Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078, USA.
Plant Physiol. 2012 Mar;158(3):1115-29. doi: 10.1104/pp.111.192393. Epub 2012 Jan 13.
Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.
尽管拟南芥（Arabidopsis thaliana）被广泛用作模式植物，但具有突变表型的拟南芥基因的经过精心整理的数据集仍有待建立。九年前在《植物生理学》上发表的一份初步清单已经过时，而全基因组表型信息仍然难以获得。我们在这里描述了一个包含 2400 个基因的综合数据集，这些基因在拟南芥中具有功能丧失型突变表型。表型描述主要是从对科学文献的手动整理中收集的。根据潜在敲除等位基因的记录表型，将基因分为优先组（必需的、形态的、细胞生物化学的和条件的）。还建立了表型类别（例如形态组中的营养、生殖和定时）和子集（例如定时类中的开花时间、衰老、昼夜节律和杂项）。基因身份被归类为已确认（通过分子互补或多个等位基因）或未确认。还探讨了突变表型与蛋白质功能、遗传冗余、蛋白质连通性和亚细胞蛋白质定位之间的关系。还编译了一个包含 401 个基因的互补数据集，这些基因只有在与假定的旁系同源物一起发生突变时才会表现出突变表型。讨论了这些基因在确认功能冗余和增强单个基因数据集价值方面的重要性。随着来自拟南芥社区的进一步投入和整理，这些数据集应该有助于解决各种重要的生物学问题，为探索被子植物基因型和表型之间的关系提供基础，增强拟南芥作为参考植物的实用性，并促进与模式遗传生物的比较研究。
