Grey Monroe

Our Research

The Monroe Lab investigates the molecular and evolutionary forces shaping plant genomes — mutation rate variation, DNA repair, chromosome biology, and somatic mutation in clonal and tissue-cultured plants. We integrate genomics, computational biology, and experimental approaches across systems ranging from wild Arabidopsis to perennial crops like pistachio and cassava.

By connecting the molecular machinery that determines where mutations land in the genome to the evolutionary outcomes that follow, our research addresses fundamental questions about the origin of adaptive variation and the persistence of populations, while informing the genomics of resilient, regenerative agriculture.

Ongoing projects

• Mutation rate variation. We have identified mechanisms influencing mutation probabilities across genomes in putatively adaptive directions. We are now advancing theory and experiments to dissect the causes of these mutation biases and their consequences for genome evolution of different plants.
• Functional Population Genomics. We are developing new computational approaches enabled by population-scale whole-genome sequence data, coupled with experimental gene editing, to accelerate the discovery of adaptive loss-of-function variation in diverse species (e.g., Arabidopsis, rice, cassava, wheat, pistachio).
• Pan Genomics of Climate-Ready Crops. Crops such as pistachio and cassava are becoming increasingly important food sources due to their tolerance to extreme events like drought. We are using emerging sequencing technologies to investigate pan-genomic diversity in these crops and working with breeders to understand and improve their adaptation to climate.

Funding

Our work has been supported by the United States Department of Agriculture, National Science Foundation, Foundation for Food and Agricultural Research, Pacific Biosciences, California Pistachio Research Board, Eco-Evo-Devo Network, and the University of California.

Select Publications

• Monroe JG, Lee C, Quiroz D, Lensink M, Oya S, Davis M, Long E, Bird KA, Pierce A, Zhao K, Runcie D. (2025) Convergent evolution of epigenome recruited DNA repair across the Tree of Life. eLife.
• Adaskaveg JA, Lee C, Wei Y, Wang F, Grilo FS, Mesquida-Pesci SD, Davis M, Wang SC, Marino G, Ferguson L, Brown PJ, Drakakaki G, Mena-Morales A, Marchese A, Giovino A, Martínez E, Marra FP, Marchante Cuevas L, Cattivelli L, Bagnaresi P, Carbonell-Bejerano P, Monroe JG, Blanco-Ulate B. (2025) In a nutshell: pistachio genome and kernel development. New Phytologist.
• Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe JG. (2024) H3K4me1 recruits DNA repair proteins in plants. The Plant Cell.
• Quiroz D, Lensink M, Kliebenstein DJ, Monroe JG. (2023) Causes of mutation rate variability in plant genomes. Annual Review of Plant Biology 74:751–775.
• Kenchanmane Raju SK, Lensink M, Kliebenstein DJ, Niederhuth C, Monroe JG. (2023) Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in Arabidopsis thaliana. New Phytologist.
• Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, et al. (2022) Mutation bias reflects natural selection in Arabidopsis thaliana. Nature602:101–105.
• Monroe JG, McKay J, Weigel D, Flood P. (2021) The population genomics of adaptive loss of function. Heredity126:383–395.
• Monroe JG, Arciniegas J, Moreno J, Sanchez F, Sierra S, Valdes S, Torkamaneh D, Chavarriaga P. (2020) The lowest hanging fruit: Beneficial gene knockouts in past, present, and future crop evolution. Current Plant Biology 24:100185.
• Monroe JG, Gill B, Turner K, McKay J. (2019) Drought regimens predict life history strategies in Heliophila. New Phytologist.
• Monroe JG, Powell T, Price N, Mullen J, Howard A, Evans K, Lovell J, McKay J. (2018) Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. eLife 7:e41038.
• Monroe JG, Markman D, Beck W, Felton A, Vahsen M, Pressler Y. (2018) Ecoevolutionary dynamics of carbon cycling in the Anthropocene. Trends in Ecology & Evolution 33:213–225.
• Monroe JG, McGovern C, Lasky J, Grogan K, Beck J, McKay J. (2016) Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana. Molecular Ecology 25:3632–3644.

Research Keywords

mutation rate variation; DNA repair; plant genome evolution; chromosome biology; somatic mutation; tissue culture and somaclonal variation; perennial crop genomics; functional population genomics; pan-genomics