In recent years, technological advances in fields such as sequencing have transformed certain aspects of biology into an information-based discipline.
To make this abundance of data—often called Big Data—useful to researchers and breeders, it needs to be organized and made accessible. Towards this goal, the Mueller lab designs and implements databases that assist scientists in their research and plant breeders in more efficient crop improvement.
Our databases and software make transcriptomic, genotypic and phenotypic data from thousands of experiments accessible to the public, often focusing on under-researched staple crops from food-insecure regions. A method called Genomic Selection that uses high-throughput genotyping technologies, such as genotyping-by-sequencing (GBS), and large phenotyping data sets allows for rapid prediction of desirable traits in new plant crosses.
Based on these tools, the Mueller laboratory collaborates on a variety of different projects. With the Nextgen Cassava project, we have created Cassavabase, a database specifically designed for cassava breeders in Africa. We coordinate the Solanaceae Genomics Network—a compilation of all the genetic information known about solanaceous plants, such as tomato, petunia and Nicotiana. We are also developing breeding databases for yam, sweet potato and the cooking banana and we work with the Genomic and Open-source Breeding Informatics Initiative (GOBII) to streamline crop breeding for five staple crops—wheat, rice, maize, sorghum and chickpea. Finally, the Mueller group is involved in multiple genome sequencing projects, including tomato, coffee, petunia and Nicotania benthamiana.
Citrus Greening Solutions
A systems-based pipeline approach for delivering commercial, grove-deployable solutions using a novel therapeutic delivery strategy and citrus transgenics.
Access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.
A breeding database designed for advanced breeding methods in banana breeding.
A collection of Root Tubers & Banana Databases, which hold genomic and phenotypic information for next generation breeding applications.
A database about breeding data for Yam (genus Dioscorea). Yam species that are being used for breeding include , Dioscorea rotundata, Dioscorea cayenensis (both are native to Africa and the major cultivated species), Dioscorea aleata (native to Southeast Asia), and Dioscorea praehensilis, as well as several other species.
- As genome sequencing becomes cheaper and faster, resulting in an exponential increase in data, the need for efficiency in predicting gene function is growing, as is the need to train the next generation of scientists in bioinformatics. Researchers in the lab of Lukas Mueller, a faculty member of the Boyce Thompson Institute (BTI), have developed […] Read more »
- It’s a dietary staple for millions of Africans, but cassava has traditionally received little attention from scientists and plant breeders in comparison to cash crops such as wheat and maize. However, researchers have recently been working to find cassava a scientific “home.” Around 100 cassava breeders, experts, and scientists from around the world, including BTI’s […] Read more »
- The new S. lycopersicoides genome sequence offers the opportunity for innovative breeding programs that may hold the ability to confer desirable traits to marketable tomato varieties. Read more »
Interns in the Mueller lab work on a variety of bioinformatics and genomics projects and gain experience in the following areas: genome assembly, structural and functional annotation, biochemical pathways, comparative genomics, ontology development and data presentation and visualization.
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