2024 IGCAST Annual Report

2024 IGCAST ANNUAL REPORT

Index Message from the IGCAST Director

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Herrera-Estrella Lab

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Tran Lab

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Lopez-Arredondo Lab

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Jiao Lab

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Liu Lab

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Janga Lab

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Patil Lab

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Funding

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Reinforcing Institutional Collaborations

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Advanced agricultural science through high-through put phenotyping system

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Dissertation Defenses

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Engagement and Outreach Programs

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IGCAST Symposium 2024

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Recognition

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IGCAST Members 2024

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IGCAST Publication list 2024

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Message from the IGCAST Director

Understanding the Genomic and Metabolic Networks that Enable Plants to Survive Stress.

Crops today face an escalating threat from abiotic stresses—environmental challenges like drought, extreme heat, and nutrient-poor or compacted soils.

These stressors are becoming more intense due to climate change, unsustainable farming practices, and over-mechanized agriculture. As a result, farmers are experiencing significant economic losses, and global food security is at increasing risk.

At IGCAST, our mission is to develop advanced tools and conduct groundbreaking research to understand how environmental factors interact with the genetic makeup of crops. This knowledge is essential for improving crop yields and creating sustainable agricultural practices capable of enduring in a rapidly changing world.

Our research focuses on decoding the intricate genomic and metabolic networks that control how plants respond to stress. We are also developing innovative technologies that make plant transformation and gene editing faster, more efficient, and more affordable to speed up plant research and crop improvement. By sequencing the genomes of plants and microalgae that thrive in extreme environments, we gain critical insights into their molecular responses using state-of-the-art techniques like transcriptomics, metabolomics, proteomics, and singlecell analysis. Additionally, we're working to reduce the reliance on harmful agrochemicals, promoting more sustainable farming practices.

A key part of our mission is to train the next generation of scientists, equipping them with the knowledge and skills to drive advances in food security and sustainability in academia and industry.

The insights we’re gaining are vital for developing more resilient crops that can withstand harsh conditions and ensure global food security in an increasingly unpredictable climate. At IGCAST, we are committed to pioneering innovative solutions to protect our food systems for future generations.

Dr. Luis Herrera-Estrella

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Herrera-Estella Lab

The Genomic and Metabolic Networks Governing Plant Responses to Abiotic Stress. Crops face a growing threat from abiotic stresses— environmental challenges such as drought, heat, and nutrient-poor or compacted soils—that reduce productivity and cause farmers significant economic losses. These stressors have become even more prevalent in recent decades, driven by climate change and excessive mechanization and grassing of land. Understanding how these environmental factors interact with a crop's genetic makeup is critical for optimizing yields and developing effective agricultural strategies.

Our research program aims to enhance the understanding of the genomic and metabolic networks that regulate plant responses to abiotic stress. We primarily focus on the role of roots in stress tolerance and strive to reveal the mechanisms that enable plants to withstand desiccation and recover after rehydration. This knowledge will be essential for improving crop resilience and ensuring food security in a changing environment climate.

Key Research Areas Gene Regulatory and Metabolic Networks in Desiccation Tolerance: Identifying and characterizing the gene networks that enable plants to tolerate desiccation, focusing on the molecular mechanisms that support survival under extreme water stress.

Phosphate Deprivation Sensing and Signaling: Investigating the sensors and signaling pathways that trigger both local and systemic responses in plants to phosphate deficiency, with the goal of enhancing nutrient use efficiency.

Genomics of Nutraceutical and Medicinal Plants: Exploring the genetic underpinnings of plant species with medicinal or nutraceutical properties to unlock their potential for human health applications.

Modulating Root Architecture for Carbon Sequestration: Developing genetic and genomic approaches to manipulate root structure to boost plant carbon sequestration and contribute to climate change mitigation.

Major discoveries Isolation of Arabidopsis mutants affected in the systemic and local sensing of phosphate.

Characterization of the gene regulatory networks involved in desiccation tolerance in Selaginella resurrection plants.

Effects of ploidy levels on changes in chromatin accessibility and its use in plant breeding.

Relevant publications Alejo-Jacuinde, G., Chávez Montes, R.A., Gutierrez Reyes, C.D., YongVillalobos, L., Simpson, J., Herrera-Estrella, L. (2024). Gene family rearrangements and transcriptional priming drive the evolution of vegetative desiccation tolerance in Selaginella. The Plant Journal, (2024). https://doi: 10.1111/tpj.17169.

Bello-Bello, E., Herrera-Estrella, L. (2024). Breaking new ground: Decoding the root’s molecular circuits to penetrate compacted soil.

Developmental Cell, Vol.59, Issue 4, page 431-433. https://doi.org/10.1016/j.devcel.2024.01.028.

Pérez-Zavala, F.G., Ojeda-Rivera, J.O., Herrera-Estrella, L., LópezArredondo, D. (2024). Beneficial Effects of Phosphite in Arabidopsis thaliana Mediated by Activation of ABA, SA, and JA Biosynthesis and Signaling Pathways. Plants 2024, Volume 13, Issue 13, 1873. https://doi.org/10.3390/plants13131873.

Research subjects Molecular elucidation of hormonal regulatory networks in plant responses to environmental stresses.

