A 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 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 approximately 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.
Cheng
Chia-Hsiung
CH
Institute of Botany, Academia Sinica, Taipei 115, Taiwan.
Chung
Mei-Chu
MC
Liu
Shu-Mei
SM
Chen
Shi-Kuang
SK
Kao
Fang-Yi
FY
Lin
Shu-Jen
SJ
Hsiao
Shin-Hsin
SH
Tseng
I-Chieh
IC
Hsing
Yue-Ie C
YI
Wu
Hong-Pang
HP
Chen
Ching-San
CS
Shaw
Jei-Fu
JF
Wu
Jianzhong
J
Matsumoto
Takashi
T
Sasaki
Takuji
T
Chen
Hong-Hwa
HH
Chow
Teh-Yuan
TY
D002503:Centromere / Q000648:ultrastructure; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D020451:Contig Mapping; D018744:DNA, Plant; D015723:Gene Library; D017343:Genes, Plant; D005821:Genetic Techniques; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D012275:Oryza / Q000235:genetics*; D020161:Physical Chromosome Mapping
D018744:DNA, Plant