Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

Abstract

BackgroundThe presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy.ResultsThe potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.ConclusionsThe negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.

Long-Term Winter Wheat (Triticum aestivum L.) Seasonal Irrigation Amount, Evapotranspiration, Yield, and Water Productivity under Semiarid Climate

“…Irmak et al [2] reported winter wheat seasonal ETc of 600 mm and 490 mm during two growing seasons in South Central Nebraska (Clay Center) with the highest ETc value obtained during the warmest season. Lower winter wheat ETc values in the range of 483-505 mm and 374-551 mm were also reported by Ko et al [24] and Luo et al [25] from their studies at in Uvalde, Texas (USA), and at Yucheng City in Shandong Province (China), respectively. Howell et al [14] reported winter wheat seasonal ETc that varied from 791 to 957 mm during the [1989][1990][1991][1992], and 1992-1993 winter wheat cropping seasons at Bushland, Texas.…”

An Autotetraploid Linkage Map of Rose (Rosa hybrida) Validated Using the Strawberry (Fragaria vesca) Genome Sequence

“…However, the high degree of homology between the closely related genomes in autopolyploid species, coupled with an equally high degree of heterozygosity within those sub-genomes precludes the assembly of WGSS for autotetraploid Rosa species [45]. Here we present the development of a linkage map for Rosa hybrida from which we have characterised all 28 linkage groups.…”

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

“…S2), and (iii) coassembly of contigs using Ae. tauschii BAC clones and clones of wheat D-genome subgenomic BAC libraries (24) (Fig. S3; SI Text).…”