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

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.香蕉（Musa sp.）是一类无性繁殖、育性较低、兼具杂交特性与多倍体特征的作物。这些特性使得该作物的育种与定向遗传改良兼具难度高、周期长的特点。全基因组关联分析（Genome-Wide Association Study, GWAS）技术目前已在作物研究中得到广泛应用，并被证实可高效挖掘目标性状的候选基因，在谷类作物中应用尤为成熟。但截至目前，该技术尚未应用于无性繁殖类作物。然而，若能在香蕉中成功应用GWAS技术，将极大助力解析目标性状的遗传基础，进而加速该作物的遗传改良进程。本研究构建了包含105份香蕉种质资源的专属研究群体，其材料可通过申请免费获取，同时附带对应的测序分型（Genotyping-by-Sequencing, GBS）数据。基于5544个高可靠性分子标记的分析结果显示，除来自巴布亚的33份种质构成的亚群外，绝大多数香蕉种质均存在较高水平的遗传混合现象。随后，针对无籽性状的全基因组关联分析在该研究群体中成功开展。通过采用TASSEL软件中针对亲缘关系与群体结构均进行校正的混合线性模型，本研究共检测到13个候选基因组区域，其中发现了多个与无籽性状（即单性结实结合雌性不育）潜在相关的基因。针对由33份巴布亚种质构成的无群体结构亚群开展的补充GWAS分析，验证了其中6个区域为候选位点。综合两次分析结果，本研究鉴定到1个与雌性不育高度相关的候选基因，其被推测为组氨酸激酶CKI1（Histidine Kinase CKI1）的直系同源基因。本研究结果证实，将GWAS技术应用于小型香蕉种质群体开展性状关联分析的可行性与应用潜力，针对由少数基因座调控的性状而言尤为如此。鉴于香蕉的表型鉴定工作需占用大量空间且耗时极久，该研究结果对于香蕉遗传改良工作而言具有尤为重要的意义。