About

Blake Meyers is a Distinguished Professor and the Director of the Department of Plant Sciences at UC Davis. He holds a Ph.D. in Genetics from the University of California, Davis, earned in 1998, and a Master's degree in Genetics from the same institution. His research focuses on small RNAs, regulation of gene expression, microRNAs and their biogenesis, phased small interfering RNAs, and their roles in crops such as maize, wheat, rice, soybean, and Arabidopsis, as well as other model species. Meyers' work also encompasses plant evolution, reproductive biology with an emphasis on anther development, genomics tools and technologies, and genome informatics. He has been recognized with numerous awards and honors, including election to the US National Academy of Sciences in 2022, the Charles Albert Shull Award from the American Society of Plant Biologists in 2017, and election as a Fellow of the American Society of Plant Biologists in 2017. Additionally, he serves as the Editor-in-Chief of The Plant Cell and has been involved in advancing plant science through his leadership and research contributions.

Research topics

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

Selected publications

• Stage‐Specific RNA Turnover Drives Small RNA Dynamics in <i>Arabidopsis</i> – <i>Colletotrichum</i> Interactions

  Plant Direct · 2026-05-01

  articleOpen access

  ABSTRACT Small RNAs (sRNAs) are key regulators of plant defense and have been implicated in cross‐kingdom interactions with pathogens. The hemibiotrophic fungus Colletotrichum higginsianum infects Arabidopsis thaliana through three stages: appressorial penetration, biotrophy, and necrotrophy. However, the dynamics of fungal and plant sRNA populations across these three stages have not been elucidated. Using high‐throughput sequencing, we profiled sRNAs from A. thaliana and C. higginsianum during in planta appressorium (PA), biotrophic (BP), and necrotrophic (NP) phases, and compared them to fungal mycelia (MY) and in vitro appressoria (VA). Our analyses revealed stage‐specific patterns in sRNA accumulation in both the plant and the pathogen. In C. higginsianum , sRNAs were dominated by 29 nt species in PA, BP, MY, and VA, but shifted to 18 nt in NP, consistent with RNA degradation during host cell death. In A. thaliana , sRNAs transitioned from 30–33 nt in PA/BP to a 21 nt dominant peak in NP. Also, TE‐derived siRNAs and other regulatory sRNAs (miRNAs, ncRNA, snoRNAs, and snRNAs) declined during NP. A total of 62 host miRNAs showed differential accumulation, including core plant developmental regulators active across infection stages, and stage‐specific miRNAs such as miR396, miR170/171, miR472, and miR858b. tRFs displayed opposite trends in host and pathogen: fungal tRFs declined in NP, while host tRFs increased. These tRFs' contrasting trends may reflect differences in RNA processing or degradation between host and pathogen. Our results provide new insights into RNA‐mediated plant–fungal interactions.

  PublisherDOI

• Long-distance transport of siRNAs with functional roles in pollen development

  Nature Plants · 2026-01-28

  articleOpen access

  Small interfering RNAs (siRNAs) play a crucial role in plant reproduction, yet their mobility and function remain incompletely understood. We report that a large proportion of siRNAs found in pollen of Capsella rubella relies on mobile siRNAs from maternal sporophytic tissues, highlighting the importance of non-cell-autonomous siRNAs in male gametophyte development. Unlike tapetal siRNAs, which guide DNA methylation and require CLASSY3 and DNA-dependent RNA polymerase IV (Pol IV) activity in the tapetum, we found that Pol IV-dependent mobile siRNAs (PMsiRNAs) mainly function post-transcriptionally and do not guide DNA methylation. Nevertheless, PMsiRNAs share key features with tapetal siRNAs, including Pol IV dependency, clustering and a size range of 21-24 nucleotides. Using a grafting approach, we show that sporophytic Pol IV-dependent siRNAs act as non-cell-autonomous mobile signals that trigger PMsiRNA formation through post-transcriptional gene silencing. This process parallels reproductive phased siRNA biogenesis, which is widespread across angiosperms but has been considered absent in Brassicaceae. Loss of PMsiRNAs causes pollen arrest, underscoring their essential role. Together, these findings highlight siRNAs as long-distance communication signals from maternal sporophytic tissues to the male gametophyte with critical functions in developmental regulation.

