Understanding Complex Traits in Maize through Structural and Functional Genomics Georgia Davis

Structural genomics n Science related to discovery of gene order and organization across the genome.

Structural Genomics n Genetic mapping n Physical mapping n In situ hybridization

Functional Genomics n Science related to the discovery and definition of the function of genes Whole plantCellular Biochemical RNA C16 C18 C20 C22 C24 C26 AldehydesAlcohols Wax Esters

Functional Genomics n Trait analysis n Gene disruption strategies –Targeted –Random n DNA microarrays n RNA profiling n Protein chips n Protein prediction algorithms

Functional Genomics n Insect Resistance –QTL Analysis –Biochemical Pathway Identified. –Major QTL With Unknown Function. n Aflatoxin Reduction –QTL Analysis –Major QTL With Unknown Function. –One Biochemical Pathway Identified.

Fall armyworm n Present east of Rockies and South of Canada. n Egg  adult in 4 weeks n One female lays several hundred eggs. n Broad host range

Hosts of Fall Armyworm

Southwestern Corn Borer n Narrow host range. n Mainly in southeastern US.

Southwestern Corn Borer Hosts

Germplasm Fall armyworm damage 10 days after infestation with 30 larvae per plant

Lepidopteran Resistance Beet armyworm European corn borer Corn ear worm Fall armyworm Southwestern corn borer

Juvenile traits n Dull epicuticular wax layer –Fatty alcohols n No leaf hairs n Adventitious roots present n No buliforme cells n Cells are rounded

Juvenile vs. Adult Leaves n Leaves maintain their phase status throughout development. n Number of juvenile leaves varies among inbreds. n A number of mutants in juvenile to adult phase change have been identified.

43% Summary of QTL Study 66% SWCB FAW Juvenility 7% 51% 27% 11%59% gl15

Gl15 n Apetala2-type transcription factor. n Regulates long-chain wax ester synthesis. n Controls epidermal juvenile to adult phase change.

Functional Genomics n Insect Resistance –QTL Analysis –Biochemical Pathway Identified. –Major QTL With Unknown Function. n Aflatoxin Reduction –QTL Analysis –Major QTL With Unknown Function. –One Biochemical Pathway Identified.

Hosts of Aspergillus flavus

Aspergillus flavus Infection via silk channel wounds in kernels cracks in kernels

Aflatoxin Aflatoxin B1  Potent carcinogen.  Associated with liver cancer in humans.

Health concerns

Aflatoxin contamination n Large environmental influence. –Drought stress increases aflatoxin level. n Correct genes in both fungus and host required for high levels of toxin formation. n Synthesis is biochemically similar to anthocyanin biosyntheis in maize.

Aflatoxin QTL Summary Mp313E favorable allele Va35 favorable allele D A DA

Anthocyanin vs. aflatoxin a2 bz1 c1-p a1 a1 sh2 a2 bt pr bz2 c1-n c sh wx in1 pr r-g sh bz wx su c2 c2 C2I-df 23X  toxin 9X  toxin 7X  toxin

Functional Genomics Whole plantCellular Biochemical RNA C16 C18 C20 C22 C24 C26 AldehydesAlcohols Wax Esters

Summary n Structural genomics provides the tools needed to support functional genomics. n In plants, future technological advancements in the areas of protein-protein interactions and site-specific knockouts on a genome- wide scale are needed.