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.
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.
Citrus Greening Solutions
A systems-based pipeline approach for delivering commercial, grove-deployable solutions using a novel therapeutic delivery strategy and citrus transgenics.
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.
Sol Genomics Network
A site for genome data of Solanaceae species such as tomato, potato, and pepper, and related to the tomato genome sequencing project.
Part of the Genomics Tools for Sweet Potato (GT4SP) Improvement Project focused on developing a set of “next generation” breeder tools for African sweetpotato breeders in Africa.
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.
Breedbase software to help speed crop improvementTo help plant breeders speed crop improvement around the world, Lukas Mueller of the Boyce Thompson Institute worked with an international team of 57 people to create Breedbase, a database […] Read more »
Wild tomato genome will benefit domesticated cousinsWild relatives of crops are becoming increasingly valuable to plant researchers and breeders. During the process of domestication, crops tend to lose many genes, but wild relatives often retain genes […] Read more »
Congratulations to BTI’s Spring 2022 Graduates!We are pleased to announce that three BTI researchers received their degrees during the Cornell University commencement ceremony on May 28. Congratulations to our newest alumni! Alex Ogbonna, Mueller lab, […] Read more »
Alex Ogbonna Wins Borlaug Scholar Award from NAPBBoyce Thompson Institute is proud to congratulate Alex Ogbonna for receiving a 2021 Borlaug Scholar Award from the National Association of Plant Breeders (NAPB). Ogbonna is a Cornell University graduate […] Read more »
Tomato’s Wild Ancestor Is a Genomic Reservoir for Plant BreedersThousands of years ago, people in the region now known as South America began domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant evolved […] Read more »
BTI Graduate Students Receive Schmittau-Novak GrantsWe would like to congratulate five BTI graduate students who are Spring 2020 Schmittau-Novak Grants Program recipients. Supported by a bequest from the estate of Jean Schmittau in honor of […] Read more »
A universal framework combining genome annotation and undergraduate educationAs 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 […] Read more »
Cassava experts gather to champion ‘orphan crop’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. […] Read more »
Open-access wild tomato genome offers valuable insights for tomato growers, crop scientistsThe 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 »
New funding supports cassava development in AfricaCornell University and BTI will expand international efforts to deliver improved varieties of cassava to smallholder farmers in sub-Saharan Africa with $35 million in new funding from the Bill & Melinda Gates Foundation and UK aid in the United Kingdom. Read more »
New ‘Tomato Expression Atlas’ dives deep into the fruit’s fleshResearchers at BTI, Cornell and USDA published a spatiotemporal map of gene expression across all tissues and developmental stages of the tomato fruit – the genetic information underlying how a fruit changes from inside to out as it ripens. Their data is available in the new Tomato Expression Atlas (TEA). Read more »
Better breeders, better yams: YamBase workshops help improve yam breedingMore than 70 participants joined in on the training sessions provided by members of BTI's Mueller Lab, October-December 2017. Read more »
BTI’s Mueller Lab and visiting researchers collaborate to improve important crop databasesDuring June and July at BTI, visiting scholars from crop breeding programs in Nigeria, Nairobi, and Uganda have been working closely with researchers in Lukas Mueller’s group to discuss ways to improve the development of online resources related to two of Africa’s most important staple crops: cassava and banana. Read more »
Global partnerships for improving cassavaCassava geneticist Ismail Yusuf Rabbi from the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria visited BTI and Cornell University last week to discuss his ongoing collaboration with NextGen Cassava. Read more »
BTI researchers share latest research at ag-genomics conferenceThe offices of data scientists at BTI emptied out earlier this month as a contingent of researchers flew to San Diego for the 25th annual Plant and Animal Genome Conference. Read more »
GOBii releases open-source tools for faster plant breedingThe collaboration works with breeding centers around the world to develop tools to make the process of adding a trait into an existing, high-yield crop variety more efficient. Read more »
SolGenomics Meeting Has Newest Advances in NightshadesMany BTI researchers will present their latest research at the 13th annual SolGenomics Conference, Sept. 12-16 in Davis, California. Read more »
“Hackathon” Breeds Momentum for Plant Breeding SoftwareAn international group of computer programmers gathered at BTI to create a single interface that will connect databases from breeding programs worldwide Read more »
