Physical maps and recombination frequency of six rice chromosomes |
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Authors: | Wu Jianzhong Mizuno Hiroshi Hayashi-Tsugane Mika Ito Yukiyo Chiden Yoshino Fujisawa Masaki Katagiri Satoshi Saji Shoko Yoshiki Shoji Karasawa Wataru Yoshihara Rie Hayashi Akiko Kobayashi Harumi Ito Kazue Hamada Masao Okamoto Masako Ikeno Maiko Ichikawa Yoko Katayose Yuichi Yano Masahiro Matsumoto Takashi Sasaki Takuji |
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Institution: | 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. |
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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. |
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Keywords: | rice genome genetic and physical map centromere gene density repetitive sequence |
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