GWAS Panel - GBS

Publication title or Reference: 

Marker type: 
SNP
Description of the dataset: 

The GWAS panel is a list of diploid accessions (composed of musa acuminata and AA) carefully selected to support Genome-Wide Association Study (GWAS) in banana in order to quickly and accurately link areas of the genome with important traits.

Accessions were fingerprinted using the Genotyping By Sequencing (GBS) method (Elshire RJ et al, 2011) using PSTI restriction enzyme ( NCBI bioproject ). A set of 129,658 unfiltered SNP markers were obtained that were sbsequently filtered with a bioinformatic workflow at South Green Galaxy to get 5,544 robut SNP markers available below

Unfiltered SNP markers from Tassel-GBS (vcf file ~80MB)
Filtered SNP markers (vcf file)   (Harvard Dataverse)

The filtered markers were deposited in dbSNP (ss#1971458520-1971464266). These SNPs mapped on DH Pahang v1 can be visualized on the JBrowse of the Banana Genome Hub (select GBS SNP panel)

The genetic tree below was calcultated using Darwin.

 

See all accessions used in this study

Showing 40 of 104 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Mambee Thu ITC0612 AA Unknown Unknown ITC
Pisang Oli ITC1157 AA Unknown Indonesia ITC
Mshale ITC1223 AA Unknown Tanzania ITC
Pamoti On ITC1229 AA Unknown Unknown ITC
Mpiajhap ITC0773 AA Unknown Papua New Guinea ITC
Inori ITC0850 AA Unknown Papua New Guinea ITC
Yangun Yefan ITC0984 AA Unknown Papua New Guinea ITC
Kokopo ITC1243 AA Unknown Papua New Guinea ITC
Maleb ITC0809 AA Unknown Papua New Guinea ITC
Hova ITC0847 AA Unknown Papua New Guinea ITC
Tainga ITC0894 AA Unknown Papua New Guinea ITC
Musa acuminata ssp. banksii ITC0897 acuminata subsp. banksii Papua New Guinea ITC
Somani ITC0603 AA Unknown Papua New Guinea ITC
Pama ITC0797 AA Unknown Papua New Guinea ITC
Sihir ITC0810 AA Unknown Papua New Guinea ITC
Kenar ITC0816 AA Unknown Papua New Guinea ITC
Mala ITC0869 AA Unknown Papua New Guinea ITC
Kwosriake ITC0882 AA Unknown Papua New Guinea ITC
Odwa ITC0889 AA Unknown Papua New Guinea ITC
Fu Des ITC0939 AA Unknown Papua New Guinea ITC
Kwaro ITC0943 AA Unknown Papua New Guinea ITC
Wiliman ITC0949 AA Unknown Papua New Guinea ITC
Hawain 3 ITC0602 acuminata subsp. banksii Papua New Guinea ITC
Borneo ITC0253 acuminata subsp. microcarpa Malaysia ITC
Spiral ITC1206 AA Unknown Papua New Guinea ITC
Garunga ITC0798 AA Unknown Papua New Guinea ITC
Sepi ITC0849 AA Unknown Papua New Guinea ITC
Wikago ITC0888 AA Unknown Papua New Guinea ITC
Adina ITC0893 AA Unknown Papua New Guinea ITC
Gorop ITC0778 AA Unknown Papua New Guinea ITC
Enar ITC0818 AA Unknown Papua New Guinea ITC
Kuspaka ITC0840 AA Unknown Papua New Guinea ITC
Awondaeke ITC0884 AA Unknown Papua New Guinea ITC
Banksii ITC0620 acuminata subsp. banksii Papua New Guinea ITC
Meinje ITC1015 AA Unknown Papua New Guinea ITC
Yalumia ITC1220 AA Unknown Papua New Guinea ITC
Mapua ITC1244 AA Unknown Papua New Guinea ITC
Akondro Mainty ITC0281 AA Unknown Unknown ITC
Waimara ITC0600 AA Unknown Papua New Guinea ITC
Navaradam ITC0770 AA Unknown Papua New Guinea ITC

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