A digital catalog of high‐density markers for banana germplasm collections

Global production of bananas, among the top 10 food crops worldwide, is under threat. Increasing use germplasm conserved in genebanks crucial. However, lack or difficult access to genetic diversity information limits efficient utilization these valuable resources. Here, we present a digital catalog high-density markers for banana at international collection. By facilitating subsets information, has potential maximize conservation and climate-ready varieties optimize breeding strategies. The extendable with data from any collection software easily deployable other crop genebanks. Crop plant managed by great value context changing needs agriculture (Smale & Jamora, 2020), but phenotypic on this insufficiently available most (McCouch et al., 2013, 2020). advent Next Generation Sequencing enabled—at an ever-decreasing cost—the sequencing reference genomes many as well genotyping large numbers samples per crop. Genotyping powerful tool help identify gaps redundancies collections, when combined phenotyping data, can be used detect correlations between genome regions agronomic traits. For some crops, massive processing have been undertaken, shown rice, wheat barley collections (Milner 2019; Sansaloni 2020; Wang 2018). These approaches represent increasingly reachable targets including CGIAR (Halewood, Lopez Noriega bananas (Musa spp.), largest ex situ maintained vitro one genebanks, International Musa Germplasm Transit Centre (ITC), comprised more than 1,600 accessions (Van den houwe Then, over 60 national worldwide conserve conduct-related research (Figure 1). Bananas (including Plantains) are arguably world's important fresh fruit major staple hundreds millions people low-income countries. With estimated world 158 million tons annually, volume gross exports worth US$12.8 billion exporting countries (FAOSTAT 2019). Furthermore, global smallholders their own consumption local trade, making it fourth-most least developed (LDCs) defined United Nations, ranked total consumption. In order increase understanding its complex genetics so boost improvement, first whole sequence was released 2012, accession belonging acuminata species (D’Hont 2012) (Table This original recently supplemented number (Rouard 2018; Wu 2016). parallel, high-throughput methods (i.e., genotyping-by-sequencing (GBS) (Elshire 2011) restriction-site associated DNA (RADSeq) (Davey 2010)) investigate single nucleotide polymorphisms (SNPs) various panels ITC genebank (Cenci Sardos addition, SNP datasets generated gene expression proteomics experiments related drought tolerance van Wesemael While variant being produced fast pace through projects processed via standardized bioinformatics workflows, main challenges management increasing raw intermediate files that handle applications. Bioinformatics workflows produce need filtered multiple ways according analysis type user perspective, working often presents those without capacity bioinformatics. Online systems coping big linked scarce (König Mansueto 2017; Raubach Ruas 2017). Moreover, continues additional factor limiting Phenotypic complex—information which they were collected indispensable, domain continuously evolving (Germeier Unger, Recognizing challenges, availability easy-to-use, interoperable flexible solutions navigate online key aim genebanks’ delivery mission documentation utilization. study, approach generate, store disseminate variants plantain ITC, https://www.crop-diversity.org/mgis/gigwa embedded system users germplasm. Material create mostly originates lyophilized leaf tissues young plants distributed ITC. Such tissue convenient way obtain acceptable quality quantity restriction enzyme-associated methods, omics techniques (Carpentier 2007). Another advantage once stock, readily distribution, whereas material takes longer average 2 months proliferating 4 rooted plantlets). sequence—short reads Illumina machines—was composed open source includes checks, read mapping genomes, calling effect genic described 2016; Cenci 2020 Eyland 2020. outputs workflow enormous text call format (VCF). every accession, another specific file gVCF) containing full list non-variant sites backed up server, allowing recall different sampling whenever necessary, thus saving significant time computing published literature (VCF files) 2) recorded non-relational database browsable web application called GIGWA (Sempéré 2019), purpose searching optimized manner. system, easy deploy platform, species-agnostic provides user-friendly interface perform advanced filtering export third-party analytical software. It seamlessly Information System (MGIS https://www.crop-diversity.org/mgis/) (Ruas 2017), situ-held resources numerous edible classified using groups relative contribution ancestral wild species. Most cultivated derived hybridization (A genome) balbisiana (B frequent combinations diploids triploids cultivars denoted: AA, AB, AAA, AAB ABB. current spans species/groups selected 2). offers sizes ranging 245,285 7 SNPs depending study. explore enables options based range parameters, (e.g., chromosome location, missing percentage, minor allele frequency, mutation effect) not only. Accession details enriched metadata such passport traits control vs. stress analyses), then become elements filtered. designed work two samples, feature which, latter case conjunction genotype pattern filters, makes straightforward discriminating particularly useful filter taxonomy certain trait contrasted genotypes reveal unique alleles held accessions. From interface, exported popular formats VCF, BED) further analyses, directly imported analyses. Alternately, content programmatically accessed Breeding API (BrAPI), computer–computer programming following standard specifications (Selby solution facilitates essential connections implemented Musabase, https://musabase.org Genesys, Plant Genetic Resources Food Agriculture (PGRFA) https://www.genesys-pgr.org). regard types catalog, support analyses studies association. Of particular interest, set panel 105 investigated provide ready genome-wide association (GWAS) obtained (Sardos concern high levels genotypic accessions, would enable new (NBTs) bypass benefit-sharing (ABS) arrangements currently distribution physical much recent attention (Aubry, Halewood, Chiurugwi Smyth At moment, researcher, breeder) them obligations, organizations already made publicly wide crops. As elaborated (Scholz challenging breed should ignored, may contribute significantly progress (Gaffney intends genomic equitable way, ultimately benefiting all, (Halewood noted does include functions, browser hub contains annotation references (Droc 2013). Nevertheless, given model plant, functional inferred homology-based prediction methods). polyploid background cultivars, expected regulation control, necessitating innovative role apparent redundancy D’Hont 2012). We yet reached stage where pick coding select interest conduct improvement. Significant still needed better understand physiology architecture banana. Phenotyping traits, quality, also missing, inhibit adoption improved hybrids (Thiele editing will fine-tuned banana, even if encouraging perspectives (Tripathi Zorrilla-Fontanesi Finally, frameworks edited legislated (Schmidt waiting future policy options, training catalogs strengthened, breeders programs supportive funding schemes. A genebank. accessible proof concept exploration datasets. adapted objective keeping connected Users browse interesting investigation programs. wondering managing scope, simple elegant solution. reasonable transaction cost, framework extrapolated Challenges addressed. First, technical side, stored clusters resulting individual studies. Merging platforms task. financial funder investment complete Given relatively small size clonal (1,600 compared 773,000 total), require investment. comply rules, developments take into account agreements (DSI) debated Convention Biological Diversity Treaty Agriculture. thank Research Program, Roots, Tubers (RTB) Directorate-general Development Cooperation Humanitarian Belgian support. M.R. led writing manuscript critical inputs J.S. N.R. S.C.C. I.V.D.H facilitated material. coordinated transcriptomics production. C.B. performed management. G.S. V.G. deployed acquired project supervised teamwork. All authors contributed draft gave final approval publication.