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.

B104是一种可转化的玉米自交系，与玉米参考自交系B73的序列相似性极高。B73与B104二者遗传背景一致，均由爱荷华硬秆合成（Iowa Stiff Stalk Synthetic）育种项目通过重组16个因配合力与秆质表现优异而被筛选出的自交系培育而来。尽管二者遗传背景相同，但B73与B104在部分表型性状上存在差异，具体包括株高、穗位高、开花期以及转化频率：B73不易进行遗传转化，而B104的转化频率相对较高。为探究创始自交系对B73与B104遗传架构的贡献，以及祖先背景差异如何调控变异模式并影响包括转座子（Transposable Element, TE）插入、甲基化模式与结构变异在内的表型变异，我们对B104开展了高质量基因组组装，并由此构建了基因模型注释集、转座子注释集、结构变异数据以及表观基因组数据；依托这些数据，我们通过在源自硬秆创始单倍型的共享与非共享单倍群内识别相关变异事件，推演出B104与B73之间结构与功能变异事件的发生时序。