Gene identification programs in bread wheat: a comparison study

Seven ab initio web-based gene prediction programs (i.e., AUGUSTUS, BGF, Fgenesh, Fgenesh+, GeneID, Genemark.hmm, and HMMgene) were assessed to compare their prediction accuracy using protein-coding sequences of bread wheat. At both nucleotide and exon levels, Fgenesh+ was deduced as the superior program and BGF followed by Fgenesh were resided in the next positions, respectively. Conversely, at gene level, Fgenesh with the value of predicting more than 75% of all the genes precisely, concluded as the best ones. It was also found out that programs such as Fgenesh+, BGF, and Fgenesh, because of harboring the highest percentage of correct predictive exons appear to be much more applicable in achieving more trustworthy results, while using both GeneID and HMMgene the percentage of false negatives would be expected to enhance. Regarding initial exon, overall, the frequency of accurate recognition of 3' boundary was significantly higher than that of 5' and the reverse was true if terminal exon is taken into account. Lastly, HMMgene and Genemark.hmm, overall, presented independent tendency against GC content, while the others appear to be slightly more sensitive if GC-poor sequences are employed. Our results, overall, exhibited that to make adequate opportunity in acquiring remarkable results, gene finders still need additional improvements.

Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes

Background

The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome.

Results

Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively.

Conclusions

In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing.

Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

Development of a deletion and genetic linkage map for the 5A and 5B chromosomes of wheat (Triticum aestivum)

The aims of the present study were to provide deletion maps for wheat ( Triticum aestivum L.) chromosomes 5A and 5B and a detailed genetic map of chromosome 5A enriched with popular microsatellite markers, which could be compared with other existing maps and useful for mapping major genes and quantitative traits loci (QTL). Physical mapping of 165 gSSR and EST-SSR markers was conducted by amplifying each primer pair on Chinese Spring, aneuploid lines, and deletion lines for the homoeologous group 5 chromosomes. A recombinant inbred line (RIL) mapping population that is recombinant for only chromosome 5A was obtained by crossing the wheat cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides and was used to develop a genetic linkage map of chromosome 5A. A total of 67 markers were found polymorphic between the parental lines and were mapped in the RIL population. Sixty-three loci and the Q gene were clustered in three linkage groups ordered at a minimum LOD score of 5, while four loci remained unlinked. The whole genetic 5A chromosome map covered 420.2 cM, distributed among three linkage groups of 189.3, 35.4, and 195.5 cM. The EST sequences located on chromosomes 5A and 5B were used for comparative analysis against Brachypodium distachyon (L.) P. Beauv. and rice ( Oryza sativa L.) genomes to resolve orthologous relationships among the genomes of wheat and the two model species.

Rapid identification of the three homoeologues of the wheat dwarfing gene Rht using a novel PCR-based screen of three-dimensional BAC pools

A high-throughput two-step PCR strategy for the identification of selected genes from a BAC library derived from hexaploid wheat (16,974 Mbp) is described. The screen is based on the pooling of DNA from BAC clones into 675 "superpools" arrayed in a three-dimensional configuration. Each BAC clone is represented in three superpools to allow the identification of candidate 384-well plates of clones after the first round of PCR; identification is facilitated by an associated Perl script. A second round of PCR detects the specific BAC clone within the candidate plate that corresponds to the gene of interest. Thus, a single copy of the target gene can be identified from the library of over 700,000 clones (approximately 5 genome equivalents) by assaying only three 384-well plates. The pooling strategy was validated by screening the library with primers specific for the reduced height (Rht-1a) gene. Using relatively stringent selection criteria, 13 Rht-containing clones were identified from 17 candidate plates, and sequence analysis of the amplified products showed that all three Rht homoeologues were represented. Furthermore, the method confirmed the estimated coverage of the BAC library. Thus, this methodology allows the rapid and cost-effective identification of genes, and their homoeologues, from large-insert libraries of complex genomes such as hexaploid wheat.