title: A comprehensive rice transcript map containing 6591 expressed sequence tag sites.
abstract: 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 approximately 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.
authors.affiliation: 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.
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.forename: Tomoko
authors.initials: T
authors.lastname: Maehara
authors.forename: Takanori
authors.initials: T
authors.lastname: Shimokawa
authors.forename: Shinichi
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Chizuko
authors.initials: C
authors.lastname: Harada
authors.forename: Yuka
authors.initials: Y
authors.lastname: Takazaki
authors.forename: Nozomi
authors.initials: N
authors.lastname: Ono
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Mukai
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Koike
authors.forename: Jyunshi
authors.initials: J
authors.lastname: Yazaki
authors.forename: Fumiko
authors.initials: F
authors.lastname: Fujii
authors.forename: Ayahiko
authors.initials: A
authors.lastname: Shomura
authors.forename: Tsuyu
authors.initials: T
authors.lastname: Ando
authors.forename: Izumi
authors.initials: I
authors.lastname: Kono
authors.forename: Kazunori
authors.initials: K
authors.lastname: Waki
authors.forename: Kimiko
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yano
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D018244:Chromosomes, Artificial, Yeast / Q000235:genetics; D003001:Cloning, Molecular; D019295:Computational Biology; D020451:Contig Mapping / Q000379:methods; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D005819:Genetic Markers; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D020080:Tandem Repeat Sequences; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D005819:Genetic Markers