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The Plant Cell, Vol. 14, 525-535, March 2002, Copyright © 2002,
American Society of Plant Biologists

GENOMICS ARTICLE

A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites

Jianzhong Wu, Tomoko Maehara, Takanori Shimokawa, Shinichi Yamamoto, Chizuko Harada, Yuka Takazaki, Nozomi Ono, Yoshiyuki Mukai, Kazuhiro Koike, Jyunshi Yazaki, Fumiko Fujii, Ayahiko Shomura, Tsuyu Ando, Izumi Kono, Kazunori Waki, Kimiko Yamamoto, Masahiro Yano, Takashi Matsumoto and Takuji Sasaki1

Rice Genome Research Program, National Institute of Agrobiological Sciences/Institute of the Society of Technoinnovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki 305-8602, Japan

1 To whom correspondence should be addressed. E-mail tsasaki{at}nias.affrc.go.jp; fax 81-298-38-2302

To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction–based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only ~21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.


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