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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 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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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. QUESTIONS & COMMENTS ?

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