mRNA Transcript Expression in the Ear Shoot Apical Meristemand Correlation with Yield
A Translational Genomics ExperimentUtilizing Next-Generation
Sequencing TechnologyAnd the B73 Genome Reference
Sequence
GENETIC MATERIALSFour homozygous lines: Ex-PVP AccessionsVery similar in rate of development (1) LH1 (2) PHG39 (3) LH123HT (4) PHG84Six F1 Hybrids
Six F2 Families
Twelve Reciprocal BC1 Families: A*B/A; A*B/B
Provides the entries for a generation means designfor the partition of genotypic variation into additive, dominance, and inter-gametic epistatic genetic effects
EXPERIMENTAL DESIGN Ear Shoot Sampling
Ear TraitPhenotyping
BC1 BC1
Parents Parents
BC1’ BC1’
F1 F1
F2 F2
Ear TraitPhenotyping
Ear Shoot Sampling
F2 F2
F1 F1
Parents Parents
BC1’ BC1’
BC1 BC1
Ear ShootSampling
Ear Trait Phenotyping
Parents Parents
F2 F2
BC1’ BC1’
BC1 BC1
F1 F1
Rep 1 Rep 2
Rep 3
• Generations blocked separately so as to eliminate unequal interplot competition effects due to differences in vigor and rateof development.• Ear shoot sampling and ear trait pheno-Typing blocked separately so as to provide Normal ear development on intact plants.• Sequencing and bioinformatics done on extracted mRNA by National Center forGenome Resources.
TRAIT WEIGHTS ON FIRST PRINCIPAL COMPONENT OF GENOTYPIC VARIATION IN
THE MATURE EAR
0.50
0.40
0.30
0.20
0.10
KernelsPer Row
GrainWeight
EarWeight
Grain Fill
CobLength
CobWeight
First principal componentaccounts for 90% of the variation in ear traits
Variation primarilyNon-additive
FREQUENCY DISTRIBUTION OF TRANSCRIPT EXPRESSION GENETIC EFFECTS AT FDR<=0.10
18,000
12,000
9,000
6,000
3,000
Genotypic Additive Dominance Inter-GameticEpistatic
ResidualGenetic
15,000
PERCENT OVER-REPRESENTATION OF GENES WITH TRANSCRIPT EXPRESSION SIGNIFICANTLY CORRELATED WITH KPR COMPONENT BY FUNCTIONAL CATEGORY
60
40
30
20
10
Oxido-Reductase
Transcription Factors
Heat ShockStress Response
AllOthers
50
RANK CORRELATIONS OF GENE EXPRESSION WITH KERNELS PER ROW COMPONENT
1.0
0.5
0
-0.5
-1.0
Ramosa1 Ramosa2 Ramosa3Chr 7
Ramosa3Chr 2Homeolog
C/EBP CREB
CCAATEnhancerBindingProtein
cAMPResponsiveElementBinding
C/EBP
Ramosa 1 Ramosa2 Ramosa3 homeolog Knox 1 ELK Pyruvate dehydrogenase Transketolase Tubby
CREB
Superoxide dismutase Detox proteins (several) Haem peroxidases (several) NADH plastoquinone Iron-sulfur protein AMP-dependent synthetase Adenine translocator AP2/EREPB
r=-1
N=451
N=394
Kernels per row
r>=0.82
r<=-0.82
r=1
r=-1
Generation of Reactive Oxygen Species (ROS) DueTo Oxido-Reductase Activity During Mitochondrial Respiration
Biosynthesis
SUMMARY• Variation in genotypic expression of the ramosa genes in the ear shoot spikelet- pair meristem is highly correlated with genotypic variation in kernels per row in the mature ear.
• Reactive oxygen species may serve as a signal acting on a gene network centered on C/EBP and CREB that regulates initiation of axillary branches in the spikelet-pair meristem.
ACKNOWLEGEMENTS
Andrew Farmer NCGRPaul Scott Iowa StateBill Beavis Iowa State
Bob Schmidt UCSDSarah Hake & Maize Infl. GroupAdrienne Lauter Iowa StateGreg May NCGRKendall Lamkey Iowa State
QUESTIONS & COMMENTS
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