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GrapeReSeq_Illumina_20K

In the frame of the PLANT-KBBE2008 " GrapeReSeq " project, an high throughput genotyping Illumina Infinium chip (20K) has been developed.

GrapeReSeq Consortium FAQ (Illumina)

GrapeReSeq_Consortium_FAQ.pdf 312.69 kB

 

A dataset obtained from the genotyping of a Vitis vinifera cultivated pool (using the SNPs of the 20k chip): see here

 

Development of a cluster file

A cluster file has been developed from the genotyping of 2278 individuals, 1450 from the Vitis vinifera species and 828 from different Vitis species or interspecific hybrids.

 

  • The current cluster file with all the SNP. The SNP that we found failed are flagged "AUX=2" in the SNP table provided above (GrapeReSeq_SNP_Table_all_180413.xlsx). The SNP with problematic clusters may give acceptable results in specific populations. They are flagged "AUX=3 to 9" in the SNP table.

 

Development of the 20K loci submitted to Illumina

  • GrapeReSeq_Illumina_20K_SNP_chip ( IGA and URGI) : 15K SNPs from Vitis vinifera genotypes and 5K SNPs from Vitis species.

 

GrapeReSeq_Illumina_20K_SNP_chip.xls (8.69 MB)

 

 

  • GrapeReSeq_Illumina_20K_SNP_chip_readme

 

GrapeReSeq_Illumina_20K_SNP_chip_readme.pdf (135.30 kB)

 

 

  • Statistics on Vitis vinifera sequences (IGA and URGI)

 

Vitis_Sequence_Stats.pdf (24.40 kB)

 

 

  • Equidistant selected SNPs for Vitis genotypes (URGI)

 

Vvinifera_SNPnumber_per_chr.pdf (24.85 kB)

 

 

  • Quality control process and cleaning (EPGV INRA; CEA/ IG-CNG)

 

README_EPGV_DataTransfer_Illumina_Sequencing.pdf (626.79 kB)

 

 

  • Technical Note to designing and ordering iSelect Genotyping Assays (Illumina)

 

Infinium_technote_iselect_design.pdf (983.25 kB)
Update: 25 Jan 2018
Creation date: 26 Oct 2012