These challenges make banana an exciting case study.
Thirdly, the vegetative mode of propagation and the high rates of clonal diversification of the crop can lead to confounding effects and spurious association due to clonal population structure. Secondly, cultivated bananas exhibit various rates of fertility, drastically reducing the occurrence of sexual reproduction and therefore limiting sample size. Firstly, most of the cultivars are polyploid, for which association studies are challenging due to a lack of appropriate analysis methods, and/or inter-specific hybrids, which complicate SNP mapping and increase genetic heterogeneity. In banana, applying GWAS is challenging due to many deviations from the assumption of Mendelian genetics. Indeed, it has led to the discovery of many candidate genes for traits related to agronomy, disease resistance, root traits or leaf architecture in cereals. With the emergence of cost-effective Next-Generation Sequencing technologies and genotyping facilities, an approach like the Genome-Wide Association Studies (GWAS) is becoming widely used in crop plants. However, quite a number of landraces cultivated in farmers’ fields are diploids. Most of the popular cultivars such as the commercial AAA Cavendish or the African staple AAB Plantain are triploids. In addition, polyploidization also occurred the initial domestication events resulted in diploids AA or AB, which was followed by the production of triploids AAA, AAB, and ABB through unbalanced meiosis. balbisiana (B genome), characterized by high levels of gene flow between these taxa followed by extensive clonal diversification, that is to say the human selection of variants ensuing from the accumulation of mutations or epigenetic changes within clones. Current cultivated bananas arose from a complex domestication scheme that involved several taxa, including different subspecies of M. In addition, banana is the fourth largest food crop in the least-developed countries, and is thus of great importance for food security. In 2012, the total production of banana in the world reached nearly 140 million tonnes, out of which close to 14% was deemed for export. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.īanana ( Musa spp.), including plantain, is a starchy crop cultivated in more than 130 countries. 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. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. parthenocarpy combined with female sterility). 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. A GWAS on the seedless phenotype was then successfully applied to the panel. 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.
We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement.
GWAS has not been applied yet to a vegetatively propagated crop. 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. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. Banana ( Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop.
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