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PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid species. PolyMarker generates a multiple alignment between the target SNP sequence and the selected reference genome (from the drop off menu in green below). It then generates a mask with informative polymorphic positions between homoeologs which are highlighted with respect to the target genome.

See About to know how to prepare your input. For wheat, we have designed primers for the iSelect 90K chip and the Axiom 820k chip.

If your request is terminated due a timeout, try with less markers and make sure the SNPs are not in low complexity regions.

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Reference

Glycine max var. Williams 82 was sequenced, assembled, and annotated by the U.S. DOE Joint Genome Institute (JGI-PGF) in collaboration with a consortium of research labs and published. Current assembly is version v2.1 and comprises a total 978 Mb The reference sequence is available in Ensembl plants Relase 50. The version of the assembly used has the repeats masked (Glycine_max.Glycine_max_v2.1.dna_rm.toplevel.fa).

The barley genome assembly presented here was produced by the International Barley Genome Sequencing Consortium (IBSC) using a hierarchical approach. Initially multiplexed short read BAC by BAC contig assemblies (N50: 79 kb) were scaffolded using physical, genetic and optical maps (N50: 1.9 Mb) and were assigned to chromosomes using a POPSEQ genetic map. Finally, the linear order and orientation of scaffold sequences was determined using chromosome-conformation capture sequencing (Hi-C). The final chromosome-scale assembly consisted of 6,347 ordered super-scaffolds composed of merged assemblies of individual BACs, representing 4.79 Gb (~95%) of the genomic sequence content, of which 4.54 Gb have beenassigned to precise chromosomal locations in the Hi-C map. The chloroplast genome component and its gene annotation are also present (KC912687). The assembly and description where downloaded from ensembl!

Tetraploid reference produced by substracting the D genome from the hexaploid wheat. A whole genome assembly has been carried out by the IWGSC in collaboration with the company NRGene. Using a proprietary algorithm DeNovoMAGIC with Illumina sequencing data a 14.5 Gb assembly was produced. Sequences have been ordered using POPSEQ data and Hi-C (chromosome conformation capture) to generate 21 pseudomolecules representing the majority of the wheat genome. Reference sequence available in URGI The assembly is described in IWGSC (2018).

The assembly was produced with a misture of Sanger BAC libraries, GS FLX Titanium (450bp) and Illumina HiSeq (100bp) and assembled with SOAP. The scaffolds where assigned to their corresponding genome by comparing the diploid progenitors and the scaffolds where anchored with the aid of genetic maps. Reference sequence available in genoscope. The assembly is described in Chalhoub, B. et al (2014)

The genomic sequence within this version of Ensembl includes 33,459 scaffolds (>200 bp) with an N50 of 850 kb that was assembled at NRC-Saskatoon using a hybrid approach from Illumina, Roche 454 and Sanger sequence data. The assembly has been orientated and assigned to the nine pseudochromosomes using dense genotype-by-sequencing genetic maps. Reference sequence available in ensembl!fasta. The assembly is described in Parkin, I. et al (2014)

The genomic sequence within this version of Ensembl includes 193 large scaffolds assembled by CAAS-IVF, which have been orientated and assigned to pseudochromosomes using publicly available genetic markers. Reference sequence available in ensembl!fasta. The assembly is described in The Brassica rapa Genome Sequencing Project Consortium (2011)

The scaffolds were constructed using the Whole Genome Shotgun (WGS) assembly of Lo7. To link WGS contigs the scaffolding software SSPACE (version 2.3) was used. The assmebly contains 1.29 million scaffolds with a cumulative length of 2.8 Gbp. Reference sequence available from IPK. The assembly is described in Bauer, E. et al (2014)

An international consortium has generated a high quality reference sequence of the modern durum wheat cultivar Svevo. Whole genome libraries were sequenced with Illumina short paired-end (2 x 250 bp) and long mate pair (up to 8-10 kb) protocols and the reads were assembly with the NR-Gene DeNovoMAGICTM pipeline. In total, a 270x coverage was obtained, and the reads were assembled into 10.5 Gb of sequence with an L50 and L90 length of 6 and 1 Mb, respectively (N50: 493; N90: 2019). The assembly scaffolds have been anchored to a high-density genetic map based on Svevo × Zavitan RIL population and merged into super-scaffolds using Hi-C data; 95% of the scaffolds have been anchored along the chromosomes and 90% oriented. Reference sequence available in InterOmics

Triticum urartu (AA) is the diploid progenitor of tetraploid and hexaploid wheat. This assembly is based on T. urartu accession G1812 (PI428198). A previous draft assembly ( Ling et al., 2013 ), created using Illumina HiSeq2000 WGS short reads, was improved using BAC-by-BAC sequencing, SMRT sequencing, a BioNano genome map, and 10x Genomics linked reads into a chromosome level assembly of T. urartu ( Ling et al., 2018 ). MBKbase.

A whole genome assembly has been carried out by the IWGSC in collaboration with the company NRGene. Using a proprietary algorithm DeNovoMAGIC with Illumina sequencing data a 14.5 Gb assembly was produced. Sequences have been ordered using POPSEQ data and Hi-C (chromosome conformation capture) to generate 21 pseudomolecules representing the majority of the wheat genome. Reference sequence available in URGI The assembly is described in IWGSC (2018). Reference sequence available in ensembl plants (reference file) The repeats are masked to avoid multiple hits in repetitive regions.

The assembly is done with the pipeline described in Clavijo, Venturini et al. 2017 10.1101/gr.217117.116 , filtering non-wheat sequences and scaffolds below 1 kbp. The assembly is available in the grassroots portal This assembly is part of a BBSRC strategic longer and larger (sLoLa) grant award between Earlham Institute (EI), John Innes Centre (JIC), European Bioinformatics Institute (EBI) and Rothamsted Research (RRes). To find the scaffold where your markers are, you can blast the sequence here.

Triticum aestivum, Fielder, 201216

Triticum turgidum, Kronos, v1.1

Triticum aestivum, Chinese Spring, IWGSC v2.1

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