About

John Mullet is the Perry L. Adkisson Chair in Agricultural Biology and a Professor in the Department of Biochemistry and Biophysics at Texas A&M University. His research focuses on developing next-generation crops through the study of genomics, gene regulatory networks, development, drought resilience, and bioenergy crop design. Mullet's laboratory collaborates with scientists from DOE Bioenergy Research Centers and the National Labs to acquire knowledge that enables the design of climate-resilient bioenergy crops using genetic, genomic, and biochemical approaches. His work includes constructing transcriptome compendiums of bioenergy sorghum, identifying gene regulatory networks, and engineering pathways to improve plant productivity, resilience, and sustainability. Additionally, his research involves engineering sorghum stems to accumulate higher levels of biopolymers such as wax, terpenoids, and starch, and studying deep roots that enhance drought resilience and reduce greenhouse gas emissions. Mullet's contributions are aimed at addressing global food, feed, biofuel, and bioproduct needs by improving crop productivity and environmental sustainability.

Research topics

• Environmental science
• Biology
• Computational biology
• Geography
• Chemistry
• Geology
• Genetics
• Geomorphology
• Soil science
• Agronomy
• Forestry

Selected publications

• Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

  The Plant Journal · 2026-05-01

  articleOpen accessSenior authorCorresponding

  Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

  PublisherDOI

• A sorghum pangenome reference improves global crop trait discovery

  Nature · 2026-03-11 · 6 citations

  articleOpen access

  Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the grain and bioenergy crop sorghum2–5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets6. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops. A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.

  PublisherDOI

• Bioenergy sorghum stem density increases threefold following internode elongation due to continued accumulation of lignified cell walls and complex regulation of genes involved in cell wall biosynthesis

  Biotechnology for Biofuels and Bioproducts · 2025-06-04 · 1 citations

  articleOpen accessSenior author

  Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates ~ 80% of its harvested biomass in ~ 4 m long stems comprised of > 40 internodes that develop sequentially during an extended vegetative growth phase. Following elongation of each internode, internode density increases ~ threefold to fourfold primarily due to the accumulation of cell walls composed of cellulose, glucuronoarabinoxylan and lignin. Lignin accumulates initially on cell walls of sclerenchyma cells surrounding vascular bundles and later on cell walls of the stem rind and stem core pith parenchyma. Many genes involved in cell wall biosynthesis were expressed continuously during the stem internode densification process whereas others showed dynamic patterns of expression (high to low, low to high). Several CESA genes involved in primary cell wall cellulose synthesis were expressed in the stem rind and core throughout the stem densification phase. In contrast, CESA genes involved in secondary cell wall biogenesis were expressed continuously in the stem rind but downregulated in the stem core shortly after completion of internode elongation. Overall, accumulation of cell wall biomass in elongated internodes during stem densification increases stem mechanical strength and biomass bulk density while modifying biomass composition in ways that could impact the amount and release of cellulosic sugars and lignin-derived bioproducts.

  PublisherOA PDFDOI

• NMR of Roots in Soil Grown in Field and Greenhouse Conditions

  2025-07-18

  book-chapter

  Intact plant roots are notoriously challenging to study, especially in natural soils due to their opacity and, even when the roots are laboriously washed, there can be breakage and loss of root biomass. Low-field MRI is a promising technology for studying roots in situ. This chapter explores hardware and methodology to do these experiments both in the agricultural field and in the greenhouse. Different magnet designs are discussed with Larmor frequencies ranging from 1.8 MHz to 20 MHz with imaging regions up to 25 cm in diameter. Root MRI in most field soils works well at these field strengths. Imaging intact roots will allow in situ phenotyping, which will, in turn, enable climate-smart plant breeding.

  PublisherDOI

• Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

  BMC Plant Biology · 2025-10-01

  articleOpen access

  BACKGROUND: Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4-5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified. RESULTS: To address these gaps, we reanalyzed a published RNA-seq dataset to identify genes with organ-preferential expression and to infer representative organ functions across major developmental stages. Our analysis revealed that the sorghum stem exhibits distinct temporal functional signatures, which correlate with the developmental dynamics of stem-specific genes and their associated regulatory elements. We further identified a set of genes with ubiquitous stem-specific expression across diverse sorghum genotypes, suggesting their universal importance and broad potential for genetic engineering applications. Among them, SbTALE03 and SbTALE04 emerged as stem hub transcription factors (TF). Both genes were empirically validated for their stem specificity across stages. Gene regulatory network analysis further indicated that these TFs participate in stage-specific transcriptional programs that maintain and regulate stem development. CONCLUSIONS: This study presents a genome-wide analysis of organ-specific gene expression, functions, and regulatory networks in sorghum, with a focus on genes preferentially-expressed in stems and their promoter motifs. We identified a set of core stem-specific genes with ubiquitous expression across genotypes and developmental stages, including two experimentally validated transcription factors with potential roles in stem development. These findings offer valuable candidates for further functional characterization and genetic engineering aimed at improving sorghum stem biomass and composition.

