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

<p>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.</p>

DOI10.1371/journal.pone.0154448
Alternate JournalPLoS ONE
PubMed ID27144345
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 India 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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