Sugary Enhancer 1 in Maize: A Presence-Absence Allelic Variant Important in Endosperm Carbohydrate Metabolism.

The sugary enhancer1 (se1) allele is a commercially important, naturally occurring recessive modifier of sugary1 (su1) endosperm mutation. Genotypes that are homozygous su1se1 have double the kernel sucrose content of su1 cultivars while retaining levels of water-soluble polysaccharide (WSP) and the characteristic creamy texture of su1. Although se1 allele has been successfully incorporated into many sweet corn varieties since its discovery in the 1970s, the gene and its function had not been characterized. We used a unique near-isogenic line pair developed in a homozygous su1 background that mendelizes the se1 locus to clone the gene. The se1 phenotype is due to a nearly complete deletion of predicted gene AC217415.3_FG004 on chromosome 2. The gene model in B73 has a predicted 522 bp ORF with a high (80%) GC content with no apparent introns. We characterized the endosperm metabolome of su1se1 relative to its su1Se1 isoline and to B73 over a time-course of development. The lipidome displayed a relatively homogenous pattern between su1Se1 and su1se1. Primary metabolites based on GC-MS platform identified remarkable differences between su1Se1 and su1se1 across time that were largely involved in starch and sucrose metabolism. Among the 86 annotated metabolites, sucrose and maltose were significantly increased in su1se1. We also found significant alterations in levels of several amino acids and secondary metabolites in su1se1. Integrating metabolic and transcriptional data, possible roles for Se1 in starch and sucrose metabolism will be discussed. This study provides new insights into mechanism controlling carbohydrate metabolism in cereal grains, and exemplifies the importance of presence-absence genome variation in phenotypic diversity and crop breeding.