- Biofuels and the Role of Maize
- Cell Wall Composition and Stalk Anatomical
Characteristics
- Tackling the Complexity of the Maize Genome
- Final Remarks
ABHISHEK ANTIBIOTICS PPT MICROBIOLOGY // USES OF ANTIOBIOTICS TYPES OF ANTIB...
Genetic Dissection of Compositional & Anatomical Characteristics Associated with Biofuel Production in Maize.
1. Genetic Dissection of Compositional &
Anatomical Characteristics Associated
with Biofuel Production in Maize
Natalia de Leon
Department of Agronomy – Univ. of Wisconsin, Madison
2. Collaborators and Sponsors
University of Wisconsin:
Shawn Kaeppler
• Marlies Heckwolf
• German Muttoni
• Jillian Foerster
• James Johnson
Edgar Spalding
• Svern Heckwolf
Michigan State University:
Robin Buell
Kevin Childs
Brieanne Vaillancourt
University of Minnesota:
Candy Hirsch
Nathan Springer
UW Graduate School
Dupont-Pioneer
Monsanto
3. Overview
Biofuels and the Role of Maize
Cell Wall Composition and Stalk Anatomical
Characteristics
Tackling the Complexity of the Maize Genome
Final Remarks
www.glbrc.org
4. Maize as a Model
Species
www.glbrc.org
Wheat
Brachypodium
Rice
Adapted from Hilu et al., 1999
Sorghum
Maize
Switchgrass
C4 photosynthesis
5. Maize
54%
Soybean
12%
Wheat
10%
Hay
23%
Sorghum
1%
Percentage from total field crop area
harvested (~300,000,000 acres)
Maize
29%
Soybean
25%
Wheat
16%
Hay
19%
Others
10%
Sorghum
1%
Field Crops Biomass Production in the US
www.glbrc.org
5
Field Crops Area Harvested 2011 (acres) Biomass Production Estimates 2011 (tons)
Percentage of biomass produced by these
major field crops
Source: USDA - National Agricultural Statistics Service
6. What Can Be Learned From Forage Breeding?
Biorefineries Ethanol
Lorenz and Coors (2008)
10. WiDiv Population and Genotypic
(RNASeq) Data Collection
WiDiv association panel (~800
diverse lines)
Lines of Midwest origin, ex-
PVPs, GEM and exotic lines
Restricted flowering – matures
in northern latitudes
Whole seedling (higher
number of expressed genes)
Targeted ~20M reads per
genotype
Goal: SNPs, non-reference
genes, expression
11. Sugar Release - WiDiV
Population
Glucose Release
(%/mg of dry biomass)
Pentose Release
(%/mg of dry biomass)
Two years
Two field reps per year
12. GWAS Sugar Release WiDiv
Glucose
Pentose
CBS domain
containing protein
Transcription
Factor
Transcription
Factor Not
annotated
CBS domain
containing protein
18. Glucose Release in Genotypes
with Extreme Anatomical Traits
n= 12-15 per groups
p= 1*10-8
p= 2.78*10-10
p= 5.88*10-8
p= 3.1*10-4
19. Pan Genome/Transcriptome
www.glbrc.org
Pan genome – full
complement of genes in a
species
Core genome – genes present
in all individuals
Dispensable genome – genes
found in only a subset of the
individuals
Dispensable and unique
genome
Pan, core and dispensable
transcriptome
Line1
Line2
Line3
Line4
Line5
Line6
Line7
Line8
20. Understanding Phenotypic Diversity
Associate genetic factors with traits of interest
Need to characterize all forms of genetic diversity that can
underlie phenotypic diversity
www.glbrc.org
Sequence Level
Variation (SNPs,
small
Insertions/Deletio
ns)
Structural Variation
(Copy Number Variation
– CNV &
Presence/Absence
Variation – PAV)
Gene Expression Variation –
Gene and Isoform level
variation (quantitative
expression differences)
RNA allows the
study of most of
these forms of
variation
21. Candice Hirsch
Novel Transcript Discovery
Line1
Line2
Line3
Map all reads from all
lines to the reference
sequence
Identified 3.2 billion
unmapped reads
B73 Reference Genome
Assemble 400k
unmapped reads
per inbred
(201.2M total)
Assembled transcript 1
Assembled transcript 2
Assembled transcript 3
>60% of reads mapped
for each line
(85% identify and coverage)
• 31,398 loci containing 102,017 transcripts
• 884 bp average size
• Used longest transcript within a loci
• representative transcript assembly (RTA)
12.5 billion reads
Hirsch et al., submitted
8,681 high confidence novel transcripts
(about 50% of those supported by sequence alignments)
22. Karyotype of the maize
chromosomes with
3,396 placed joint RTAs
www.glbrc.org
= RTAs expressed in
every line
= RTAs not expressed
in every inbred line but
expressed in B73
= RTAs not expressed
in every inbred line and not
expressed in B73
~77% of the RTAs with at
least one SNP - placed to a
single place in the reference
24. Juvenile to Adult Transition
www.glbrc.org
Poethig 2003. Phase Change and the Regulation
of Developmental Timing in Plants. Science
301:334-336
Phenotype: Last leaf with
juvenile (dull) wax -
TRANSITION
Jillian Foerster
Juvenility has been associated with lower recalcitrance & increased starch content
25. QTL and GWAS of Transition
www.glbrc.org
Novel gene
glossy15
A.
GRMZM2G362718
B.
GRMZM2G096016
?
-log10(p-value)
FROM
PREVIOUS
WORK:
NAM Popn.
WiDiv
Panel
26. glossy15
A.
GRMZM2G362718
B.
GRMZM2G096016
GRMZM2G104610
C.
Pairwise LD − Chr 2 Region
GRMZM
Association Mapping with SNP Markers
glossy15
A.
GRMZM2G362718
B.
GRMZM2G096016
GRMZM2G104610
C.
Pairwise LD − Chr 2 Region
G
GRMZM2
GRMZM2G09596
Association Mapping with Quantitative Expression
?
-log10(p-value)-log10(p-value)
WiDiv
Panel
27. Final Remarks
Considerable natural variation observed for sugar
release and anatomical traits
Genotypes with low sugar yields have wider stalks, a
thicker rind & less bundles
Ability to characterize different source of genetic
diversity is critical to explain the observed phenotypic
diversity
RTA are not represented in the reference and
therefore appropriate sampling of those variants is
missed in QTL and association analysis
Transcriptome level PAV is extensive and can predict
genomic level PAV, in the case of maize
www.glbrc.org
