A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop.

TitleA Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop.
Publication TypeJournal Article
Year of Publication2016
AuthorsSardos J, Rouard M, Hueber Y, Cenci A, Hyma KE, van den Houwe I, Hribova E, Courtois B, Roux N
JournalPLoS One
Volume11
Issue5
Paginatione0154448
Date Published2016
ISSN1932-6203
Abstract

Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.

DOI10.1371/journal.pone.0154448
Alternate JournalPLoS ONE
PubMed ID27144345
Showing 24 of 104 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Akondro Mainty ITC0281 AA Unknown Unknown ITC
Waimara ITC0600 AA Unknown Papua New Guinea ITC
Navaradam ITC0770 AA Unknown Papua New Guinea ITC
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
Musa acuminata ssp. banksii ITC0896 acuminata subsp. banksii Papua New Guinea ITC
Saing Todloh ITC0316 AA subgr. Pisang Jari Buaya Philippines 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
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 Indonesia 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

Pages

Evaluation traits: