Sequencing, Assembly and Annotation of B104. Sequencing, Assembly and Annotation of B104

B104 is a transformable maize inbred line which shows high sequence similarity with the reference maize line B73. Both B73 and B104 inbred lines share the same background; they were developed as part of the Iowa Stiff Stalk Synthetic breeding program by recombining 16 inbred lines that were selected for their above average combining ability and stiff quality. Although they share the same background, B73 and B104 differ in certain phenotypic traits such as plant height, ear height, flowering time, and frequency of transformation: B73 is not readily transformable whereas B104 shows a relatively high frequency of transformation.To explore the contribution of the founder lines to the genetic architecture of both B73 and B104 and how the difference in ancestries governs patterns of variation and contributes to phenotypic variation, including TE insertions, methylation patterns, and structural variation, we generated a high-quality assembly of B104 from which we have generated a gene model annotation set, TE annotations, structural variation data, and epigenomic data, which we used to deduce the timing of structural and functional variation events between B104 and B73 by identifying these events within shared and non-shared haplogroups derived from the stiff-stalk founder haplotypes.