EST map

A YAC-Based Rice Transcript Map Containing 6591 EST Sites

A comprehensive rice YAC-based EST map is established (Wu et al, Plant Cell 14, 2002). Clone-specific primer pairs designed from 6713 unique EST sequences (3' end) derived from 19 cDNA libraries were screened on YAC clones and used for map construction in combination with genetic analysis. The map is composed of 2782 YAC clones, containing 364 YAC contigs with 6591 assigned EST sites from 6421 unique sequences, and covers 80.8% of the rice genome as summarized in Table 1.

Table 1. Summary of Rice EST Mapping Results

Chr No. YAC
Clones YAC
Contigs Total Length of
YAC Contigs (Mb) Coverage
(%)^a EST Sites Ave EST Density
(EST/100 kb)^b

1 303 36 39.09 76.5 977 2.50

2 293 32 34.65 78.1 781 2.25

3 296 28 34.36 73.5 963 2.80

4 261 31 30.29 83.2 476 1.57

5 199 25 26.45 77.0 555 2.10

6 206 25 27.87 78.5 522 1.87

7 238 30 27.80 83.4 503 1.81

8 213 29 27.64 81.2 446 1.61

9 168 19 18.58 70.7 296 1.59

10 191 28 22.83 97.0 369 1.62

11 197 34 25.79 76.8 328 1.27

12 193 34 26.46 86.0 322 1.22

Unknown 24 13 5.46 1.3 53 0.97

Total 2782 364 347.27 80.8 6591 1.90

^aTotal length(Mb) of YAC contigs/genetic length of chromosome (cM) x 430 Mb/1,530.4 cM x 100
^bNumber of ESTs/total length of YAC contigs

We provide here the detailed contents of the YAC-based rice transcript map with the following tables and figures (together Microsoft Excel format and pdf format for your download). We hope that it will be greatly helpful for researchers not only to isolate the genes of agronomic importance but also to understand the complicated structures of rice chromosomes and accelerate the completion of its genome sequencing. Tables contain the detailed results of PCR-based YAC screening with the clone-specific EST primers. From left to right in each table: anchor (genetic markers used for YAC landing), chromosome number, genetic distance (cM), EST (cDNA), DDBJ accessions of the EST clones (Forward and/or reverse sequences), positive YACs, primer, amplified PCR band size, annealing temperature (Ann T) and primer sequences (5' and 3' primers, each 20 bases) are shown. Figures contain the rice genetic and YAC physical maps with the assigned EST sites. From left to right in each YAC contig: anchor (genetic markers used for YAC landing), genetic distance (cM), estimated physical distance (kb) of YAC contigs, YAC contig and EST sites (multiple sites of an EST are indicated by alphabets after the name) are shown. Vertical bars on the left of EST names indicate the estimated distribution range of sites where the relative order of each site could be changeable. Relative order as well as direction of YAC contigs anchored by the genetic markers with the same genetic distance (often observed in the regions around the centromeres) also could be changeable.

  Notes
  #; floating markers on the genetic map
  c; chimeric YAC clones
  *; PCR band size longer than predicted 
  Ann T; 60 -C unless otherwise indicated
  NI; YACs with unknown insert
  brown color; EST clones (or sequence) corresponding to the genetic markers

Tables

All Chromosomes -MicrosoftExcel format (3.6MB)

Figures -

All Chromosomes -PDF format (490KB)

All Chromosomes -html

Chromosome unknown(13 contigs)

Both EST (cDNA) and YAC clones are available for distribution. For EST clones, contact the DNA bank at the Ministry of Agriculture, Forestry and Fisheries of Japan (http://rgp.dna.affrc.go.jp/htdocs/Cloneaccess.html). For YAC clones, contact T. Sasaki at tsasaki@nias.affrc.go.jp. If you have any other questions, please contact T. Sasaki (tsasaki@nias.affrc.go.jp) or J. Wu ( RICE GENOME RESEARCH PROGRAM (RGP) HOME PAGE