fine physical map of the rice chromosome 5

A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence t...

Full description

Saved in:
Bibliographic Details
Published in:Molecular genetics and genomics : MGG 2005-11, Vol.274 (4), p.337-345
Main Authors: Cheng, C.H, Chung, M.C, Liu, S.M, Chen, S.K, Kao, F.Y, Lin, S.J, Hsiao, S.H, Tseng, I.C, Hsing, Y.I.C, Wu, H.P
Format: Article
Language:English
Subjects:
Artificial chromosomes
bacterial artificial chromosomes
Centromere - ultrastructure
centromeres
Chromosome Mapping
chromosomes
Chromosomes, Artificial, Bacterial
clones
Contig Mapping
DNA probes
DNA, Plant
fluorescence in situ hybridization
Gene Library
Genes, Plant
Genetic Techniques
Genetics
Genome, Plant
Genomics
In Situ Hybridization, Fluorescence
Oryza - genetics
Oryza sativa
Physical Chromosome Mapping
PI-derived artificial chromosomes
rice
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for ~150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.
ISSN:1617-4615
1617-4623
DOI:10.1007/s00438-005-0039-y