Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny.
The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2 cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10x redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score >/= 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome.
Singh
Nagendra K
NK
Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012, New Delhi, India.
Raghuvanshi
Saurabh
S
Srivastava
Subodh K
SK
Gaur
Anupama
A
Pal
Ajit K
AK
Dalal
Vivek
V
Singh
Archana
A
Ghazi
Irfan A
IA
Bhargav
Ashutosh
A
Yadav
Mahavir
M
Dixit
Anupam
A
Batra
Kamlesh
K
Gaikwad
Kishor
K
Sharma
Tilak R
TR
Mohanty
Amitabh
A
Bharti
Arvind K
AK
Kapur
Anita
A
Gupta
Vikrant
V
Kumar
Dibyendu
D
Vij
Shubha
S
Vydianathan
Ravi
R
Khurana
Parul
P
Sharma
Sulabha
S
McCombie
W Richard
WR
Messing
Joachim
J
Wing
Rod
R
Sasaki
Takuji
T
Khurana
Paramjit
P
Mohapatra
Trilochan
T
Khurana
Jitendra P
JP
Tyagi
Akhilesh K
AK
D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D005819:Genetic Markers; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny; D014908:Triticum / Q000235:genetics*
D005819:Genetic Markers