Introduction

The Next Generation Cassava Breeding aims to significantly accelerate genetic improvement of cassava breeding and unlock the full potential of cassava, a staple crop central to food security and livelihoods across Africa (http://www.nextgencassava.org/about.html).

Cassavabase (www.cassavabase.org) was created to centralize information tracking, genotypic and phenotypic data, and Genomic Selection prediction analyses.

Data is being collected on evaluation sheets and field notebooks which

might be altered or misplaced pointing to the fact that evaluated data are not protected.

In addition, it takes longer time for the collected data to be entered into the computer, cleaned and prepared for analysis, giving room for error during data entering if proper care is not taken by the curator.

NRCRI uses Fieldbook application and Android tablet for phenotype collection in the field for it routine germplasm development.

The Android tablet is convenient because data files can easily be

transferred; it gives a reasonable time for data collection and has little glare while being used in the field during data recording.

Cassavabase ultimately aims to achieve and facilitate unhindered

sharing of information, which means overcoming the traditional reluctance of researchers to share data.

Acknowledgments We thank National Root Crops Research Institute, Umudike, Nigeria and Boyce Thompson Institute, Ithaca, New York for their support. Funding for this project was provided by the Next Generation Cassava Project.

Conclusions

Alex Ogbonna1,2, Chiedozie Egesi1*, Adeyemi Olojede1, Ezenwanyi Uba1, Nneka Okereke1, Emmanuel Okogbenin1, Lukas Mueller2

1National Root Crops Research Institute (NRCRI), Umudike, Nigeria; 2Boyce Thompson Institute for Plant Research Ithaca, New York, U. S. A.

Corresponding author email address: aco46@cornell.edu, Registrant ID # 4593

Use Case 6: Breeding Outcome

NR110370, NR110036 and NR110005 were ranked as the top producing lines from the analysis.

Figure 1. Cassavabase homepage.

The use of cassavabase: a tool for cassava genomics at NRCRI, Nigeria.

Objectives To develop a data management strategy for routine germplasm development

that will aid data accessing, sharing and retrieval at NRCRI, Umudike, Nigeria.

To carry out data analysis using genomic prediction models on the cassavabase server.

Case Study: Use of Cassavabase for 2012 Training Population (TP) Trial.

A total of 500 pre-selected genotypes from NRCRI germplasm were evaluated at western farm of NRCRI, Umudike, Nigeria. The genotypes were properly curated and uploaded into Cassavabase. The trial was created on Cassavabase, transferred to android tablet and setup with fieldbook app for phenotyping. The use of the newly developed cassava traits ontology was fully implemented for this trial. Cassavabase genomics selection pipeline was used to carry out genomic selection for this trial (population).

Figure 7. Data recording at western

farm of NRCRI ,Umudike ,Nigeria.

The use of Cassavabase at NRCRI Cassava Breeding Program, has given hope to data accessing, sharing, retrieval and managing which brings about data integration and utilization.

It has a data management component for phenotypic data generated by evaluation and testing.

The solGS and genome browser component has a pipeline for performing genomic selection (GS) and viewing the genomes at any scale with dozens of aligned annotation tracks respectively..

Cassavabase has given our breeding scheme a new look, ending the era of having trial information on field books and on the shelf of scientists. However, Cassavabase will ensure an open data policy for accelerating research on Cassava.

Figure 5. Showing Fieldbook App phenotyping page.

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Genomic selection is the use of statistical methodology to predict the merit (GEBVs, figure 2) of a genotype using genotypic information from it self and it’s relatives and phenotypic information from it relatives. Cassavabase implements genomic selection algorithms for analysis of field trials and estimation of GEBVs.

Figure 6. Showing the use of Android Fieldbook App for data recording at the 2012 TP trial field.

Figure 10. Showing data analysis result and exploration for fresh root yield trait. Panel A shows an interactive scatter plot of phenotype data, panel B displays the frequency of the same phenotype data, panel C gives the GEBVs of the individuals in the training population and panel D shows the relationship between GEBVs and phenotype values for fresh root yield trait.

A B

C D

Fig. 9. Cassava Genomic Selection Scheme.

Source: Heffner et al. 2009 Crop Sci. 49:1–12

Use Case 1: Trial Creation.

Figure 2. Showing list of accessions used for 2012 TP trial

Figure 3. Cassavabase trial creation dialog showing the creation of 2012 TP trials

Figure 4. Trial detail page for 2012 TP trial.

Use Case 2: Data Collection

Use Case 3: Data Uploading

Figure 7. Showing phenotype upload for 2012 TP trial recorded data.

Figure 8. Showing the uploaded phenotype on the trial detail for 2012 TP trial.

Use Case 5: Data Analysis Output

Use Case 4: Data Analysis

Figure 11. Cassavabase Ontology browser page showing cassava trait ontology

Cassava Trait Ontology

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