Lukas Mueller

About

Lukas Mueller is an adjunct professor in the School of Integrative Plant Science, Plant Breeding and Genetics Section. His lab designs and implements databases that assist scientists in their research and plant breeders in more efficient crop improvement. The databases and software developed by his group 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. Mueller's research involves the use of Genomic Selection, which employs high-throughput genotyping technologies such as genotyping-by-sequencing (GBS) and large phenotyping data sets to rapidly predict desirable traits in new plant crosses. His lab collaborates on various projects, including the creation of Cassavabase for cassava breeders in Africa, coordinating the Solanaceae Genomics Network, and developing breeding databases for crops like yam, sweet potato, and banana. He is involved in multiple genome sequencing projects for crops such as tomato, coffee, petunia, and Nicotiana benthamiana. His work aims to organize and make accessible the large amounts of biological data generated by advances in sequencing technologies, thereby facilitating crop improvement and supporting research in food-insecure regions.

Research topics

• Genetics
• Biology
• Computational biology
• Botany
• Evolutionary biology

Selected publications

• Graph pangenome captures missing heritability and empowers tomato breeding

  Nature · 2022 · 506 citations

  . Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largel…

  DOI

• Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

  Nature Communications · 2020 · 156 citations

  Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles un…

  DOI

• The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

  Nature Genetics · 2024-04-01 · 81 citations

  articleOpen access

  Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenom…

  PublisherOA PDFDOI

• MangoBase: A Genomics Portal and Gene Expression Atlas for Mangifera indica

  Plants · 2023-03-10 · 21 citations

  articleOpen access

  Mango (Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated in more than 100 countries, with a production of more than 40 million tons. Recently the genome sequences of several mango varieties have been released, but there are no bioinformatics platforms dedicated to mango genomics and breeding to host ma…

  PublisherOA PDFDOI

• Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize

  Genetics · 2024-03-12 · 8 citations

  articleOpen access

  Design randomizations and spatial corrections have increased understanding of genotypic, spatial, and residual effects in field experiments, but precisely measuring spatial heterogeneity in the field remains a challenge. To this end, our study evaluated approaches to improve spatial modeling using high-throughput phenotypes (HTP) via unoccupied aerial vehicle (UAV) imagery. The normalized difference vegetation index was measured by a multispectral MicaSense camera and processed using ImageBreed.…

  PublisherOA PDFDOI

Frequent coauthors

• Surya Saha

  Ithaca College

  281 shared

• Prashant S. Hosmani

  Ithaca College

  179 shared

• Mirella Flores-Gonzalez

  Ithaca College

  159 shared

• Naama Menda

  Ithaca College

  137 shared

• Wayne B. Hunter

  U.S. Horticultural Research Laboratory

  115 shared

• Susan J. Brown

  108 shared

• Susan R. Strickler

  Center for Plant Conservation

  108 shared

• Tom D’Elia

  101 shared

Awards & honors

• Cornell CALS faculty recognized among most influential scien…

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