Li Guotian, Jain Rashmi, Chern Mawsheng, Pham Nikki T, Martin Joel A, Wei Tong, Schackwitz Wendy S, Lipzen Anna M, Duong Phat Q, Jones Kyle C, Jiang Liangrong, Ruan Deling, Bauer Diane, Peng Yi, Barry Kerrie W, Schmutz Jeremy, Ronald Pamela C
Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616.
Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
Plant Cell. 2017 Jun;29(6):1218-1231. doi: 10.1105/tpc.17.00154. Epub 2017 Jun 2.
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake ( ssp ), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
全基因组测序突变群体的可获得性以及每个株系单核苷酸分辨率的突变编目有助于功能基因组分析。为此,我们在模式水稻品种北陆(粳稻亚种)中生成并测序了一个快中子诱导的突变群体,该品种在9周内完成其生命周期。我们以45倍覆盖度对1504个突变株系进行了测序,鉴定出91513个影响32307个基因的突变,即占所有水稻基因的58%。我们平均每个株系检测到61个突变。突变类型包括单碱基替换、缺失、插入、倒位、易位和串联重复。我们观察到功能丧失突变的比例很高。我们在一个突变株系中鉴定出一个影响单个基因的倒位是短粒表型的致病突变。这一结果揭示了该资源对于高效、经济地鉴定赋予特定表型的基因的有用性。为了便于公众获取这一遗传资源,我们建立了一个名为KitBase的开放获取数据库,该数据库提供序列数据和种子库的访问。这个群体补充了其他现有的突变体库和基因编辑技术。这项工作展示了如何应用廉价的下一代测序来生成高密度的突变编目。