The genome sequence and structure of rice chromosome 1

Abstract

viruses were injected to follicles on both wings for later studies. Chickens were raised in cages and observed on a daily basis over a two-month period. The regenerated feathers were plucked and examined with a dissection or scanning electron micrograph microscope for abnormalities compared with normal primary remiges. Histology and in situ hybridizationParaffin sections (5 mm) were stained with haematoxylin and eosin or prepared for in situ hybridization following routine procedures 26 . Cryostat sections (10 mm) were stained with X-gal. TUNEL staining was performed using a kit (Roche). Nonradioactive wholemount or section in situ hybridization or section in situ hybridization was performed according to the protocol described 22,26 . After hybridization, sections were incubated with an antidigoxigenin Fab conjugated to alkaline phosphatase (Boehringer Mannheim). Colour was detected by incubating with a Boehringer Mannheim purple substrate (Roche).

Physical maps and recombination frequency of six rice chromosomes

“…There was no clear relationship between recombination frequency and G C content in either hotspot or coldspot regions (Table 4). Although two hotspot regions showed comparatively high G C content, the average values from the hotspot and coldspot regions were 44.3 and 43.9%, respectively, that is almost the same as the base composition of the overall chromosome (Sasaki et al, 2002). All six hotspot regions (13±99 kbp) showed a high density of predicted genes (those predicted and also supported by homologous sequences from the public databases containing proteins or rice ESTs) and had less repetitive sequences, consisting mainly of miniature invertedrepeats transposable elements (MITE).…”

“…Construction of a physical map of chromosome 1 by PCR screening of RGP PAC and BAC libraries with rice sequencetagged site (STS)/EST markers was reported previously by Sasaki et al (2002). We newly mapped eight additional PAC and BAC clones on this chromosome, facilitating both the closure of 1 gap on the long arm and the narrowing of the gap region, particularly at the centromere.…”

“…The physical sizes of all gap regions on chromosome 1, as determined by the FISH method, have been reported previously by Sasaki et al (2002). Results obtained from YAC physical maps were used to estimate the physical sizes of the gaps on each arm of the other ®ve chromosomes (Wu et al, 2002).…”

“…To achieve this goal, IRGSP has adopted the clone-by-clone sequencing strategy and adheres to the policy of immediate release of sequence data (Sasaki and Burr, 2000). The genomic sequences of rice chromosomes 1, 4, and 10 have been completed, and this work has led to detailed characterization of the genome, such as the discovery of the presence of many tandemly duplicated genes, as well as the chromosomal distribution of repetitive sequences and the chromosomal integration of organelle DNA sequences (Feng et al, 2002;Sasaki et al, 2002;The Rice Chromosome 10 Sequencing Consortium, 2003). These important features could not be revealed by the draft sequence data obtained by the whole-genome shotgun method.…”

Update and challenges on proteomics in rice

“…indica [3] and for O. sativa L. ssp. japonica [4], and the complete map-based sequences of chromosome 1 [5] and chromosome 4 [6] for O. sativa L. cv. Nipponbare provide a rich resource for understanding the biological processes of rice.…”