A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system

Funding Information: Acknowledgements This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Green Technology Project EF-1004). We are grateful to Dr. Takuji Sasaki for his encouragement throughout the project and his excellent advice on the improvement of this manuscript, and to Dr. Shoshi Kikuchi for providing useful information on rice FL-cDNAs. We thank Professors Kokichi Hinata, Atsushi Hirai, Hiroshi Kamada and Masashi Ugaki for their encouragement, critical comments and helpful suggestions, and Drs. Hisato Okuizumi and Hiroyuki Kawahigashi for their administrative support throughout the project. We also thank Mayumi Akagawa, Hiroko Abe, Keiko Mori, Etsuko Sugai, Yumiko Nakane, Ken-ichi Watanabe, Mayumi Takeya, and Kana Miyata for their technical assistance; the members of the Technical Support Section of the National Institute of Agrobiological Sciences for their help in the care of the FOX-rice plants; Haruko Onodera and Kazuko Ono for their technical assistance and advice on rice transformation; Inplanta Innovations Inc. for their technical help on the construction of theThe latest report has estimated the number of rice genes to be ∼32 000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13 980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12 000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene, confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.publishersversionPeer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead