A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites

Abstract

To determine the chromosomal positions of expressed rice genes, we have performed an expressed sequence tag (EST) mapping project by polymerase chain reaction-based yeast artificial chromosome (YAC) screening. Specific primers designed from 6713 unique EST sequences derived from 19 cDNA libraries were screened on 4387 YAC clones and used for map construction in combination with genetic analysis. Here, we describe the establishment of a comprehensive YAC-based rice transcript map that contains 6591 EST sites and covers 80.8% of the rice genome. Chromosomes 1, 2, and 3 have relatively high EST densities, approximately twice those of chromosomes 11 and 12, and contain 41% of the total EST sites on the map. Most of the EST-dense regions are distributed on the distal regions of each chromosome arm. Genomic regions flanking the centromeres for most of the chromosomes have lower EST density. Recombination frequency in these regions is suppressed significantly. Our EST mapping also shows that 40% of the assigned ESTs occupy only approximately 21% of the entire genome. The rice transcript map has been a valuable resource for genetic study, gene isolation, and genome sequencing at the Rice Genome Research Program and should become an important tool for comparative analysis of chromosome structure and evolution among the cereals.

Physical maps and recombination frequency of six rice chromosomes

“…Previous studies have demonstrated signi®cant differences in recombination frequency along the length of each rice chromosome (Chen et al, 2002;Wu et al, 2002; Zhao et al, 2002). As these differences were detected by using whole YAC or BAC contigs rather than the interval region between each neighboring marker, this information on recombination frequency is of limited value for studies on gene isolation by map-based cloning.…”

“…During construction of the rice yeast arti®cial chromosome (YAC) physical map, the positions of the centromeres for 11 rice chromosomes were characterized by using the ricecentromere-speci®c sequence RCS2 as a probe (Wu et al, 2002). Recently, an extensive study was performed by thē uorescence in situ hybridization (FISH) technique with the aim of understanding the location, quantity, and organization of sequences of the CentO satellite (previously named RCS2) and Centromeric Retrotransposon of Rice (CRR ) within the rice centromere region .…”

“…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). There were ®ve gaps where no YAC clones were mapped.…”

“…The marker-sequence database contains a total of 11 593 rice STS/EST (Harushima et al, 1998;Wu et al, 2002). The BAC end-sequence database contains a total of 127 459 rice BAC end sequences collected from the CUGI website at http://www.genome.clemson.edu/projects/rice/rice_bac_end/.…”

“…Only clones comprising the minimum tiling path (MTP) were selected for additional sequencing to meet the IRGSP standard of 10-fold sequence redundancy. The second step was to select new clones from RGP PAC and BAC libraries, using primer pairs generated from those STS/EST marker sequences not matched by any Monsanto BAC sequences, with the PCR screening method described previously by Wu et al (2002). Either end sequencing or ®ngerprinting of PCR-screened PAC/BAC clones was conducted.…”