Abstract
BackgroundPlant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change.ResultsWe have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium.ConclusionsWe show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-259) contains supplementary material, which is available to authorized users.
Highlights
Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes
We describe the subsequent development of a pedigree visualization tool that was implemented in close collaboration with domain experts
Layout algorithms Plant pedigrees often form what we describe as a pedigree net, whereby there is structure to the graph but it’s not as simple as traditional top-down pedigree representation that is seen in humans and to a lesser extent in farmed animals (Figure 2)
Summary
Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. Derivation of the inheritance of such traits by traditional molecular techniques is expensive and time consuming, even with recent developments in high-throughput technologies This is especially true in industrial settings where, due to time constraints relating to growing seasons, many thousands of plant lines may need to be screened quickly, efficiently and economically every year. Post-study questionnaires (attitudinal and open ended) After carrying out our main interaction study the users were asked to fill in a series of questions that asked them to compare Helium to pedigree tools, or methods of handling pedigree data that they are familiar with using, and to get feedback on what they found easy and difficult to understand or perform with Helium These were obtained from feedback gained in our post-study questionnaire
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
