GWAS Panel - GBS

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
Malaysian Blood ITC0568 AA Unknown Unknown ITC
Selangor 2 ITC0629 acuminata Unknown Unknown ITC
Kluai Lep Mu Nang ITC0533 AA Unknown Unknown ITC
Pisang Sapon ITC0679 AA Unknown Indonesia ITC
Pa (Musore) no.2 ITC0668 acuminata Unknown Thailand ITC
Sena ITC1013 AA Unknown Papua New Guinea ITC
Uyam ITC0819 AA Unknown Papua New Guinea ITC
Pisang Madu ITC0258 AA Unknown Unknown ITC
Pisang Bangkahulu ITC0689 AA Unknown Indonesia ITC
Bata Bata ITC0974 AA Unknown Unknown ITC
Type 2 ITC0069 acuminata Unknown Unknown ITC
Ngu ITC1358 AA subgr. Sucrier Vietnam ITC
Sowmuk ITC0266 AA Unknown Unknown ITC
Pa (Musore) no.3 ITC0406 acuminata Unknown Thailand ITC
Pisang Cici Alas ITC0415 acuminata Unknown Indonesia ITC
Waigu ITC0465 acuminata subsp. banksii Unknown ITC
Calcutta 4 ITC0249 acuminata subsp. burmannicoides Unknown ITC
Pahang ITC0609 acuminata subsp. malaccensis Unknown ITC
Lidi ITC0395 AA Unknown Unknown ITC
Pisang Berlin ITC0611 AA Unknown Unknown ITC
Pisang Jari Buaya ITC0312 AA subgr. Pisang Jari Buaya Malaysia ITC
Tudlo Tumbaga ITC1231 AA Unknown Unknown ITC
Uwati ITC0373 AA Unknown Papua New Guinea ITC
Racadag ITC0434 AA Unknown Philippines ITC
Higa ITC0378 acuminata Unknown Unknown ITC
Pisang Serun 404 ITC1348 acuminata subsp. malaccensis Unknown ITC
Pisang Serun 400 ITC1349 acuminata subsp. malaccensis Malaysia ITC
Khae (Phrae) ITC0660 acuminata subsp. siamea Thailand ITC
Zebrina (G.F.) ITC0966 acuminata subsp. zebrina Unknown ITC
Morong Princesa ITC1150 AA Unknown Unknown ITC
AAcv Rose ITC0712 AA Unknown Indonesia ITC
Diploide EMBRAPA 204 ITC1192 AA Unknown Brazil ITC
Pu-te La-Bum ITC0446 AA Unknown Malaysia ITC
Pisang Pipit ITC0685 AA Unknown Indonesia ITC
Pa (Songkhla) ITC0408 acuminata Unknown Unknown ITC
Pisang Kermian ITC0437 AA Unknown Malaysia ITC
Binaktong ITC1181 AA Unknown Unknown ITC
Te'engi ITC0951 AA Unknown Papua New Guinea ITC
Morong Princesa ITC0310 AA subgr. Pisang Jari Buaya Unknown ITC
Tomolo ITC1187 AA Unknown Papua New Guinea ITC

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