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 24 of 104 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Himone ITC0886 AA Unknown Papua New Guinea ITC
Grupnai ITC0887 AA Unknown Papua New Guinea ITC
Pai ka ITC0892 AA Unknown Papua New Guinea ITC
Yapu Yapu ITC0923 AA Unknown Papua New Guinea ITC
Banksii ITC0806 acuminata subsp. banksii Papua New Guinea ITC
Musa acuminata ssp. banksii ITC0896 acuminata subsp. banksii Papua New Guinea ITC
Selangor ITC1060 acuminata subsp. malaccensis Unknown ITC
Saing Todloh ITC0316 AA subgr. Pisang Jari Buaya Unknown ITC
Truncata ITC0393 acuminata subsp. truncata Unknown ITC
Tjau Lagada ITC0090 AA Unknown Unknown ITC
Diploide EMBRAPA 205
ITC1193 AA Unknown Brazil ITC
IRFA 905
ITC1267 AA Unknown Nigeria ITC
NBA 14
ITC0267 AA Unknown Unknown ITC
Djum Tau
ITC0292 AA Unknown Indonesia ITC
Pitu
ITC0294 AA Unknown Unknown ITC
Guyod
ITC0299 AA Unknown Philippines ITC
Pu-te Wey
ITC0447 AA Unknown Malaysia ITC
Pisang Tongat
ITC0063 AA Unknown Unknown ITC
A3617/9
ITC0530 acuminata Unknown Unknown ITC
Hybrid
ITC0606 acuminata Unknown Unknown ITC
Hybrid
ITC0608 acuminata Unknown Unknown ITC
Malaccensis
ITC0074 acuminata subsp. malaccensis Unknown ITC
Not Named
ITC0318 AA subgr. Pisang Jari Buaya Indonesia ITC
Pisang Buntal
ITC0480 AA subgr. Sucrier Malaysia ITC

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