Various large breeding projects have been developed to modernize sweetpotato breeding with new ambitious targets and new genomicGenomics methods. As the data sources that these methodologies rely on grow in volume, so grows the importance of an efficient data management system. In this chapter, we introduce a digital breeding ecosystem centered around Sweetpotatobase, a database platform tailored for sweetpotato breeders across the globe to manage their breeding data effectively. We highlight a handful of complementary Android applications designed for data collection: Field BookField Book, for phenotypic data, Coordinate, for genotypic data, and Intercross, for crossing data. We discuss the importance of roundtripping, and how BrAPI, a standard for breeding data transfer, can facilitate this via automated transfers. We present some of the many features of Sweetpotatobase that can be leveraged once the ecosystem is up and running—the Search Wizard, which explores and retrieves data intuitively and efficiently, the Pedigree Viewer, which can visualize allele inheritance patterns through pedigrees, the sweetpotatoSweet potato ontology, which defines standardized and measurable traits. Lastly, we discuss how Sweetpotatobase is empowered with analysis features, from a mixed model tool to genomeGenome-wide association studies (GWAS), principal component analysis (PCA), and stability analysis.

错误:搜索内容不能为空,请输入英文关键词
错误:关键词超出字数限制,请精简
高级检索

Sweetpotato Breeding in the Genomic Age: Harnessing Databases, Bioinformatics, Digital Tools, and Genomic Insights

  • Bryan J. Ellerbrock,
  • Christiano C. Simoes,
  • Srikanth Kumar Karaikal,
  • Christine M. Nyaga,
  • Lukas A. Mueller

摘要

Various large breeding projects have been developed to modernize sweetpotato breeding with new ambitious targets and new genomicGenomics methods. As the data sources that these methodologies rely on grow in volume, so grows the importance of an efficient data management system. In this chapter, we introduce a digital breeding ecosystem centered around Sweetpotatobase, a database platform tailored for sweetpotato breeders across the globe to manage their breeding data effectively. We highlight a handful of complementary Android applications designed for data collection: Field BookField Book, for phenotypic data, Coordinate, for genotypic data, and Intercross, for crossing data. We discuss the importance of roundtripping, and how BrAPI, a standard for breeding data transfer, can facilitate this via automated transfers. We present some of the many features of Sweetpotatobase that can be leveraged once the ecosystem is up and running—the Search Wizard, which explores and retrieves data intuitively and efficiently, the Pedigree Viewer, which can visualize allele inheritance patterns through pedigrees, the sweetpotatoSweet potato ontology, which defines standardized and measurable traits. Lastly, we discuss how Sweetpotatobase is empowered with analysis features, from a mixed model tool to genomeGenome-wide association studies (GWAS), principal component analysis (PCA), and stability analysis.