  PublisherDOI

• The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat <i>Triticum turgidum</i> cv Kronos

  New Phytologist · 2026-02-22

  articleOpen access

  Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. 3000 exome-capture (EC) and promoter-capture (PC) datasets linked to mutagenized seed stocks, along with extensive transcriptomic and phenotypic resources. However, the absence of a reference genome has constrained their full utility. We assembled a chromosome-scale reference genome for Kronos, with high-confidence annotations, including manual curation of over 1000 disease resistance (nucleotide-binding leucine-rich repeat (NLR)) genes and genome-wide identification of microRNAs and phasiRNAs. We additionally reanalyzed EC and PC data to capture mutational landscapes across ethyl methane sulphonate-mutagenized Kronos populations. We revealed previously hidden NLR diversity and resolved their genomic organization at chromosomal ends. Re-analysis of capture datasets enabled high-resolution mutation discovery in genes and regulatory regions, providing a more comprehensive view of the variations detectable in the Kronos mutant populations. Collectively, these resources provide a reference-quality genomic framework for Kronos and position it as a versatile platform for functional and translational wheat research.

  PublisherOA PDFDOI

• A multi-omics approach to maize ( <i>Zea mays</i> ) tassel development

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-02

  articleOpen access

  The development of the male inflorescence in maize ( Zea mays L.) is a complex and highly regulated process that is essential for reproductive success and yield. To gain a comprehensive understanding of the regulatory programs involved in tassel formation, including the initial specification of anther cell types, the transcriptomes, small RNAs (sRNAs), and proteomes were profiled at four developmental stages (0.5–2.0 cm). The RNAseq analysis indicates dynamic shifts in gene expression underlying the transition from indeterminate meristems to organ initiation and germinal cell determination by 2.0 cm. Complementing these data, sRNA sequencing uncovered 182 microRNAs (miRNAs) with distinct temporal patterns. A core set of 126 miRNAs was expressed throughout tassel development, while others displayed strong stage-specific enrichment. Notably, families of miRNAs that target auxin signaling were dynamically regulated, suggesting fine-tuning of hormone signaling in relation to meristem activity. Later stages were enriched for miR2275 and miR11969, which previously have both been associated with meiocytes, indicating the onset of reproductive sRNA pathways during the early stages of anther differentiation. Together, these datasets provide a broad overview of tassel development and form a backbone to enrich existing RNAseq and single cell RNAseq data sets of specific steps in tassel and initial anther development, while also adding new data on sRNA expression.

  PublisherOA PDFDOI

• Stage-Specific RNA Turnover Drives Small RNA Dynamics in <i>Arabidopsis</i> – <i>Colletotrichum</i> Interactions

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-27

  articleOpen access

  Abstract Small RNAs (sRNAs) are key regulators of plant defense and have been implicated in cross-kingdom interactions with pathogens. The hemibiotrophic fungus Colletotrichum higginsianum infects Arabidopsis thaliana through three stages: appressorial penetration, biotrophy, and necrotrophy. However, the dynamics of fungal and plant sRNA populations across these three stages have not been elucidated. Using high-throughput sequencing, we profiled sRNAs from A. thaliana and C. higginsianum during in planta appressorium (PA), biotrophic (BP), and necrotrophic (NP) phases, and compared them to fungal mycelia (MY) and in vitro appressoria (VA). Our analyses revealed stage-specific patterns in sRNA accumulation in both the plant and the pathogen. In C. higginsianum , sRNAs were dominated by 29 nt species in PA, BP, MY, and VA, but shifted to 18 nt in NP, consistent with RNA degradation during host cell death. In A. thaliana , sRNAs transitioned from 30-33-nt in PA/BP to a 21 nt dominant peak in NP. Also, TE-derived siRNAs and other regulatory sRNAs (miRNAs, ncRNA, snoRNAs and snRNAs) declined during NP. A total of 62 host miRNAs showed differential accumulation, including core plant developmental regulators active across infection stages, and stage-specific miRNAs such as miR396, miR170/171, miR472, and miR858b. tRFs displayed opposite trends in host and pathogen: fungal tRFs declined in NP, while host misc-tRFs, 5′-tRFs, and 3′-tRFs increased, suggesting contrasting regulatory roles. These results provide new insights into RNA-mediated plant-fungal interactions.

