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 meristem and correlation with yield

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

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

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

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

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


Mrna transcript expression in the ear shoot apical meristem and correlation with yield

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

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


Mrna transcript expression in the ear shoot apical meristem and correlation with yield

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

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

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

QUESTIONS & COMMENTS

?


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