplitude-Specific Gene Clusters in
ABA-Treated Roots
10000
10
A
B
1000
1
100
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0.1
1.
0.1
0.01
100000
100
D
C
10000
1000
10
100
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1
1
100000
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E
10000
1000
100
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G
H
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0.1
0.1
0.01
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0.00
0 h 3 h 27 h
0 h 3 h 27 h
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Himmelbach et al., 2003
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rab16/17 Genes from Sorghum, Maize and Rice
16MY
50MY
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A
Sb17/Zm17
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-10
-30
-50
Fold difference
-70
-90
-110
Control3R
ABA3R
ABA27R
Control3S
ABA3S
ABA27S
seed
B
16B/16C
16A/OS17
Zm17/Os17
20
15
10
5
Fold difference
0
-5
-10
Control3R
ABA3R
ABA27R
Control3S
ABA3S
ABA27S
seed
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Sb Zm ( Os) Comparisons

• Gene complement
• differential gene family expansion
• Biochemical pathways
• MetaCyc enabled pathway comparison
• RiceCyc
• SorghumCyc
• Gene regulation
• regulon structure, cis-elements, etc.
• Traits, QTL, eQTL, CNS

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Acknowledgements
Genome Map Construction
Gene Expression
Project PIs

• Jeong-soon Kim
• Monica Menz
• Bin Zhou
• Jeff Brady
• Karen Harris
• Natalie Unruh
• Julie McCollum

• Daryl Morishige
• Jeff Brady
• Karen Harris
• Brock Weers
• Sanghyun Lim
• Christina Buchanan
• Ron Salzman

• Patricia Klein
• John Mullet
• Robert Klein

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Collaborators

• Andy Borrell and David Jordan (DPI) Drought
  tolerance and midge resistance
• Bill Rooney (TAMU) Yield, maturity, fertility
  restoration, grain mold, biomass production
• David Stelly and Jim Price (TAMU) Molecular
  cytogenetics
• Leon Kochian (USDA) Al tolerance
• Jurandir Magalhaes (EMBRAPA Maize and Sorghum)
  Al tolerance
• Darrell Rosenow and Henry Nguyen (TAMU and MU)
  Drought tolerance
• Mitch Tuinstra (KS) Seedling vigor at low
  temperature
• Daryl Pring (USDA) Fertility restoration
• John Burke (USDA) Thermotolerance
• Georgia Davis (MU) Root architecture under
  drought conditions
• Lincoln Stein (CSHL) and Doreen Ware (USDA/ARS,
  CSHL) Incorporation of sorghum data into
  Gramene SorghumCyc pathway development
• Lee Pratt and Marie-Michele Pratt (UGA) Sorghum
  EST production, expression profiling, database
  development
• Catherine Feuillet (Univ. of Zurich) Rph7 locus
• Jeff Bennetzen (UGA) Mapping the Pc locus
• Doreen Ware (USDA/ARS, CSHL) Comparative
  analysis of rice, maize and sorghum
• Stephen Kresovich (Cornell) Sorghum panicle
  architecture, sorghum biomass production

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Funding Sources

• NSF Plant Genome Program
• Texas AM University System
• USDA-ARS
• Texas Advanced Technology Program
• Australia QDPI, GRDC
• USAID
• Perry Adkission Chair