New Hot Paper Comment by Takuji Sasaki

Takuji Sasaki answers a few questions about this month's new hot paper in the field of Plant & Animal Science.

From •>>March 2004

Field: Plant & Animal Science
Article Title: The genome sequence and structure of rice chromosome 1
Authors: Sasaki, T;Matsumoto, T;Yamamoto, K;Sakata, K;Baba, T;Katayose, Y;Wu, JZ;Niimura, Y;Cheng, ZK;Nagamura, Y;Antonio, BA;Kanamori, H;Hosokawa, S;Masukawa, M;Arikawa, K;Chiden, Y;Hayashi, M;Okamoto, M;Ando, T;Aoki, H;Arita, K;Hamada, M;Harada, C;Hijishita, S;Honda, M;Ichikawa, Y;Idonuma, A;Iijima, M;Ikeno, M;Ito, S;Ito, T;Ito, Y;Ito, Y;Iwabuchi, A;Kamiya, K;Karasawa, W;Katagiri, S;Kikuta, A;Kobayashi, N;Kono, I;Machita, K;Maehara, T;Mizuno, H;Mizubayashi, T;Mukai, Y;Nagasaki, H;Nakashima, M;Nakama, Y;Nakamichi, Y;Nakamura, M;Namiki, N;Negishi, M;Ohta, I;Ono, N;Saji, S;Sakai, K;Shibata, M;Shimokawa, T;Shomura, A;Song, JY;Takazaki, Y;Terasawa, K;Tsuji, K;Waki, K;Yamagata, H;Yamane, H;Yoshiki, S;Yoshihara, R;Yukawa, K;Zhong, HS;Iwama, H;Endo, T;Ito, H;Hahn, JH;Kim, HI;Eun, MY;Yano, M;Jiang, JM;Gojohori, T
Journal: NATURE
Volume: 420
Page: 312-316
Year: NOV 21 2002
* Natl Inst Agrobiol Sci, Rice Genome Res Program, 1-2 Kannondai 2 Chome, Tsukuba, Ibaraki 3058602, Japan.
* Natl Inst Agrobiol Sci, Rice Genome Res Program, Tsukuba, Ibaraki 3058602, Japan.
* Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba, Ibaraki 3058602, Japan.
* Natl Inst Genet, Ctr Informat Biol, Mishima, Shizuoka 4118540, Japan.
* Natl Inst Genet, DNA Data Bank Japan, Mishima, Shizuoka 4118540, Japan.
* Univ Wisconsin, Dept Hort, Madison, WI 53706 USA.
* Tokyo Med & Dent Univ, Dept Bioinformat, Bunkyo Ku, Tokyo 1138510, Japan.
* Natl Inst Agr Sci & Technol, Rice Genome Sequencing Project, RDA, Suwon 441707, South Korea.

Why do you think your paper is highly cited?

“The publication of this article has led many rice and plant scientists to recognize the advantages of a high-quality rice genome sequence for basic research in genetics and molecular biology to illuminate numerous features of plant biology, and most importantly in agriculture to facilitate the breeding of high-yielding and better-quality varieties of rice.”

I believe that all of us are deeply concerned about our daily staple foods, which consist mainly of the major cereal crops such as rice, wheat, corn, oats, and rye. Although these crops are supposed to have diverged from a common ancestral species about 60 million years ago, their genome structures are highly conserved with a well-defined syntenic relationship. However, each species has evolved differently and their phenotypes and genome sizes have diverged significantly from the common ancestor. Among them, rice has the smallest genome size of 400 Mb and is considered as a model cereal crop. It is widely cultivated in Asia, Africa, and Latin America thereby supporting almost half of the world population. To secure a stable food supply in these areas and to meet the needs of an ever-increasing population, new knowledge and technology in breeding based on genomics is indispensable. The rice genome sequence provides the fundamental information to accomplish this innovation in breeding not only for rice but for other cereal crops as well. With this goal, the International Rice Genome Sequencing Project (IRGSP) was organized in 1997 to obtain a highly accurate sequence of the rice genome. Japan is leading this collaboration of 10 countries and is responsible for sequencing six chromosomes which correspond to almost half of the genome. This article is the first report of a completely sequenced chromosome from the international sequencing collaboration. The publication of this article has led many rice and plant scientists to recognize the advantages of a high-quality rice genome sequence for basic research in genetics and molecular biology to illuminate numerous features of plant biology, and most importantly in agriculture to facilitate the breeding of high-yielding and better-quality varieties of rice. With the publication of this paper, complete sequencing of the remaining 11 rice chromosomes is further accelerated and studies on rice functional genomics are encouraged.

Does it describe a new discovery or new methodology that's useful to others?

This article describes the construction of a precise rice PAC/BAC physical map as a template for genome sequencing, i.e., a thorough characterization of the nucleotide sequence, genome structure, gene composition as well as the gene multiplication along the chromosome. The analysis of the sequence is supported by details which can be accessed on the web which describes the details of predicted gene models along the rice chromosome 1. This information is very useful for understanding the functional genomics of rice and other cereal crops. Additionally, the entire sequence is deposited in public databases and is freely available to the scientific community.

What were some of the circumstances that led you to do this research?

Rice is a major crop in Japan and the Japanese government has always put priority on rice-related research. I believe that as a plant scientist working on rice, it provides a certain advantage to be involved in a novel and innovative research that will address basic human needs while at the same time making discoveries in the area of basic science. When we initiated the rice molecular genetic analysis in Japan in 1991, very few anticipated the culmination of the project in rice genome sequencing. However with the success of this project, Japan and the international rice research community has been motivated to pursue genome sequencing and establish rice as a model monocot plant in the same manner that Arabidopsis is considered as a model dicot plant.

Could you summarize the significance of your paper in layman's terms?

All the genetic information of an organism, including the instructions needed for growth, development and reproduction—as well as those which develop in response to varied environmental conditions—are hidden in a sequence of four types of letters in the DNA. Although this paper provides only a part of the entire genome sequence, the complete set of rice DNA will provide the blueprint necessary to tackle the challenges in rice improvement programs dealing with yield, eating quality, flowering time, resistance to diseases, and other agronomically important characteristics. The complete genome sequence will provide the ultimate genetic map which, when combined with functional genomics tools, will tell us the position of all genes and what they do, and ultimately facilitate in developing innovative breeding tools on how to manipulate these genes in order to increase rice production and develop better quality rice.

Takuji Sasaki, Ph.D.
Director
Genome Research Department
National Institute of Agrobiological Sciences (NIAS)
Tsukuba, Ibaraki, Japan

ESI Special Topics, March 2004
Citing URL - http://www.esi-topics.com/nhp/2004/march-04-TakujiSasaki.html