Ken Naito / Associate Professor / Division of Transdisciplinary Sciences
Department of Integrated Biosciences / / Genetic resource of genus Vigna

Career Summary
2001: B.A. in Agriculture - Kyoto University
2003: M.A. in Agriculture - Graduate School of Kyoto University
2007: Ph.D. in Agriculture - Kyoto University
2008-10: Postdoctoral Research Associate - University of Georgia
2011-15: Research Scientist - National Institute of Agrobiological Sciences
2012-17: Research Fellow - JST PRESTO
2016: Principal Investigator - National Institute of Agrobiological Sciences
2016: Associate Professor - University of Tokyo
Educational Activities
Graduate school: Applied Bioresources
Research Activities
Irradiation-induced chromosomal deletions in Arabidopsis thaliana (2002-03):
Deletions induced by irradiation were much larger than considered before (ref 12).
Massive transposition of a transposable element in rice (2004-10):
I found that a rice transposon, mPing, was bursting in a specific rice strain (ref 11). We developed a simple and easy marker system using this transposon (ref 10). We then surveyed insertion sites on the genomic scale and found the genetic load caused by the burst of transposon to be unexpectedly benign (ref 9).
Wild genetic resources of genus Vigna (2011-):
Genus Vigna is a family of cowpea that comprises lots of wild species, many of which live in severe environments such as ocean beaches and limestone karsts. We are working to identify stress tolerance genes from these wild species using genetics and genomics. We are also attempting to de novo domesticate such wild species to turn them into neo-crops (refs 1-8).
1) Wang, Kikuchi, Muto, Naito, Isemura, Ishimoto, Cheng, Kaga, and Tomooka: Reciprocal translocation identified in Vigna angularis dominates the wild population in East Japan. Journal of plant research, in press (2015).

2) Yoshida, Marubodee, Ogiso-Tanaka, Iseki, Isemura, Takahashi, Muto, Naito, Kaga, Okuno, Ehara, and Tomooka: Salt tolerance in wild relatives of adzuki bean, Vigna angularis (Willd.) Ohwi et Ohashi. Genetic Resources and Crop Evolution, in press (2015).

3) Sakai, Naito, Ogiso-Tanaka, Takahashi, Iseki, Muto, Satou, Teruya, Shiroma, Shimoji, Hirano, Itoh, Kaga, and Tomooka: The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome. Scientific Reports, in press (2015).

4) Marubodee, Ogiso-Tanaka, Isemura, Chankaew, Kaga, Naito, Ehara, and Tomooka: Construction of an SSR and RAD marker-based molecular linkage map of Vigna vexillata (L.) A. Rich. PloS one, 10e0138942 (2015).

5) Chankaew, Isemura, Naito, Ogiso-Tanaka, Tomooka, Somta, Kaga, Vaughan, and Srinives: QTL mapping for salt tolerance and domestication-related traits in Vigna marina subsp. oblonga, a halophytic species. Theoretical and Applied Genetics, 127691-702 (2014).

6) Tomooka, Isemura, Naito, Kaga, Vaughan: Vigna Species. Broadening the Genetic Base of Grain Legumes. pp175-208 (2014)

7) Tomooka, Naito, Kaga, Sakai, Hiroaki; Isemura, Ogiso-Tanaka, Iseki, and Takahashi: Evolution, domestication, and neo-domestication of the genus Vigna. Plant Genetic Resources, 12, S168-S171 (2014).

8) Naito, Kaga, Tomooka, and Kawase: De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. Breeding Science, 63, 176-184 (2013).

9) Naito, Zhang, Tsukiyama, Saito, Hancock, Richardson, Okumoto, Tanisaka, and Wessler: Unexpected consequences of sudden and massive transposon amplification on rice gene expression. Nature, 461, 1130-1134 (2009).

10) Monden, Naito, Okumoto, Saito, Oki, Tsukiyama, Ideta, Nakazaki, Wessler, and Tanisaka: High potential of a transposon mPing as a marker system in japonica-japonica cross in rice. DNA Research 16, 131-140 (2009).

11) Naito, Cho, Yang, Campbell, Yano, Okumoto, Tanisaka, and Wessler: Dramatic amplification of a rice transposable element during recent domestication. Proceedings of the National Academy of Sciences, 103, 17620-17625 (2006).

12) Naito, Kusaba, Shikazono, Takano, Tanaka, Tanisaka, and Nishimura: Transmissible and nontransmissible mutations induced by irradiating Arabidopsis thaliana pollen with ő≥-rays and carbon ions. Genetics, 169, 881-889 (2005).
Other Activities
Future Plan
Currently, we are sequencing whole genomes of fantastic wild species to develop a database. In addition, we are developing mapping populations by crossing a stress-tolerant species to sensitive species. Using the genome database and the population, we will go on to isolate stress tolerance genes and apply them to crop species.
Messages to Students
What is your most burning question? What is the most important problem in the world? If you know the question, why donít you start working on the answer?