  PublisherOA PDFDOI

• Chromosome-level genome assembly of Triticum turgidum var 'Kronos' additional datasets

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-20

  datasetOpen access

  This data is made available under the Toronto Agreement. All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you agree to: respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication. not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories. contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses. fully cite the prepublication data along with any applicable versioning details. understand that this data as accessed is precompetitive and is not patentable in its present state. This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). https://doi.org/10.1038/461168a If you have questions about the use of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu Updates in Zenodo v6This release includes ~70 Mb of putative NLR loci together with transcriptomic data mapped to these regions, which were used for manual curation and validation. These datasets can be directly loaded into standard genome browsers (e.g., IGV), allowing users to visually inspect annotation models and match them to supporting transcriptomic evidence. Note that a small subset of gene models underwent additional post-processing and may not be fully represented in this dataset. Acknowledgement This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726). Please, feel free to reach out to us regarding this datasets

  PublisherDOI

• Reproductive phasiRNAs are the piRNAs of plants

  Trends in Genetics · 2026-01-27

  articleOpen accessSenior author

  Small RNAs are fundamental to gene expression regulation, with specialized classes playing critical roles in reproduction. This review compares animal PIWI-interacting RNAs (piRNAs) and plant reproductive phased small interfering RNAs (phasiRNAs), which show remarkable similarities. Both originate from Pol II-transcribed precursors but have distinct biogenesis pathways. piRNA processing in metazoans is Dicer-independent, involving PIWI-clade proteins for amplification via 'ping-pong' and phased cleavage. Reproductive phasiRNAs are Dicer-dependent and are initiated by miRNA-guided cleavage to generate phased sRNAs. A well-defined piRNA function is transposon silencing, but roles for nontransposon-targeting piRNAs and most reproductive phasiRNAs remain unresolved. Comparing these independently evolved systems reveals common strategies for reproductive success and highlights key unresolved questions regarding their molecular targets, functions, and evolutionary pressures that shaped them.

  PublisherDOI

• <i>DICER-LIKE 5</i> loss causes thermosensitive male sterility in durum wheat and reveals an AU-rich motif guiding 24-nt phasiRNA biogenesis

  Proceedings of the National Academy of Sciences · 2025-07-30 · 4 citations

  articleOpen accessSenior authorCorresponding

  Reproductive, male-enriched small RNAs are present in flowering plants and animals, yet their role in plants remains underexplored. We generated dicer-like 5 ( dcl5 ) mutants in durum wheat ( Triticum turgidum ssp. durum 2n = 4× = 28; AABB), revealing temperature-sensitive genic male sterility. Loss of DCL5 depleted premeiotic and meiotic 24-nt phasiRNA production, correlating with sterility under standard growth conditions and partial fertility recovery at higher temperatures. A single functional DCL5 allele restored complete fertility, presenting a promising alternative to current methods for hybrid production. We demonstrate that premeiotic 24-nt phasiRNA biogenesis is independent of miRNA-mediated cleavage and driven by a conserved motif initiating DCL5 activity. In the dcl5 mutant developing under sterility-inducing conditions, developmental defects are observed during pollen maturation, rather than at peak 24-nt phasiRNA accumulation in premeiotic and meiotic anthers. Although no visible morphological abnormalities were apparent during early development, single-cell RNA sequencing revealed that dcl5 mutant cells exhibit transcriptional profiles distinct from those of wild-type cells, when premeiotic 24-nt phasiRNAs are accumulating at the early developmental stage. Finally, the coexpression of Argonaute ( AGO1b , AGO4a, and AGO6 ) homeologs in 24-nt phasiRNA-producing cells identifies candidate effectors and suggests a role for 24-nt phasiRNAs in transcriptional gene silencing.

