Presentation on theme: "MRNA Transcript Expression in the Ear Shoot Apical Meristem and Correlation with Yield A Translational Genomics Experiment Utilizing Next-Generation Sequencing."— Presentation transcript:
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 Very similar in rate of development (1) LH1 (2) PHG39 (3) LH123HT (4) PHG84 Six F 1 Hybrids Six F 2 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 Ear Shoot Sampling Ear Trait Phenotyping BC1 Parents BC1 F1F1 F1F1 F2F2 F2F2 Ear Trait Phenotyping Ear Shoot Sampling F2F2 F2F2 F1F1 F1F1 Parents BC1 Ear Shoot Sampling Ear Trait Phenotyping Parents F2F2 F2F2 BC1 F1F1 F1F1 Rep 1 Rep 2 Rep 3 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.
TRAIT WEIGHTS ON FIRST PRINCIPAL COMPONENT OF GENOTYPIC VARIATION IN THE MATURE EAR 0.50 0.40 0.30 0.20 0.10 Kernels Per Row Grain Weight Ear Weight Grain Fill Cob Length Cob Weight First principal component accounts for 90% of the variation in ear traits Variation primarily Non-additive
FREQUENCY DISTRIBUTION OF TRANSCRIPT EXPRESSION GENETIC EFFECTS AT FDR<=0.10 18,000 12,000 9,000 6,000 3,000 GenotypicAdditive Dominance Inter- Gametic Epistatic Residual Genetic 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 Shock Stress Response All Others 50
RANK CORRELATIONS OF GENE EXPRESSION WITH KERNELS PER ROW COMPONENT 1.0 0.5 0 -0.5 Ramosa1 Ramosa2 Ramosa3 Chr 7 Ramosa3 Chr 2 Homeolog C/EBP CREB CCAAT Enhancer Binding Protein cAMP Responsive Element Binding
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