IC4R003-Phenomics-2007-17701278

From RiceWiki
Jump to: navigation, search

Project Title

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

The Background of This Project

Figure 1. Examples of variation in T1 plant morphology.
  • 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.

Plant Culture & Treatment

  • An isolated net field, located at the Taiwan Agriculture Research Institute (TARI), Wufeng, Taiwan, specific for GM crops, was used for growth and propagation of rice T-DNA mutants. The rice growing season in Taiwan each year is about 10 months, with two cropping seasons of about 4–5 months each. Since the rice variety used in this study is not sensitive to day length or temperature, T0 and T1 plants can be grown continuously.
  • The planting density was 25 · 25 cm 2 , and all plants were of single-seed descent. Each of the two regions contained approximately 4,000 T0 plants and 2,500 T1 lines. Approximately 0.2 ha was used for T0 plants and 0.7 ha for T1 plants each season. T0 plants were grown in the region closest to the entrance and T1 lines in the rest of the area. The area for T0 plants was large, and some empty space was prepared for new seedlings.
  • Approximately 1,000 T0 seedlings with 4–5 leaves were sent from the tissue culture lab each month. During this time, leaf samples were collected for the subsequent flanking sequence analysis. All seedlings were tagged with a barcode and then transplanted to the field. A total of 8,000 T0 plants each year were transplanted continuously from February to August with a growing season of approximately 4 months. T1 lines were transplanted twice a year, in mid-February and late July. Thirty seeds per line were used for germination. The seedling phenotypes were recorded at three-leaf stage, and 12 seedlings were then transplanted into the field in blocks of 3 · 4 plants. All seeds from each plant were harvested, cleaned, and stored in the National Plant Genetic Resource Center (NPGRC) at TARI.

IC4R003-Phenomics-2007-17701278-1.png

Research Findings

  • The mutant phenotypes and segregation ratio of the three sublines in a T1 mutant line M0028606 was shown in Table 2. Three phenotype traits were recorded for M0026806_B and seven for M0028606_C. Although M0026806_B and M0026806_C plants share common phenotypic traits such as semidwarfism, M0026806_C plants showed several different traits such as late heading and sterile seeds. The plant types also differ—spread-out type in the B group and erect type in the C group. Of the 12 plants grown, 8, 3, and 1 plants belonged to the M0026806, M0026806_B, and M0026806_C groups, respectively. The seeds from dif- ferent groups were harvested separately. The phenotypes of the T1 lines were scored in a similar manner and then recorded systematically. Of the 4,065 lines showing mutated phenotypes, 3,740 have one mutant group, 303 and 22 lines have two and three mutant groups, respectively.
  • The photos of eight plants transplanted at the same time for the same growth period was shown in Figure 1. The wild-type plant is at early heading stage, contains approximately 20 tillers and is almost 100 cm tall (panel A). Panels B to H illustrate mutants with decreased height (C, D) or tiller number (E), changes in leaf angle (G), tiller angle (B), leaf shape (C, D, F), and plant type (F, H). The seed of the wild type illustrated in Fig. 2A is awnless and contains short glumes at both sides, and one lemma (wider) and one palea to protect the kernel inside. The length-to-width ratio of the seed is approximately 1.7, and the color is yellowish. Several obvious mutants show changes in seed size (C, E, F), seed shape (C, D), open hull (E, F), and presence of long glume (G, H), or awn (I, J).
  • The seed of the wild type was illustrated in Figure2. A is awnless and contains short glumes at both sides, and one lemma (wider) and one palea to protect the kernel inside. The length-to-width ratio of the seed is approximately 1.7, and the color is yellowish. Several obvious mutants show changes in seed size (C, E, F), seed shape (C, D), open hull (E, F), and presence of long glume (G, H), or awn (I, J).

Figure 2.Examples of variations in T2 seed morphology.

Labs working on this Project

  • Taiwan Agricultural Research Institute, Wufeng, Taichung 41301, Taichung 41354, Taiwan
  • Department of Biotechnology and Bioinformatics, Asia University, Wufeng, Taichung 41354, Taiwan
  • Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan

Corresponding Author

Yue-Ie C. Hsing(E-Mail: bohsing@gate.sinica.edu.tw)