  PublisherOA PDFDOI

• Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-30 · 1 citations

  preprintOpen access

  Background Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 meters in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified. Results To address these gaps, we reanalyzed a published RNA-seq dataset to identify genes with organ-preferential expression and to infer representative organ functions across major developmental stages. Our analysis revealed that the sorghum stem exhibits distinct temporal functional signatures, which correlate with the developmental dynamics of stem-specific genes and their associated regulatory elements. We further identified a set of genes with ubiquitous stem-specific expression across diverse sorghum genotypes, suggesting their universal importance and broad potential for genetic engineering applications. Among them, SbTALE03 and SbTALE04 emerged as stem hub transcription factors (TF). Both genes were empirically validated for their stem specificity across stages. Gene regulatory network analysis further indicated that these TFs participate in stage-specific transcriptional programs that maintain and regulate stem development. Conclusions This study presents a genome-wide analysis of organ-specific gene expression, functions, and regulatory networks in sorghum, with a focus on genes preferentially-expressed in stems and their promoter motifs. We identified a set of core stem-specific genes with ubiquitous expression across genotypes and developmental stages, including two experimentally validated transcription factors with potential roles in stem development. These findings offer valuable candidates for further functional characterization and genetic engineering aimed at improving sorghum stem biomass and composition.

  PublisherOA PDFDOI

• Amino acid substrate specificities and tissue expression profiles of the nine <scp>CYP79A</scp> encoding genes in <i>Sorghum bicolor</i>

  Physiologia Plantarum · 2025-01-01 · 8 citations

  articleOpen access

  Cytochrome P450s of the CYP79 family catalyze two N-hydroxylation reactions, converting a selected number of amino acids into the corresponding oximes. The sorghum genome (Sorghum bicolor) harbours nine CYP79A encoding genes, and here sequence comparisons of the CYP79As along with their substrate recognition sites (SRSs) are provided. The substrate specificity of previously uncharacterized CYP79As was investigated by transient expression in Nicotiana benthamiana and subsequent transformation of the oximes formed into the corresponding stable oxime glucosides catalyzed by endogenous UDPG-glucosyltransferases (UGTs). CYP79A61 uses phenylalanine as a substrate, whereas CYP79A91, CYP79A93, and CYP79A95 use valine and isoleucine as substrates, with CYP79A93 showing the ability also to use phenylalanine. CYP79A94 uses isoleucine as a substrate. Analysis of 249 sorghum transcriptomes from two different sorghum cultivars showed the expression levels and tissue-specific expression of the CYP79As. CYP79A1 is the committed gene in dhurrin formation and was the highest expressed gene in most tissues/organs. CYP79A61 was primarily expressed in fully developed leaf blades and leaf sheaths. CYP79A91 and CYP79A92 were expressed mainly in roots >200 cm below ground, while CYP79A93 and CYP79A94 were most highly expressed in the leaf collar and leaf sheath, respectively. The possible signalling effects of the oximes and their metabolites produced in different sorghum tissues are discussed.

  PublisherDOI

• Developing future resilience from signatures of adaptation across the sorghum pangenome

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-06 · 1 citations

  preprintOpen access

  While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum, and many other crops that were not homogenized during the green revolution, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

  PublisherOA PDFDOI

• Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

  Frontiers in Plant Science · 2024-10-21 · 1 citations

  articleOpen accessSenior authorCorresponding

  Bioenergy sorghum’s large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop’s resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7 th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17 th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation ( WOX4 ), auxin transport ( LAX2, PIN4 ), meristem activation ( NGAL2 ), and genes involved in cell proliferation. Expression of WOX11 and WOX5 , genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5 , SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO , a gene involved in root cap formation, and GATA19 , BBM , LBD29 and RITF1 /RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.

  PublisherDOI

• Correction for Mechan-Llontop et al., “Genome-sequenced bacterial collection from sorghum epicuticular wax”

  Microbiology Resource Announcements · 2024-07-01

  erratumOpen access

  Vol. 12, no. 12, e00484-23, 2023, https://journals.asm.org/doi/10.1128/mra.00484-23. Page 3, Table 1: Isolate ID SORGH_AS_961 identified as “Pseudacidovorax intermedius” should read “Chryseobacterium sp.”

  PublisherDOI

Recent grants

• NIH Grant R01GM037987

  NIH · $1.8M · 2000

• Gene Mapping in Sorghum Using Direct Selection Technology

  NSF · $740k · 2000–2003

Frequent coauthors

• Robert R. Klein

  Southern Plains Agricultural Research Center

  121 shared

• Kankshita Swaminathan

  HudsonAlpha Institute for Biotechnology

  110 shared

• Daryl T. Morishige

  Texas A&M University

  109 shared

• Amy Marshall‐Colón

  University of Illinois Urbana-Champaign

  109 shared

• Lee H. Pratt

  73 shared

• Marie‐Michèle Cordonnier‐Pratt

  University of Georgia

  72 shared

• Henry T. Nguyen

  University of Missouri

  69 shared

• Feng Sun

  Institute of Plant Protection

  68 shared

Education

• B.S.

  Colgate University

• Ph.D.

  University of Illinois

• Other

  Rockefeller University