IC4R005-Microarray-2012-22419825

Project Title

• Efficacy of Microarray Profiling Data Combined with QTL Mapping for the Identification of a QTL Gene Controlling the Initial Growth Rate in Rice

The Background of This Project

• Nowadays, and especially in the tropics, the rice cropping system is shifting from transplanting to direct sowing because it is less labor intensive (Erguiza et al. 1990). For the establishment of such a direct sowing system, strong seedling vigor is one of the most important agronomic traits. The level of seedling vigor is determined by many morphological and physiological traits, among which the germination rate and early seedling growth are the major targets in a breeding program (Williams and Peterson 1973, Sasahara et al. 1986). Moreover, several studies have suggested that phytohormones, such as gibberellin and auxin, are important for their control (Oikawa et al. 2004, Chhun et al. 2007, Lo et al. 2008).
• Microarray-based transcriptome profiling studies have been primarily used to address gene regulations related to morphological and physiological traits of animals and　plants. However, results from these studies tend to identify a large number of differentially expressed genes due to　the complex interactions between various signaling pathways.　Previously, a report　combining expression profiling using　microarrays with genetic mapping significantly contributed to　the isolation of genetic factors in animal research (Aitman　et al. 1999). However, the identification of QTL genes　using this approach has never been reported in plants.
• This study is the first to use this new approach for the isolation of QTL genes in rice; we conducted combined QTL mapping and microarray profiling analyses to identify QTL genes for seedling vigor at the initial growth stage. Our QTL analysis identified two QTLs, early-stage plant develop- ment1/2 (qEPD1 and qEPD2) for increasing plant height and/ or leaf sheath length at the initial growth stage. By combining QTL mapping and microarray profiling, we predicted that qEPD1 or qEPD2 correspond to gibberellin 20 oxidase-1 or -2 genes (OsGA20ox1, 2), respectively, and confirmed this prediction by complementation analysis. Our study demonstrated that the integration of QTL mapping and expression profiling could be a powerful method to narrow down the number of candidate genes for QTL(s) of interest.

Plant Materials & Treatment

• The researchers used a population of 82 BILs (BC 1 F 12 ) derived from a cross between Koshihikari (japonica) and Habataki (indica) to identify QTLs for seedling traits at the initial growth stage and CL at the heading stage. Seeds of all the lines were immersed in water for 2 d and then sown into the cell plug tray (cell count,　14 × 32; tray size, 540 × 280 mm; depth of cell, 30 mm). These　lines were first grown under greenhouse conditions (15 h of　daylight, 25 × C) until 30 d after the germination to evaluate　seedling traits; then, they were　transplanted to the paddy　field to measure CL at the heading stage. The phenotypic evaluation in BILs was conducted in three or four replicates. SLs were　selected from the BC4F2　generation.

Labs working on this Project

• Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601 Japan
• Honda Research Institute Japan Co., Ltd., Japan
• RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan

Corresponding Author

Koichiro Aya (Email: koichi.a@agr.nagoya-u.ac.jp )