Research Express@NCKU - Articles Digest
Research Express@NCKU Volume 23 Issue 4 - February 8, 2013 [ http://research.ncku.edu.tw/re/articles/e/20130208/3.html ]
The map-based sequence of the rice genome
HONG-HWA CHEN
Department of Biology, College of Bioscience and Biotechnology, National Cheng Kung University [email protected]
Nature 436, 793-800 (2005)
Times Cited: 1,268 (from Web of Science 2013/01/22)
Rice, one of the world’s most important food plants, has important syntenic
relationship with the other cereal species and is a model plant for the grasses. Rice has been chosen as the first crop genome sequencing by an international rice genome sequencing consortium, IRGSP (International Rice Genome Sequencing Project) for the following reasons: (1) Rice is an important crop in the world, feeding about one half of the world’s population; (2) Rice genome size, 430 Mb, is the smallest among crops; (3) Rice linkage and physical maps have been established, and over 120,000 expressed
sequence tags (ESTs) reported and mostly mapped. A yeast artificial chromosome (YAC) library that has been fingerprinted and ordered with mapped markers currently covers 60% of the rice genome. Several bacterial artificial chromosome (BAC) libraries and P1-derived artificial chromosome (PAC) libraries have also been described. (4) The transgenic technology for rice has been established, and rice has become the easies of all cereal plants to transform genetically. (5) Rice shares a co-linear gene organization of the other grasses. IRGSP was founded at 1997 and started function at 1998. Ten members were working together to decode the rice
chromosome, they are Japan, USA, China, Taiwan, France, India, Korea, Thailand, UK, and Brazil. Taiwan picked up chromosome 5 because of the following reasons: less repetitive sequence, high YAC contig coverage, and with many god agronomic traits in this chromosome.
Only five countries complete the sequence work of at least one chromosome, and Taiwan is one of them. Japan has finished 50%, USA 22%, China 9%, Taiwan 8%, and France 7%. Several PIs of Institute of Botany, Academia Sinica started this project. Later on, my lab in Dept. of Biology, National Cheng-kung University joined it. IRGSP decided to speed up the sequencing work, so VGH-YMU Genome Center and Vitagenomics Company also joined this team. This team has registered 38.5 Mb rice chromosome 5 sequence to the public database and completes the high quality of chromosome. In this paper, we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis.
It is now post-genomics era and rice functional genomics research becomes a cutting-edge topic. With the exponential increase in the world population, the crop production would be very critical in the next decades. On the other hands, less chemicals, including fertilizers/herbicides/insecticides, should be applied to our environment for the purpose of sustainable development. To fulfill this, scientists have to fine ways to improve crop
performance within a certain time. Functional genomics research would facilitate to fine out new genes responsible for stress resistance, high quality grains, and many important agronomic traits.
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Research Express@NCKU - Articles Digest
Figure 1. Maps of the twelve rice chromosomes.
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