title: Physical maps and recombination frequency of six rice chromosomes.
abstract: We constructed physical maps of rice chromosomes 1, 2, and 6-9 with P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-specific repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR)- and RIce RetroElement 7 (RIRE7)-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.
authors: Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan.
authors: Jianzhong
authors: J
authors: Wu
authors: Hiroshi
authors: H
authors: Mizuno
authors: Mika
authors: M
authors: Hayashi-Tsugane
authors: Yukiyo
authors: Y
authors: Ito
authors: Yoshino
authors: Y
authors: Chiden
authors: Masaki
authors: M
authors: Fujisawa
authors: Satoshi
authors: S
authors: Katagiri
authors: Shoko
authors: S
authors: Saji
authors: Shoji
authors: S
authors: Yoshiki
authors: Wataru
authors: W
authors: Karasawa
authors: Rie
authors: R
authors: Yoshihara
authors: Akiko
authors: A
authors: Hayashi
authors: Harumi
authors: H
authors: Kobayashi
authors: Kazue
authors: K
authors: Ito
authors: Masao
authors: M
authors: Hamada
authors: Masako
authors: M
authors: Okamoto
authors: Maiko
authors: M
authors: Ikeno
authors: Yoko
authors: Y
authors: Ichikawa
authors: Yuichi
authors: Y
authors: Katayose
authors: Masahiro
authors: M
authors: Yano
authors: Takashi
authors: T
authors: Matsumoto
authors: Takuji
authors: T
authors: Sasaki
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D022201:Chromosomes, Artificial / Q000235:genetics; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D005819:Genetic Markers; D017404:In Situ Hybridization, Fluorescence; D012275:Oryza / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*
chemical_list: D005819:Genetic Markers