Mrna transcript expression in the ear shoot apical meristem and correlation with yield
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mRNA Transcript Expression in the Ear Shoot Apical Meristem and Correlation with Yield. A Translational Genomics Experiment Utilizing Next-Generation Sequencing Technology And the B73 Genome Reference Sequence. GENETIC MATERIALS. Four homozygous lines: Ex-PVP Accessions

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mRNA Transcript Expression in the Ear Shoot Apical Meristem and Correlation with Yield

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mRNA Transcript Expression in the Ear Shoot Apical Meristemand Correlation with Yield

A Translational Genomics Experiment

Utilizing Next-Generation

Sequencing Technology

And the B73 Genome Reference Sequence


GENETIC MATERIALS

Four homozygous lines: Ex-PVP Accessions

Very similar in rate of development

(1) LH1

(2) PHG39

(3) LH123HT

(4) PHG84

Six F1 Hybrids

Six F2 Families

Twelve Reciprocal BC1 Families: A*B/A; A*B/B

Provides the entries for a generation means design

for the partition of genotypic variation into additive, dominance,

and inter-gametic epistatic genetic effects


EXPERIMENTAL DESIGN

Rep 1

Rep 2

  • Generations blocked separately so as to

  • eliminate unequal interplot competition

  • effects due to differences in vigor and rate

  • of 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 for

  • Genome Resources.

Rep 3


TRAIT WEIGHTS ON FIRST PRINCIPAL COMPONENT OF GENOTYPIC VARIATION IN THE MATURE EAR

First principal component

accounts for 90% of the variation

in ear traits

Variation primarily

Non-additive

0.50

0.40

0.30

0.20

0.10

Ear

Weight

Cob

Length

Cob

Weight

Grain

Weight

Grain

Fill

Kernels

Per Row


FREQUENCY DISTRIBUTION OF TRANSCRIPT EXPRESSION GENETIC EFFECTS AT FDR<=0.10

18,000

15,000

12,000

9,000

6,000

3,000

Residual

Genetic

Dominance

Inter-

Gametic

Epistatic

Genotypic

Additive


PERCENT OVER-REPRESENTATION OF GENES WITH TRANSCRIPT EXPRESSION SIGNIFICANTLY CORRELATED WITH KPR COMPONENT BY FUNCTIONAL CATEGORY

60

50

40

30

20

10

Heat Shock

Stress Response

Oxido-

Reductase

Transcription

Factors

All

Others


RANK CORRELATIONS OF GENE EXPRESSION WITH KERNELS PER ROW COMPONENT

cAMP

Responsive

Element

Binding

CCAAT

Enhancer

Binding

Protein

1.0

0.5

0

-0.5

-1.0

C/EBP

CREB

Ramosa1

Ramosa2

Ramosa3

Chr 2

Homeolog

Ramosa3

Chr 7


Ramosa 1

Ramosa2

Ramosa3 homeolog

Knox 1 ELK

Pyruvate dehydrogenase

Transketolase

Tubby

N=394

Biosynthesis

r>=0.82

C/EBP

r=1

Kernels per row

r=-1

r=-1

CREB

r<=-0.82

Superoxide dismutase

Detox proteins (several)

Haem peroxidases (several)

NADH plastoquinone

Iron-sulfur protein

AMP-dependent synthetase

Adenine translocator

AP2/EREPB

Generation of Reactive Oxygen Species(ROS) DueTo Oxido-Reductase Activity During Mitochondrial Respiration

N=451


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 NCGR

Paul Scott Iowa State

Bill Beavis Iowa State

Bob Schmidt UCSD

Sarah Hake & Maize Infl. Group

Adrienne Lauter Iowa State

Greg May NCGR

Kendall Lamkey Iowa State


QUESTIONS & COMMENTS

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