Population Structure of the sugaryenhancer1 (se1) Haplotype in a Collection of Sweet Maize

Sweet corn is consumed around the world as a fresh vegetable. In the late 1970s a new major mutation that confers high eating quality in sweet corn was characterized. This sugaryenhancer1 (se1) gene was recently fine mapped. With this information we are now able to examine the history of the integration of this major gene into the germplasm. The se1 allele was originally reported in a single inbred line, Ill677a, and it is thought to have penetrated a large breeding pool from this single source. Here, we examine the history of this allele in a modern population and examine the impacts of a single inbred in the background of a breeding pool. To explore the source and history of se1 in modern sweet corn, we compared 120 of the publicly available sweet maize lines in the Ames panel, to 10 inbred lines closely related to Ill677a, and 40 modern high quality inbreds from the University of Wisconsin-Madison sweet corn breeding program, which we genotyped using Genotyping-by-Sequencing. We were able to identify a single extended shared haplotype surrounding the se1 locus, that matched with the molecular marker for the locus in all cases and matches the Ill677a haplotype. We then scanned across the genome to find any other regions that were similar to Ill677a in the modern population using a combination of LD, Fst and the IHS (Integrated Haplotype Statistic) based tests. We found strong evidence for long Ill677a haplotypes around the se1 locus as expected. Unexpectedly, we also found many regions of extended haplotypes throughout the genome including a region around the su1 locus showing a monomorphic haplotype throughout all of the sweet maize germplasm that encompasses nearly half of chromosome 4. Here we have confirmed the source of this allele in a modern commercial pool of germplasm, and provided an example of the integration of important lines into breeding programs, and the slow rate of decay of haplotypes in an actively bred population.