Showing papers by "Devinder Sandhu published in 2002"

Gene-Containing Regions of Wheat and the Other Grass Genomes

Abstract: Deletion line-based high-density physical maps revealed that the wheat (Triticum aestivum) genome is partitioned into gene-rich and -poor compartments. Available deletion lines have bracketed the gene-containing regions to about 10% of the genome. Emerging sequence data suggest that these may further be partitioned into "mini" gene-rich and gene-poor regions. An average of about 10% of each gene-rich region seem to contain genes. Sequence analyses in various species suggest that uneven distribution of genes may be a characteristic of all grasses and perhaps all higher organisms. Comparison of the physical maps with genetic linkage maps showed that recombination in wheat and barley (Hordeum vulgare) is confined to the gene-containing regions. Number of genes, gene density, and the extent of recombination vary greatly among the gene-rich regions. The gene order, relative region size, and recombination are highly conserved within the tribe Triticeae and moderately conserved within the family. Gene-poor regions are composed of retrotransposon-like non-transcribing repeats and pseudogenes. Direct comparisons of orthologous regions indicated that gene density in wheat is about one-half compared with rice (Oryza sativa). Genome size difference between wheat and rice is, therefore, mainly because of amplification of the gene-poor regions. Presence of species-, genera-, and family-specific repeats reveal a repeated invasion of the genomes by different retrotransposons over time. Preferential transposition to adjacent locations and presence of vital genes flanking a gene-rich region may have restricted retrotransposon amplification to gene-poor regions, resulting into tandem blocks of non-transcribing repeats. Insertional inactivation by adjoining retro-elements and selection seem to have played a major role in stabilizing genomes.

Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley.

Abstract: Barley (Hordeum vulgare L.) is one of the most important large-genome cereals with extensive genetic resources available in the public sector. Studies of genome organization in barley have been limited primarily to genetic markers and sparse sequence data. Here we report sequence analysis of 417.5 kb DNA from four BAC clones from different genomic locations. Sequences were analyzed with respect to gene content, the arrangement of repetitive sequences and the relationship of gene density to recombination frequencies. Gene densities ranged from 1 gene per 12 kb to 1 gene per 103 kb with an average of 1 gene per 21 kb. In general, genes were organized into islands separated by large blocks of nested retrotransposons. Single genes in apparent isolation were also found. Genes occupied 11% of the total sequence, LTR retrotransposons and other repeated elements accounted for 51.9% and the remaining 37.1% could not be annotated.

Structural and functional organization of the '1S0.8 gene-rich region' in the Triticeae.

Abstract: Plant Molecular Biology49: 791–804, 2002 Table 1 of this article was wrongly printed. The correct version is printed overleaf.

Identification of expressed sequence markers for a major gene-rich region of wheat chromosome group 1 using RNA fingerprinting-differential display

Abstract: This study demonstrates a successful application of RNA fingerprinting-differential display technique in identifying expressed sequence markers for a small targeted region of the wheat (Triticum aestivum L.) genome. Wheat genes are present in clusters spanning about 10% of the genome. One of the important gene-rich regions is present on the short arm of wheat homoeologous group I chromosomes around fraction length 0.8 ('1S0.8 region'). The region is about 0.1% of the wheat genome and is flanked by the breakpoints of deletion lines 1BS-4 and 1BS-19. The objective of this study was to identify expressed sequence markers for the region. First-strand cDNA of poly A + mRNA pooled from various developmental stages of the two deletion lines were PCR amplified in the presence of 35 S by means of 90 pair-wise combinations of 19 primers. Amplification products were size-separated on a denaturing polyacrylamide urea gel. A total of 6840 fragment bands were amplified, of which 65 were present in the deletion line 1BS-4, but missing in 1BS-19. These 65 fragment bands were cut out of the gel, reamplified, and used as probes for gel-blot DNA analysis of group 1 nullisomic-tetrasomic lines and the two deletion lines. Nineteen of the 65 fragment bands detected a smear pattern and thus were not mapped. Of the remaining 46 probes, 22 mapped to wheat homoeologous group 1 and seven mapped to the '1S0.8 region'. The same approach can be used to target other wheat gene-rich regions bracketed by deletion breakpoints.