Portal de Periódicos da CAPES

Physical maps and recombination frequency of six rice chromosomes

2003; Wiley; Volume: 36; Issue: 5 Linguagem: Inglês

10.1046/j.1365-313x.2003.01903.x

1365-313X

Jianzhong Wu, Hiroshi Mizuno, Mika Hayashi‐Tsugane, Yukiyo Ito, Yoshino Chiden, Masaki Fujisawa, Satoshi Katagiri, Shoko Saji, Shoji Yoshiki, Wataru Karasawa, Rie Yoshihara, Akiko Hayashi, Harumi Kobayashi, Kazue Ito, Masao Hamada, Masako Okamoto, Maiko Ikeno, Yoko Ichikawa, Yūichi Katayose, Masahiro Yano, Takashi Matsumoto, Takuji Sasaki,

Genomics and Phylogenetic Studies

Summary 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.