Deletion Mapping of Homoeologous Group 6-Specific Wheat Expressed Sequence Tags

Abstract

To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin. C OMMON wheat (Triticum aestivum L.) is an alloimportant cereals, the wheat genome with 16,000 Mb is hexaploid (2n ϭ 6x ϭ 42, AABBDD) containing the largest and rice (Oryza sativa L.) with 415 Mb is the three homoeologous genomes (Sears 1954

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

“…Large-scale EST sequence comparisons using binmapped wheat ESTs and rice pseudomolecules had previously indicated colinearity between W3 and R1 and between W6 and R2 chromosomes (Sorrells et al 2003; La Rota and Sorrells 2004;Munkvold et al 2004;Randhawa et al 2004). Their centromere homology was confirmed in this study.…”

“…W3-R1 and W6-R2 chromosomes and their centromeres have maintained perfect synteny (Figure 3). The remaining wheat and Triticeae chromosomes are associated with linkage blocks corresponding to two or three rice chromosomes (Ahn et al 1993;Gale and Devos 1998;Sorrells et al 2003;Conley et al 2004;Hossain et al 2004;La Rota and Sorrells 2004;Linkiewicz et al 2004;Miftahudin et al 2004;Peng et al 2004;Randhawa et al 2004;Salse et al 2008). Chromosome W1 arose from the fusion of chromosomes with homology to R5 and R10 but its centromere was derived from R5 ( Figure 3).…”

Comparative Analyses Between Lolium/Festuca Introgression Lines and Rice Reveal the Major Fraction of Functionally Annotated Gene Models Is Located in Recombination-Poor/Very Recombination-Poor Regions of the Genome

“…It is these orthologous markers that have then been bin mapped in Lolium/Festuca. The reasons for the absence of genes in the proximal regions of wheat and sorghum could therefore possibly result from (1) only partially representative EST libraries or (2) an inability to detect ESTs as a result of low sequence polymorphism (Sorrells et al 2003 andRandhawa et al 2004 reported between 24 and 45% of loci as monomorphic and therefore that could not be mapped to either nulli-tetrasomic or deletion lines).…”

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

“…BAC DB009O11 had three genes that matched mapped wheat ESTs (BE497888, BE500611 and BE490512). These three ESTs have been mapped to the same co-localized bins (6AL4-0.55-0.90, 6BL5-0.40-1.00, and 6DL5-0.29-0.47) located on the long arm of wheat chromosome 6A, 6B and 6D, respectively Randhawa et al 2004). …”