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 40 of 104 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Tomolo ITC1187 AA Unknown Papua New Guinea ITC
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
Te'engi ITC0951 AA Unknown Papua New Guinea 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 Unknown ITC
Spiral ITC1206 AA Unknown Papua New Guinea ITC
Katual Vunalir ITC0788 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
Banksii ITC0806 acuminata subsp. banksii Papua New Guinea ITC
Meinje ITC1015 AA Unknown Papua New Guinea ITC
Mapua ITC1244 AA Unknown Papua New Guinea ITC

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