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

Abstract

BackgroundAs for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.ResultsUsing a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.ConclusionsHere, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.

The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements

“…Assuming that genes located on the same or overlapping BAC clones constitute “islands” of genes [16, 18], organization of the gene space along 5DS also demonstrated dominance of gene islands over isolated genes along each deletion bin (Fig. 8, Table 3), consistent with previous findings [10, 16, 18].…”

“…The average contig size of the 5DS preliminary map was 1,078 kb, with the longest contig size being 6,649 kb, comparable to the LTC-constructed physical maps of 1AL, 1BL and 1BS which ranged between 5.8 Mb to over 7 Mb [15, 16, 18]. A total of 58 of the 164 contigs were longer than 1 Mb.…”

“…While the number of anchored contigs to the genetic map of 5DS was considerably higher than that of 1AL physical map [15], more recent physical maps of 1BS, 1BL, and 6A reported similar percentages of contigs integrated with the genetic maps, as 77.4 %, 74 %, and 79 %, respectively [16, 18, 19]. Among these contigs, 63 were ordered within the deletion bins utilizing primarily the shared extensive homology between Ae.…”

Plant genomics: sowing the seeds of success

“…Although whole genome shotgun sequencing allowed the recent assembly of the bread wheat gene set [3], a complete bread wheat genome will be necessary to determine the full effect of genomic variation on wheat phenotypes. Philippe et al [4] describe the application of BAC-by-BAC sequencing to generate a physical map of wheat chromosome 1BL, which has the highest marker density to-date with 11 markers per Mb, and also has high levels of anchoring and contig ordering. It is hoped that applying the methods employed in Philippe et al .…”

Dissection of barley chromosomes 1H and 6H by the gametocidal system

“…Although it is based on a high-redundancy BAC library (approximately 14-fold genome coverage), the physical map may still have errors due to the repetitive nature of cereal genomes. For the determination of physical positions of the contigs, deletion lines (Endo and Gill, 1996) have been successfully utilized in wheat genomics (Paux et al, 2008;Breen et al, 2013;Lucas et al, 2013;Philippe et al, 2013;Raats et al, 2013;Choulet et al, 2014).…”