Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these “classical” maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5–12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of “grasses as a single genetic system,” where what is learned in one grass may be applied to another.

并非所有基因均具有同等的生物学特性。尽管有序列保守性与表达数据作为支撑，但许多基因的纯合敲除突变体在至少实验室条件下未表现出可见表型。我们已鉴定出一组玉米（Zea mays L.）基因，这些基因在玉米基因组数据库（MaizeGDB）收录的相关文献中占比远超平均水平。我们将这些"经典"玉米基因手动锚定至B73参考基因组的基因模型中，并在其他禾本科植物基因组中鉴定出了共线性同源基因。除了对最新的玉米基因模型版本2进行验证外，我们还发现，其中一部分在克隆前通过形态学表型鉴定的基因，在整个禾本科植物的共线性区域中的保留水平远高于普通表达的玉米基因；且即便在相反的亚基因组上仍保留有重复拷贝，这些基因仍优先定位于maize1亚基因组。maize1亚基因组是指玉米谱系在5~12百万年前发生全基因组复制后，基因丢失程度更低的亚基因组；定位于该亚基因组的基因在现代玉米中的表达水平通常更高。我们用于禾本科共线性分析的网页版分析工具链接，将为后续研究以及玉米遗传学研究史相关教学提供有力支撑。本研究结果印证了"禾本科作为统一遗传系统"的概念，即从一种禾本科植物中获得的研究结论可推广应用至其他禾本科物种。