Functional Genomics of Maize Endosperm Maturation and Protein Quality

Quality Protein Maize (QPM) is a hard kernel variant of the high-lysine mutant, opaque2. Using γ-irradiation, we created opaque QPM variants to identify opaque-2 modifier genes and to investigate deletion mutagenesis combined with Illumina sequencing as a maize functional genomics tool. A K0326Y-QPM deletion mutant (line 107) was null for the 27and 50-kD γ-zeins and abolished vitreous endosperm formation. Illumina exonand RNA-seq revealed a 1.2 Mb deletion encompassing the 27and 50-kD γ-zein genes on chromosome 7, and a deletion of at least 232 Kb on chromosome 9. Protein body number was reduced by over 90% while protein body size is similar to wild type. Kernels hemizygous for the γ-zein deletion had intermediate 27and 50-kD γ-zein levels and were semi-vitreous, indicating haploinsufficiency of these gene products in opaque-2 endosperm modification. We showed that such haploinsufficiency for 27-kD γ-zein function does not apply to the modification in B73 wild type vitreous endosperm formation. The γ-zein deletion further increased lysine in QPM in its homozygous and hemizygous states. This work identifies 27-kD γ-zein as an opaque-2 modifier gene within the largest QPM QTL, and may suggest the 50-kD γ-zein also contributes to this QTL. It further demonstrates that genome-wide deletions in non-reference maize lines can be identified through a combination of assembly of Illumina reads against the B73 genome and integration of RNA-seq data.