Demarcating the gene-rich regions of the wheat genome

Abstract

By physically mapping 3025 loci including 252 phenotypically characterized genes and 17 quantitative trait loci (QTLs) relative to 334 deletion breakpoints, we localized the gene-containing fraction to 29% of the wheat genome present as 18 major and 30 minor gene-rich regions (GRRs). The GRRs varied both in gene number and density. The five largest GRRs physically spanning <3% of the genome contained 26% of the wheat genes. Approximate size of the GRRs ranged from 3 to 71 Mb. Recombination mainly occurred in the GRRs. Various GRRs varied as much as 128-fold for gene density and 140-fold for recombination rates. Except for a general suppression in 25-40% of the chromosomal region around centromeres, no correlation of recombination was observed with the gene density, the size, or chromosomal location of GRRs. More than 30% of the wheat genes are in recombination-poor regions thus are inaccessible to map-based cloning.

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

“…The mapping of ESTs to sets of overlapping deletion lines further suggests that genecontaining BACs are clustered in the genome to form gene-rich regions that can be cytologically defined (24). A similar study, but using a larger number of deletion lines and combining the data across the three homoeologous genomes, has reported that 29% of the genome contains 94% of the genes, with 60% of the genes being concentrated in only 11% of the genome (25). Assuming that this is an accurate representation of the gene distribution in wheat, identification of 94% of the genes would require sequencing of some 5,000 Mb of DNA of the hexaploid wheat genome with a BAC by BAC approach.…”

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

“…Colinearity in the order of loci in the wheat genomes is largely conserved except for a 4A-5A-7B translocation, a putative 2B-6B translocation, and two inversions on chromosome 4A (Hossain et al 2004a;Peng et al 2004). Gene density in wheat tends to increase with relative distance from the centromere, with some of the highest densities observed in several distal regions of the chromosomes (Akhunov et al 2003;Erayman et al 2004). However, the overall relationship between gene density and relative position on the chromosome is weak (Akhunov et al 2003).…”

“…Recombination rate increases with approximately the square of the relative distance of a given segment from the centromere (Akhunov et al 2003). Due to this uneven distribution of recombination, significant variation in genetic to physical distance ratios along the length of a given chromosome is evident ranging from $17 Mb/ cM in the most proximal region to $1 Mb/cM in the most distal intervals (Akhunov et al 2003;Erayman et al 2004). A weak correlation was observed between relative gene density and recombination rate (Akhunov et al 2003;Erayman et al 2004).…”

“…Due to this uneven distribution of recombination, significant variation in genetic to physical distance ratios along the length of a given chromosome is evident ranging from $17 Mb/ cM in the most proximal region to $1 Mb/cM in the most distal intervals (Akhunov et al 2003;Erayman et al 2004). A weak correlation was observed between relative gene density and recombination rate (Akhunov et al 2003;Erayman et al 2004). By some estimates onefourth to one-third of the wheat genome, primarily around the centromeres, accounts for ,1% of total recombination (Lukaszewski and Curtis 1993;Akhunov et al 2003;Erayman et al 2004).…”

“…A weak correlation was observed between relative gene density and recombination rate (Akhunov et al 2003;Erayman et al 2004). By some estimates onefourth to one-third of the wheat genome, primarily around the centromeres, accounts for ,1% of total recombination (Lukaszewski and Curtis 1993;Akhunov et al 2003;Erayman et al 2004). Thus, development of high-resolution genetic maps through the use of traditional recombination methods for at least onefourth of the wheat genome will be extremely difficult.…”