From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

Raubach, Sebastian; Kilian, Benjamin; Dreher, Kate; Amri, Ahmed; Bassi, Filippo M.; Boukar, Ousmane; Cook, Douglas R.; Cruickshank, Alan; Fatokun, Christian; Haddad, N. I.; Humphries, Alan; Jordan, David R.; Kehel, Zakaria; Kumar, Shiv; Labarosa, Sandy Jan; Nguyen, Loi Huu; Mace, Emma; McCouch, Susan R.; McNally, Kenneth L.; Marshall, David; Mikwa, Erick Owuor; Milne, Iain; Odeny, Damaris Achieng; Plazas, Mariola; Prohens, Jaime; Rieseberg, Loren H.; Schafleitner, Roland; Sharma, Sunny; Stephen, Gordon; Tin, Huynh Quang; Togola, Abou; Warschefsky, Emily; Werner, P.; Shaw, Paul; Partners, All our Cwr Pre‐Breeding

doi:10.1002/csc2.20248

Cited by 34 publications

(32 citation statements)

References 47 publications

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“…In addition, finger millet breeders assembled 49 improved varieties, inbred lines, and popular landraces in Kenya, making the total number of all accessions used in the study as 101 (Supplemental Table S1). More details on the genotypes used in the current study can be found in the Germinate3 website (https://ics.hutton.ac.uk/cwr/fingermillet) (Raubach et al., 2020).…”

Section: Methodsmentioning

confidence: 99%

Novel sources of resistance to blast disease in finger millet

et al. 2021

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Finger millet (Eleusine coracana (L.) Gaertn. subsp. coracana) is the most important millet in eastern Africa and perhaps the oldest domesticated cereal grain in Africa. One of the major factors limiting finger millet production is blast disease caused by the fungus Magnaporthe grisea. Crop wild relatives and landraces present a potential source of novel genes. This study investigated the response of cultivated and wild relatives of finger millet to an isolate of blast disease from western Kenya. Previous germplasm collections were purified through two generations of single‐seed descent before screening alongside improved and farmer‐preferred varieties (FPVs) under a screen house across three seasons. Farmer‐preferred varieties were identified through participatory varietal selection (PVS). The plants were inoculated twice during each growth period using hand‐spraying method and data on disease incidence recorded at grain‐filling stage. Genotypic data was generated using diversity arrays technology (DArT) sequencing and data analysis done using Genstat 18.2 and TASSEL 5.2.58. We observed high heritability (81%), indicating that the variation observed was predominantly genetic. Wild accessions were generally more resistant to the disease in comparison to the cultivated accessions. Preliminary genome‐wide association study (GWAS) using general linear model with principal component analysis led to the identification of 19 markers associated with blast disease that will be be developed into assays for genotype quality control and trait introgression. Wild accessions and landraces of finger millet present a good reservoir for novel genes that can be incorporated into crop improvement programs.

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Section: Methodsmentioning

confidence: 99%

Novel sources of resistance to blast disease in finger millet

et al. 2021

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“…High-throughput approaches for crop genotyping and phenotyping are becoming popular approaches to understanding plant genetics and breeding. Databases such as Germinate 3 have been developed in an effort to store, visualize and analyze data from crops such as potatoes, barley and wheat ( 44 ). This publicly available database allows for queries of the data to optimize knowledge gains for the user to facilitate desired crop cultivation.…”

Section: Nutri-informatics Progress Toward Improved Disease Managemenmentioning

confidence: 99%

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

et al. 2021

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Informatics has become an essential component of research in the past few decades, capitalizing on the efficiency and power of computation to improve the knowledge gained from increasing quantities and types of data. While other fields of research such as genomics are well represented in informatics resources, nutrition remains underrepresented. Nutrition is one of the most integral components of human life, and it impacts individuals far beyond just nutrient provisions. For example, nutrition plays a role in cultural practices, interpersonal relationships and body image. Despite this, integrated computational investigations have been limited due to challenges within nutrition informatics (nutri-informatics) and nutrition data. The purpose of this review is to describe the landscape of nutri-informatics resources available for use in computational nutrition research and clinical utilization. In particular, we will focus on the application of biomedical ontologies and their potential to improve the standardization and interoperability of nutrition terminologies and relationships between nutrition and other biomedical disciplines such as disease and phenomics. Additionally, we will highlight challenges currently faced by the nutri-informatics community including experimental design, data aggregation and the roles scientific journals and primary nutrition researchers play in facilitating data reuse and successful computational research. Finally, we will conclude with a call to action to create and follow community standards regarding standardization of language, documentation specifications and requirements for data reuse. With the continued movement toward community standards of this kind, the entire nutrition research community can transition toward greater usage of Findability, Accessibility, Interoperability and Reusability principles and in turn more transparent science.

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“…Platforms for combining and analysing the data from the different domains are also essential, and can be adapted to the needs of projects or communities. A promising and already successfully used approach is the platform Germinate, developed by the James Hutton Institute, which is used in various projects to represent their data [ 64 ].…”

Section: Challengesmentioning

confidence: 99%

Document or Lose It—On the Importance of Information Management for Genetic Resources Conservation in Genebanks

Weise

Lohwasser

Oppermann

2020

Plants

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Genebanks play an important role in the long-term conservation of plant genetic resources and are complementary to the conservation of diversity in farmers’ fields and in nature. In this context, documentation plays a critical role. Without well-structured documentation, it is not possible to make statements about the value of a resource, especially with regard to its potential for breeding and research. In particular, comprehensive information management is a prerequisite for the further development of genebank collections. This requires detailed information about the composition of a collection, thus allowing statements about which species and/or regions of origin are under-represented. This task is of strategic importance, especially due to the threats to crop plants and their wild relatives caused by advancing climate change. Both the actual conservation management and the fulfilment of legal obligations depend on information. Hence, documentation units have been established in almost all genebanks worldwide. They all face the challenge that knowledge about genebank accessions must be permanently managed and passed on across generations. International standards such as Multi-Crop Passport Descriptors (MCPD) have been established for the exchange of data between genebanks, and allow the operation of international information systems, such as the World Information and Early Warning System on Plant Genetic Resources for Food and Agriculture (WIEWS), the European Search Catalogue for Plant Genetic Resources (EURISCO) or Genesys.

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From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

Cited by 34 publications

References 47 publications

Novel sources of resistance to blast disease in finger millet

Novel sources of resistance to blast disease in finger millet

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

Document or Lose It—On the Importance of Information Management for Genetic Resources Conservation in Genebanks

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