2019-7-17 Meeting Notes EiB Polyploid Working Group

 Andrzej – review experiences /  approaches with polyploids

absent - comments by email

Liz asked for some comments on the experience with the polyploids and I can say that most of our clients breeding polyploids use either DArTcap or DArTseqLD. In both cases the source of markers is based on DArTseq whole genome profiling and neither of these methods can accommodate specific markers discovered using other methodsfor DArTag work with animals and therefore diploids, but we have developed successful assay for a number of plant species including for polyploids with marker pools sizes varying from 500 - 10,000. I think the largest volume of service in polyploids was for cultivated cotton which is pretty tricky and our main (large) customer settled on DArTag after comparing its performance against what was available on the market.

Controls are G12 and H12 for DArT and Intertek can handle this

In cassavabase have an ordering form to create Intertek and DArT orders

DArT can provide a vcf as well as tab delimited

Have a script to convert vcf to genotyping files

In cassavabase will use vcf dosage data in GS ie user doesn't have to do anything

Have loaded 20,000 samples for DArT-LD already

Polyploids - can store dosage in cassavabase but not sure how to handle downstream tools

Elisa - can Guillaume share ontologies with potato base for molecular markers? Maybe have a follow up meeting on this? eg protocols, platform 

DArT-LD get 6-10,000 markers with good coverage - approx 20% missing data. Loading data as-is and imputing.

Dorcus - used DArT-seq for sweet potato. Ask for raw fastq files and use this for polyploid calling. Using a different vendor too optimized for polyploids. 

Jeff - need allele depth - need to communicate to DArT. Top on wish-list for Guillaume too. 

Dorcus - when call data with dosage the quality is not very high - need 3-4 times higher depth

For Yam just used the standard protocol

Jeff - have used intertek for KASP for potato - results were consistent with in-house results. For genome wide markers = have provided a set of SNPs for primer design 1,200-1,300 primers ordered. Waiting for wet-lab to see which will be working

Jeff - Dart wants the DNA of reference genome to set up for internal QC for development of plex. 

Guillaume - 100 bp sequence each side and they design sequence.

Correct and complete order form - will be generated by Sample Manager in future

Shipments of multiple of 16 x 96 plates. 

Agreed quality and quantity of sample

Agreed plasticware - Rajaguru would have this info and we can send it out 

Fixed plate layouts
Payment via Charge account

Agreed SNPs with VERY GOOD Assessment class (for KASP)