A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat  

Abstract

To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2-fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

“…The proportion of UniGenes mapped to 1BS that were non-syntenic in model grass genomes was 55% to 65% compared to only 35% to 42% of genes mapped to 3B [34], 23% to 30% to 3A [55], and 20% to 45% to 1AL, 1BL and 1DL [35]. Our results support the recent findings of Wicker et al .…”

“…[41] proposed more active mechanisms for gene island formation, which involve gene duplication and translocation. A similar pattern of non-syntenic gene distribution, with a two-fold increase towards the telomeric parts, was found in chromosome 3B [34]. However, in contrast to 1BS, the increase in size of 3B was found to be homogeneous along the proximal and distal regions [41].…”

“…[34]. After signal quantification, normalization and data deconvolution, 1,063 UniGenes were unambiguously assigned to 1,568 1BS clones (Additional file 2) from the scaffolds representing 262 Mb of 1BS.…”

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

“…These results suggest a lower proportion of non-syntenic genes on chromosome 3B compared to chromosome 1BL (approximately 60%). Moreover, no peak of synteny was observed on wheat chromosomes 3BL and 3BS,in which there is a continuous increase in the proportion of non-syntenic genes along the chromosome arms towards the telomeres [15]. These differences aredue to the different evolutionary origin of homoeologous group 3 chromosomesin wheat, which, in contrast to chromosomes of group 1, originate directly from a single ancestral chromosome (proto-chromosomeA1)[78].…”

“…These differences aredue to the different evolutionary origin of homoeologous group 3 chromosomesin wheat, which, in contrast to chromosomes of group 1, originate directly from a single ancestral chromosome (proto-chromosomeA1)[78]. Despite these differences, the density and proportion of gene islands,the gradient of gene density from the centromere to the telomere,and thecorrelation with the density of non-syntenic genes or the recombination rate remained very similar between chromosome 1BL andchromosome 3B [15]. Thus, our results show that wheat chromosomes display a superimposition of evolutionary patterns.…”