About

Zhantao Chen is an Assistant Professor in the Walker Department of Mechanical Engineering at The University of Texas at Austin. He leads the Group for AI in Materials Modeling and Analytics (GAMMA). Prior to joining UT Austin in 2025, Dr. Chen was a Research Associate at SLAC National Accelerator Laboratory from 2022 to 2025. He earned his Ph.D. in Mechanical Engineering from the Massachusetts Institute of Technology in 2022. His research develops artificial intelligence and machine learning methods for materials modeling, characterization, and discovery, with the vision of enabling AI-driven autonomous research platforms. His long-term goal is to integrate design, synthesis, and characterization into closed-loop, intelligent workflows that accelerate materials discovery and advance fundamental materials science.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Agronomy
• Cell biology
• Ecology
• Endocrinology
• Botany
• Computational biology

Selected publications

• Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance

  The Plant Genome · 2025-06-01 · 5 citations

  reviewOpen access1st authorCorresponding

  Advancements in genomic and epigenetic research in both plants and animals have transformed breeding methods and biotechnological strategies for crop improvement, particularly in the face of extreme weather challenges. These breakthroughs in plant biology and agriculture have laid a strong foundation for ensuring food security, promoting environmental sustainability, enhancing nutritional health, and driving basic science advances, as exemplified by Mendel's discovery of genetic principles and McClintock's discovery of transposable elements. Plant epigenetics has held a transformative potential for developing high-yielding and resilient crops. In this review, I will examine various relevant epigenetic phenomena, including nucleolar dominance, paramutation, imprinting, somaclonal variation, and transgenerational epigenetic inheritance, to explore strategies for overcoming yield limitations in an increasingly volatile climate. This perspective aligns with the vision for plant breeding and sustainable agriculture championed by the late Professor Ronald L. Phillips.

  PublisherOA PDFDOI

• <scp>SCL15</scp> Regulates the Release of Seed Dormancy in <scp> <i>Arabidopsis thaliana</i> </scp> by Integrating the Circadian Clock, Hormonal Signals and Cell Wall Remodelling

  Physiologia Plantarum · 2025-09-01 · 2 citations

  articleOpen access

  Dormancy release and germination of the seed are two separate, but continuous phases controlled by both external (e.g., light and temperature) and internal (e.g., circadian clock and hormones) cues. In eudicot seeds, the endosperm tissues play a key role in dormancy release and germination through dynamic modulation of wall components and biomechanics. However, the mode of action by which the circadian oscillator influences dormancy release by modulation of endosperm wall biomechanics remains elusive. SCARECROW-LIKE15 (SCL15) represses embryonic gene expression in seedlings through interaction with HISTONE DEACETYLASE19 (HDA19) in Arabidopsis thaliana. Here, we report that SCL15 plays a positive role in primary dormancy release, which is associated with gene expression changes in circadian, abscisic acid, auxin and cell wall (CW) remodelling pathways, based on studies using SCL15 mutant and Napin promoter-driven SCL15 expression lines. SCL15 was found to affect the expression of genes whose products modify endosperm wall biomechanical features, possibly through regulation of local auxin accumulation and evening-phased clock components. RNA-seq analysis supported the notion that dormancy release is associated with changes in the expression of genes associated with circadian and hormone-mediated pathways, which in turn affect CW structure.

  PublisherOA PDFDOI

• Transgenerational epigenetic inheritance during plant evolution and breeding

  Trends in Plant Science · 2024-05-28 · 52 citations

  reviewOpen accessSenior author
  PublisherOA PDFDOI

• Genome resources for three modern cotton lines guide future breeding efforts

  Nature Plants · 2024-05-30 · 32 citations

  articleOpen access

  Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

  PublisherOA PDFDOI

• Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

  Communications Biology · 2024-05-16 · 50 citations

  reviewOpen accessSenior authorCorresponding

  As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.

