Lukas Mueller

Professor
Lukas Mueller
lam87@cornell.edu
Office/Lab: 221
Phone: 607-255-6557
Office/Lab: 221
Email: lam87@cornell.edu
Office Phone: 607-255-6557
Affiliations: Adjunct Professor / Section of Plant Breeding and Genetics / School of Integrative Plant Science / Cornell University
Graduate Fields: Plant Breeding
Research Overview

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.

Links:

Cassavabase
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.

Musabase
A breeding database designed for advanced breeding methods in banana breeding.

Rtbbase
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.

Sweetpotatobase
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.

Yambase
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.

Intern Projects
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.

Internship Program | Projects & FacultyApply for an Internship
Current status and impending progress for cassava structural genomics.
2022.
Lyons, J.B., Bredeson, J.V., Mansfeld, B.N., Bauchet, G.J., Berry, J., Boyher, A., Mueller, Lukas A.…
Plant Mol Biol..
109
:
177–191
Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae.
2022.
Powell, A.F., Zhang, J., Hauser, D., Vilela, J.A., Hu, A., Gates, D.J., Mueller, Lukas A., Li, Fay-W…
Plant Genome.
:
Graph pangenome captures missing heritability and empowers tomato breeding.
2022.
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., Zhang, …
Nature.
606
:
527–534
Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn’s disease
2022.
Zhang, S., Morgan, X., Dogan, B., Martin, F.P., Strickler, S., Oka, A., Herzog, J., Liu, B., Dowd, S…
JCI Insight.
7
:
Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data
2022.
Mann, M., Saha, S., Cicero, J.M., Pitino, M., Moulton, K., Hunter, W.B., Cano, L.M., Mueller, Lukas …
Gigascience.
11
:
1–16
A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity.
2022.
Powell, A.F., Feder, A., Li, J., Schmidt, M.H., Courtney, L., Alseekh, S., Jobson, E.M., Vogel, A., …
Plant J..
:
Breedbase: a digital ecosystem for modern plant breeding.
2022.
Morales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., Powell, …
G3.
:
Chromosome length genome assembly of the redbanded stink bug, Piezodorus guildinii (Westwood)
2022.
Saha, S, Allen, K.C., Mueller, Lukas A., Reddy, G.V.P., Perera, O.P.
BMC Res Notes..
15
:
115
Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication.
2021.
Ogbonna, A.C., Braatz de Andrade, L.R., Mueller, Lukas A., de Oliveira, E.J., Bauchet, G.J.
Theor Appl Genet..
134
:
1343–1362
Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? – A Case Study With Hydrogen Cyanide in Cassava
2021.
Torres, L.G., de Oliveira, E.J., Ogbonna, A.C., Bauchet, G.J., Mueller, Lukas A., Azevedo, C.F., Sil…
Front Plant Sci..
12
:
742638
A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)
2021.
Ogbonna, A.C., Ramu, P., Esuma, W., Nandudu, L., Morales, N., Powell, A., Kawuki, R., Bauchet, G., J…
Sci Rep..
11
:
23520
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
2021.
Foerster, H., Battey, J.N.D., Sierro, N., Ivanov, N.V., Mueller, Lukas A.
Brief Bioinform..
22
:
bbaa136
The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago.
2021.
Raharimalala, N., Rombauts, S., McCarthy, A., Garavito, A., Orozco-Arias, S., Bellanger, L., Morales…
Sci Rep..
11
:
8119
Annotation of segmentation pathway genes in the Asian citrus psyllid, Diaphorina citri
2021.
Miller, S., Shippy, T.D., Hosmani, P.S., Flores-Gonzalez, M., Mueller, Lukas A., Hunter, W.B., Brown…
Gigabyte.
1
:
The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality
2021.
Mango Genome Consortium, Bally, I.S.E., Bombarely, A., Chambers, A.H., Cohen, Y., Dillon, N.L., Inne…
BMC Plant Biol..
:
Current status and impending progress for cassava structural genomics
2021.
Lyons, J.B., Bredeson, J.V., Mansfeld, B.N., Bauchet, G.J., Berry, J., Boyher, A., Mueller, Lukas A.…
:
Large-scale GWAS using historical data identifies a conserved genetic architecture of cyanogenic glucosides content in cassava (Manihot esculenta Crantz.) root
2021.
Ogbonna, A.C., Braatz de Andrade, L.R., Rabbi, I.Y., Mueller, Lukas A., de Oliverira, E.J., Bauchet,…
Plant J..
105
:
754–770
PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens
2020.
Fernandez-Pozo, N., Haas, F.B., Meyberg, R., Ullrich, K.K., Hiss, M., Perroud, P.F., Hanke, S., Krat…
:
Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
2020.
Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P.S., Saha, S., Zhang, J., Mainiero, S., Str…
Nat Commun.
11
:
5817
Draft Genome Sequence Resource of the Citrus Stem-End Rot Fungal Pathogen Lasiodiplodia theobromae CITRA15
2020.
Zheng, Q., Ozbudak, E., Liu, G., Hosmani, P.S., Saha, S., Flores-Gonzales, M., Mueller, Lukas A., Ro…
Phytopathology.
:

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