A rice phenomics study—phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population

Abstract

With the completion of the rice genome sequencing project, the next major challenge is the largescale determination of gene function. As an important crop and a model organism, rice provides major insights into gene functions important for crop growth or production. Phenomics with detailed information about tagged populations provides a good tool for functional genomics analysis. By a T-DNA insertional mutagenesis approach, we have generated a rice mutant population containing 55,000 promoter trap and gene activation or knockout lines. Approximately 20,000 of these lines have known integration sites. The T0 and T1 plants were grown in net ''houses'' for two cropping seasons each year since 2003, with the mutant phenotypes recorded. Detailed data describing growth and development of these plants, in 11 categories and 65 subcategories, over the entire four-month growing season are available in a searchable database, along with the genetic segregation information and flanking sequence data. With the detailed data from more than 20,000 T1 lines and 12 plants per line, we estimated the mutation rates of the T1 population, as well the frequency of the dominant T0 mutants. The correlations among different mutation phenotypes are also calculated. Together, the information about mutant lines, their integration sites, and the phenotypes make this collection, the Taiwan Rice Insertion Mutants (TRIM), a good resource for rice phenomics study. Ten T2 seeds per line can be distributed to researchers upon request.

Mutant Resources in Rice for Functional Genomics of the Grasses

“…T-DNA AT populations have been developed using vectors with cauliflower mosaic virus 35S enhancer multimers, the inserts characterized by FSTs and phenomic data for forward and reverse genetics screens (Jeong et al, 2002;Chern et al, 2007;Hsing et al, 2007;Wan et al, 2009). Recently, an Ac-Ds AT system has also been developed (Qu et al, 2008) using convenient markers for selection of multiple transposants from a few starter transformed lines.…”

Growth Platform-Dependent and -Independent Phenotypic and Metabolic Responses of Arabidopsis and Its Halophytic Relative, Eutrema salsugineum, to Salt Stress

“…However, the challenge will remain to accurately associate changes in these molecules with quantifiable developmental and physiological stress adaptation phenotypes and thus allow genotype-tophenotype predictions to be made. To achieve this goal, deep phenotyping (phenomics) is essential to allow compilation of precise multidimensional, morphological, physiological, and molecular phenotypes of plant responses (Boyes et al, 2001;Granier et al, 2006;Chern et al, 2007;Miyao et al, 2007;Kuromori et al, 2009;Furbank and Tester, 2011). Although Arabidopsis and E. salsugineum possess some fundamental differences in developmental program such as a vernalization requirement for promotion of flowering in E. salsugineum (Bressan et al, 2001), their developmental growth stages from seed to rosette leaves to production of flowering bolts are similar, a feature that facilitates phenotypic comparison between the two species.…”

Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

“…Jeon et al (2000) have investigated the phenotypic variation of rice T-DNA tagging lines and found that up to 17% of the lines were sterile and various mutant phenotypes were observed including dwarfing, leaf-pigment alterations, tallness and so on. Chern et al (2007) reported 11 categories of the visible phenotypic variations with the ratio at around 18%. Miyao et al (2007) have investigated around 50,000 Tos17 insertion lines and found that nearly half of the lines showed mutant phenotype.…”