Students Become Gene Detectives to Fight Citrus GreeningA group of students and experts work together through video conferencing to identify the genes in the genome of the newly sequenced Asian citrus psyllid, the insect that spreads the bacterium that causes citrus greening disease. Read more »
Wild Parents’ Genomes Reveal Complex Genetic Past for Garden Variety PetuniasAn international consortium of researchers has sequenced the two wild parent species of the domesticated petunia Read more »
Jonathan Gomes Selman Recognized as Distinguished YouthTompkins County has awarded Gomes Selman, a 2015 high school intern at BTI, its Distinguished Youth award for his numerous academic and volunteer commitments. Read more »
Researchers Uncover Core Set of Genes for Plant-Fungal SymbiosisBTI researchers used a genome comparison approach to identify genes necessary for beneficial plant-fungal relationships, which may lead to better crop plants that require less fertilizer input. Read more »
GOBii Workshop Seeks Solutions to Big Data ProblemThe GOBII project gathered researchers from breeding centers around the world to make a plan to develop the architecture for a genomics database for five staple crops. Read more »
From Flower to Fruit: Study Reveals Details of Tomato FormationBTI Researchers pinpointed which genes are important at different stages of tomato fruit development by monitoring how gene expression changed in the first four days after a flower becomes pollinated. Read more »
The Perks of Being a MentorSummer internships at BTI let students try on the life of a scientist for a few months, while attending a variety of talks, trainings and social events. But what’s in it for the mentors, who painstakingly train them? Read more »
BTI Welcomes New Crop of Summer InternsBTI welcomes 20 college-level interns for 10 weeks of research in Plant Genome Research Program, the Bioinformatics Program or the Bioenergy Education Program. Read more »
18.5 Million Grant Will Help Bring Genomic Technology to Small FarmersBTI Professor Lukas Mueller will participate in an international collaboration to expedite crop breeding for five worldwide staple crops—wheat, rice, maize, sorghum and chickpea. Read more »
BTI at Plant and Animal Genome ConferenceBTI researchers attended, presented and led workshops at 23rd Annual Plant Animal Genome Conference (PAG) 2015 in San Diego. Read more »
Transatlantic Collaboration Builds a Better Database"Biology is becoming a data science," said Ruiz. "Biologists need to learn to use bioinformatics tools." Read more »
Lukas Mueller: Ace of BasesThe Yambase database will allow users to access the yam genome browser hosted by the Iwate Biotechnology Research Center in Japan and will house information about desirable yam characteristics and tools for breeders. Read more »
BTI Professors Present to Bill GatesBTI professors David Stern, Zhangjun Fei, and Lukas Mueller were able to brief Bill Gates and his team on their Gates funded projects and issues of biotechnology and plant science while he was at Cornell on October 1, 2014. Read more »
New Bioinformatics Alliance between CGIAR and BTIGraham Thiele, RTB Program Director at CGIAR Research Program on roots, tubers, and bananas recently met with Boyce Thompson Institute's Lukas Mueller to plan expansion of bioinformatics platforms and databases. Read more »
$4.7 Million to SIPS and BTI for More Tomato ResearchJocelyn Rose, professor of plant biology and director of Cornell’s Institute of Biotechnology, with BTI co-PI's Carmen Catala, Zhangjun Fei, James Giovannoni, and Lukas Mueller will research ripening mechanisms & drought tolerance. Read more »
BTI Tomato and Fruit Biology Group Awarded USDA Secretary of Agriculture HonorBTI researchers led team that pioneered international tomato gene sequencing and genetic basis of fruit ripening. Congrats to Vrebalov, Van Eck, Mueller, Giovannoni, Fei. Read more »
Bioinformatics Progress at BTIBTI provides bioinformatics consulting in-house. Read more »
BTI Cassavabase Project in AfricaMueller Lab at BTI coordinates Cassavabase web site to pool data from cassava field trials in Africa to improve plant breeding. Read more »
New Website Is Portal for Nicotiana benthamiana Experimental ResourcesThis Nicotiana benthamiana web site shares papers, results, tools, protocols, and other materials from researchers using NB as a study plant. Read more »
A Wild Relative of Tobacco Offers Insight into Molecular Plant Biology at BTIThe genome of an experimentally important relative of tobacco has been sequenced by US and Canadian researchers. Read more »
Cornell Receives $25.2M in Funding for Next Generation Cassava BreedingCassava, a rough and ready root crop that has long been the foundation of food security in Africa is finally getting the respect it deserves. Read more »
Scientists Find Clues into More Disease-Resistant Watermelons, Genome DecodedAre juicier, sweeter, more disease-resistant watermelons on the way? Read more »
Tomato Genome Becomes Fully Sequenced – Paving the Way for Healthier PlantsFor the first time, the genome of the tomato, Solanum lycopersicum, has been decoded. Read more »
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