  PublisherOA PDFDOI

• Genetic variation in a tandemly duplicated <scp>TPS</scp> gene cluster contributes to the diversity of aroma in lychee fruit

  New Phytologist · 2025-03-27 · 11 citations

  articleOpen access

  Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

  PublisherOA PDFDOI

• Transcriptional dynamics of nitrogen fixation and senescence in soybean nodules: A dual perspective on host and <i>Bradyrhizobium</i> regulation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-06

  preprintOpen access

  ABSTRACT The Soybean– Bradyrhizobium symbiosis enables symbiotic nitrogen fixation (SNF) within root nodules, reducing reliance on synthetic N-fertilizers. However, nitrogen fixation is transient, peaking several weeks after Bradyrhizobium colonization and declining as nodules senesce in coordination with host development. To investigate the regulatory mechanisms governing SNF and senescence, we conducted a temporal transcriptomic analysis of soybean nodules inoculated with Bradyrhizobium diazoefficiens USDA110. Weekly nodule samples (2–10 weeks post-inoculation, wpi) were analyzed using RNA and small RNA sequencing, while acetylene reduction assays assessed nitrogenase activity from 4 to 7 wpi. We identified three major nodule developmental phases: early development (2–3 wpi), nitrogen fixation (3–8 wpi), and senescence (8–10 wpi). Soybean showed extensive transcriptional reprogramming during senescence, whereas Bradyrhizobium underwent major transcriptional shifts early in development before stabilizing during nitrogen fixation. We identified seven soybean genes and several microRNAs as candidate biomarkers of nitrogen fixation, including lipoxygenases ( Lox ), suggesting roles for oxylipin metabolism. Soy hemoglobin-2 ( Hb2 ), previously classified as non-symbiotic, was upregulated during senescence, implicating oxidative stress responses within aging nodules. Upregulation of the Bradyrhizobium paa operon and rpoH during senescence suggested metabolic adaptation for survival beyond symbiosis. Additionally, Bradyrhizobium NIF gene expression showed stage-specific regulation, with nifK peaking at 2 wpi, nifD and nifA at 2 and 10 wpi, and nifH , nifW , and nifS at 10 wpi. These findings provide insights into SNF regulation and nodule aging, revealing temporal gene expression patterns that could inform breeding or genetic engineering strategies to enhance nitrogen fixation in soybeans and other legume crops.

  PublisherOA PDFDOI

Recent grants

• Understanding the Rice Epigenome: From Genes to Genomes

  NSF · $5.9M · 2007–2013

• IOS: The Function and Evolution of Plant Phased siRNAs in Signaling Pathways and Microbial Interactions

  NSF · $423k · 2016–2018

• Deep Transcriptional Profiling of Rice Using Signature Sequencing

  NSF · $4.2M · 2003–2008

• Signature Sequencing for Quantitative Expression Analysis and Gene Discovery

  NSF · $967k · 2001–2002

• RCN: An International Arabidopsis Informatics Consortium

  NSF · $500k · 2011–2016

Frequent coauthors

• Jixian Zhai

  Southern University of Science and Technology

  152 shared

• Pamela J. Green

  124 shared

• Kan Nobuta

  86 shared

• Kun Huang

  First Affiliated Hospital of Harbin Medical University

  81 shared

• Rui Xia

  Tsinghua University

  77 shared

• Stacey A. Simon

  University of Delaware

  73 shared

• Sandra M. Mathioni

  73 shared

• Siwaret Arikit

  72 shared

Education

• PhD, Genetics

  University of California Davis

  1998

• MS, Genetics

  University of California Davis

  1995

• BA, Biology

  University of Chicago

  1992

Awards & honors

• Elected Member, US National Academy of Sciences (2022)
• University of Missouri Award for Faculty Excellence (2022)
• Editor-in-Chief, The Plant Cell (2020 – 2024)
• Elected Fellow, American Society of Plant Biologists (ASPB)…
• Charles Albert Shull Award, American Society of Plant Biolog…