The opaque2 (o2) mutation increases the Lys content of maize (Zea mays) endosperm by reducing the synthesis of zein storage proteins and increasing the accumulation of other types of cellular proteins. Elongation factor 1A (eEF1A) is one of these proteins, and its concentration is highly correlated with the amount of other Lys-containing proteins in the endosperm. We investigated the basis for this relationship by comparing patterns of protein accumulation and gene expression between a high (Oh51Ao2) and a low (Oh545o2) eEF1A inbred, as well as between high and low eEF1A recombinant inbred lines obtained from their cross. The content of a-zein and several cytoskeletal proteins was measured in high and low eEF1A inbred lines, and the levels of these proteins were found to correlate with that of eEF1A. To extend this analysis, we used an endosperm expressed sequence tag microarray to examine steady-state levels of RNA transcripts in developing endosperm of these genotypes. We identified about 120 genes coordinately regulated in association with eEF1A content. These genes encode proteins involved in several biological structures and processes, including the actin cytoskeleton, the endoplasmic reticulum, and the protein synthesis apparatus. Thus, higher levels of eEF1A in o2 mutants may be related to a more extensive cytoskeletal network surrounding the rough endoplasmic reticulum and increased synthesis of cytoskeleton-associated proteins, all of which contribute significantly to the Lys content of the endosperm.The discovery that the opaque2 (o2) mutation almost doubles the Lys content of maize (Zea mays) endosperm (Mertz et al., 1964) led to extensive efforts to develop genotypes with better nutritional quality for human and animal diets. Unfortunately, the inferior agronomic traits associated with this mutation, including reduced yield and protein content, soft kernels, and pathogen susceptibility, made it difficult to develop o2 in breeding programs (Glover and Mertz, 1987). To overcome these problems, maize breeders at International Center for Development of Maize and Wheat, Mexico (Villegas et al., 1992) and the University of Natal, South Africa (Gevers and Lake, 1992) developed modified o2 mutants called Quality Protein Maize (QPM). These genotypes combine the improved nutritional quality trait of o2 with those responsible for vitreous endosperm and normal yield. However, additional improvement of protein quality is required for Quality Protein Maize to meet the minimal Lys content (5 mg/100 mg of protein) recommended for human nutrition (Young et al., 1998).Several studies have documented a broad range of variability in Lys content among normal, o2, and modified o2 maize genotypes (Moro et al., 1996;Zarkadas et al., 2000), showing that the effect of the mutation is highly dependent on the genetic background. These studies suggested the Lys content of the kernel can be improved by appropriate selection. However, identification of more nutritional maize genotypes has been limited by knowledge of the genetic...