  PublisherOA PDFDOI

• Cytoplasmic genome contributions to domestication and improvement of modern maize

  BMC Biology · 2024-03-13 · 8 citations

  articleOpen accessSenior author

  BACKGROUND: Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated. RESULTS: Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes. CONCLUSIONS: Our results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.

  PublisherOA PDFDOI

• Imprinting but not cytonuclear interactions determines seed size heterosis in Arabidopsis hybrids

  PLANT PHYSIOLOGY · 2024-02-06 · 5 citations

  articleOpen accessSenior author

  The parent-of-origin effect on seeds can result from imprinting (unequal expression of paternal and maternal alleles) or combinational effects between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding factors, we produced cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in Arabidopsis (Arabidopsis thaliana) ecotypes Col-0 and C24. These CNS lines differed only in the nuclear genome (imprinting) or cytoplasm. The CNS reciprocal hybrids with the same cytoplasm displayed ∼20% seed size difference, whereas the seed size was similar between the reciprocal hybrids with fixed imprinting. Transcriptome analyses in the endosperm of CNS hybrids using laser-capture microdissection identified 104 maternally expressed genes (MEGs) and 90 paternally expressed genes (PEGs). These imprinted genes were involved in pectin catabolism and cell wall modification in the endosperm. Homeodomain Glabrous9 (HDG9), an epiallele and one of 11 cross-specific imprinted genes, affected seed size. In the embryo, there were a handful of imprinted genes in the CNS hybrids but only 1 was expressed at higher levels than in the endosperm. AT4G13495 was found to encode a long-noncoding RNA (lncRNA), but no obvious seed phenotype was observed in lncRNA knockout lines. Nuclear RNA Polymerase D1 (NRPD1), encoding the largest subunit of RNA Pol IV, was involved in the biogenesis of small interfering RNAs. Seed size and embryos were larger in the cross using nrpd1 as the maternal parent than in the reciprocal cross, supporting a role of the maternal NRPD1 allele in seed development. Although limited ecotypes were tested, these results suggest that imprinting and the maternal NRPD1-mediated small RNA pathway play roles in seed size heterosis in plant hybrids.

  PublisherOA PDFDOI

• Ploidy variation induces butterfly effect on chromatin topology in wheat

  The Plant Journal · 2024-07-14 · 4 citations

  articleOpen access

  Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.

  PublisherOA PDFDOI

• Faculty Opinions recommendation of Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.

  Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2023-04-11

  dataset1st authorCorresponding
  PublisherDOI

• Faculty Opinions recommendation of Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers.

  Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2023-04-03

  dataset1st authorCorresponding
  PublisherDOI

Recent grants

• EAGER: Dosage and Small RNA Regulation of Imprinting and Seed Development

  NSF · $359k · 2011–2015

• Functional and Sequence Analysis of Fiber Development in Allotetraploid Cotton

  NSF · $3.9M · 2010–2017

• Sequencing a Reference-grade Genome of the Domesticated Allotetraploid Cotton: the World's Largest Source of Renewable Textile Fiber

  NSF · $2.2M · 2015–2019

• Genomic and Functional Analysis of Circadian Rhythms and Growth Vigor in Maize

  NSF · $1.5M · 2013–2018

• Genetic and Functional Genomic Analysis of Early Events in Cotton Fiber Development

  NSF · $2.2M · 2005–2010

Frequent coauthors

• Qingxin Song

  Nanjing Agricultural University

  62 shared

• Wenxue Ye

  Nanjing Agricultural University

  32 shared

• Shuai Cao

  21 shared

• Tongwen Han

  Shandong Agricultural University

  17 shared

• Misook Ha

  Samsung (South Korea)

  15 shared

• David M. Stelly

  Mitchell Institute

  15 shared

• Longfei Wang

  Nanjing Agricultural University

  15 shared

• Atsumi Ando

  The University of Texas at Austin

  14 shared

Education

• Ph.D., Mechanical Engineering

  Massachusetts Institute of Technology

  2022