Large-scale phenomics analysis of a T-DNA tagged mutant population

Abstract

Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.

Keywords: T-DNA insertional mutants; flanking sequence; large-scale phenomics; rice; sequence analysis.

Figure 1:

Example of search results for the trait “yellow leaf” in the TRIM resource.

Figure 2:

Trait percentages for the 4 high abundant phenotype categories in the TRIM resource: (A) plant stature; (B) leaf morphology; (C) leaf color; and (D) panicle.

Figure 3:

Example of TRIM flanking sequence integration sites revealed by use of genome browsers. The 20-kb region locates at 13 781 735 to 13 801 735 bp of chromosome 3. The upper section illustrates the flanking sequence tag in TRIM, the second section genes annotated by RAP-db [8], the third section genes annotated by the MSU Rice database [35], and the last section repeat sequences annotated by MSU Rice.