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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