Whole‐genome profiling and shotgun sequencing delivers an anchored, gene‐decorated, physical map assembly of bread wheat chromosome 6A

Abstract

Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the ‘decoration’ of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome.

Wheat Landrace Genome Diversity

“…This could hint at the presence of a genetic element controlling recombination rate that is specific for that chromosome. It was shown that recombination greatly increased from the centromere toward the telomeres on chromosome 6A ( p oursarebani et al 2014), as expected for plants with large genomes. Moreover, it was shown that a recent translocation (6VS:6AL) led to a suppression of recombination rate on 6AL ( x ie et al 2012), which could be due to the knockout of a locus involved in recombination.…”

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

“…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.…”

Genomics as the key to unlocking the polyploid potential of wheat

“…Current efforts aim to generate physical maps based on BAC minimum tiling paths developed from flow-sorted chromosome arms (Paux et al, 2008) and to fully sequence these regions by 2017. So far, a single wheat chromosome has been fully sequenced (chromosome 3B; Choulet et al, 2014), while physical maps are being generated for most of the remaining 20 chromosomes (Philippe et al, 2013;Poursarebani et al, 2014). The fully sequenced and annotated 3B chromosome represents an excellent resource for wheat researchers and will serve as a benchmark for the remaining wheat chromosomes.…”