Roles of hormone and non-hormone signaling molecules in environmental stress adaptation.

Elucidation and exploration of plant-microbe interactions for improvement of plant responses and adaptation to environmental stresses.

Functional genomics of food crops for improvement of crop productivity in adverse conditions.

Figure 1. Model of the molecular mechanisms modulating the inhibition of root elongation and penetration in compacted soil.

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Tran Lab

The world population has been rapidly increasing, making food security a major issue in many countries. In addition, climate change also puts a great burden on food production. Environmental stresses, such as drought, extreme temperatures, high salinity, nutrient deficiency, soil erosion, and pollutants affect crop production yield and stability, thereby threatening sustainable agriculture.

Our research group has interests in (i) studying the roles of signaling molecules and their interactions in plant responses and adaptation to environmental stresses, (ii) plant-microbe interactions for improvement of plant responses and adaptation to environmental stresses, as well as (iii) translational genomics aiming to enhance crop productivity under adverse environmental stress conditions.

Research subjects Molecular elucidation of hormonal regulatory networks in plant responses to environmental stresses.

Roles of hormone and non-hormone signaling molecules in environmental stress adaptation.

Elucidation and exploration of plant-microbe interactions for improvement of plant responses and adaptation to environmental stresses.

Functional genomics of food crops for improvement of crop productivity in adverse conditions.

Relevant publications Le TD, Ha CV, Nguyen KH, Chu HD, Zhu C, Li W, Watanabe Y, Kojima M, Takebayashi Y, Sakakibara H, Mochida K, Tran L-SP (2024). Altering endogenous cytokinin content by GmCKX13 as a strategy to develop drought-tolerant plants. Plant Stress 11:100678.

Gupta, A., Li, L., Zhu, C., Kun, K.,Jia, K.,Miao, Y., Li, W.,Tran, L.-S. P. (2024).

Differential modulation of hormonal pathways by strigolactone and karrikin signaling. Plant Growth Regul 104, 1197–1205. https://doi.org/10.1007/s10725-024-01227-w.

Rahman, M.M., Mostofa, M.G., Keya, S.S., Ghosh, P.K., Abdelrahman, M., Anik, T.R., Gupta, A., Tran, L.-S.P. (2024). Jasmonic acid priming augments antioxidant defense and photosynthesis in soybean to alleviate combined heat and drought stress effects. Plant Physiology and Biochemistry, Volume 206. https://doi.org/10.1016/j.plaphy.2023.108193.

Major discoveries We discovered that GmCKX13 from soybean is an excellent gene for developing drought-tolerant crops by altering endogenous cytokinin levels and abscisic acid responsiveness when being driven by a drought-responsive promoter.

We provided evidence that despite the structural similarities, strigolactone signaling and karrikin signaling exhibit significant distinctions in regulating the metabolism and signal transduction events controlled by other hormones in plants.

We demonstrated that exogenous jasmonic acid application alleviated the effects of combined heat and drought stress effects in soybean plants by optimizing their photosynthetic performance and protecting them against oxidative stress.

Improvement of drought tolerance of Arabidopsis transgenic plants (RD29A:GmCKX13) ectopically expressing GmCKX13 gene from soybean using the drought-inducible RD29A promoter. (A) 3-weekold wild-type (WT) and RD29A:GmCKX13 L1 and L3plants before being subjected to a drought stress.

(B) WT and RD29A:GmCKX13 plants were subjected to drought stress for 14 days and then rewatered for 3 days. Inflorescences were removed from the surviving plants before photographing. (C) For control, WT and RD29A:GmCKX13 plants were grown in parallel with the drought test under wellwatered conditions. (D) Survival rates of WT and transgenic plants. Means and standard errors from data pooled from three independent experiments (n = 3 experiments, 30 per genotype per experiment) are shown. Asterisks indicate significant differences as determined by a Student’s t-test (* P < 0.05; ** P < 0.01).

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Lopez-Arredondo Lab Unraveling regulatory networks behind biotic and abiotic stresses in plants and microalgae: the driving force of domestication and trait improvement Our research group is interested in studying plants and microalgae responses to environmental stressors and fluctuating growing conditions, e.g., phosphorus and nitrogen starvation, and pathogens. We use molecular biology, metabolomics, lipidomics, transcriptomics, and genomics, to unravel the mechanisms behind those responses and gain insights into their regulation. But we do not stop there, our major goal is to go beyond by taking advantage of this knowledge to design strategies to solve real problems. We study the regulatory networks controlling Fusarium and root-knot nematode resistance in cotton to identify genes that can be used to speed up breeding programs to improve resistance to these pathogens. Similarly, in microalgae, we study the metabolic and regulatory networks controlling the biosynthesis of lipids for biofuels and novel molecules with potential herbicidal and nematocidal effects, and design strategies to enhance their production via synthetic biology strategies.

Research subjects

Relevant publications Pérez-Zavala, F.G., Ojeda-Rivera, J.O., Herrera-Estrella, L., López-Arredondo, D. (2024). Beneficial Effects of Phosphite in Arabidopsis thaliana Mediated by Activation of ABA, SA, and JA Biosynthesis and Signaling Pathways. Plants 2024, Volume 13, Issue 13, 1873. https://doi.org/10.3390/plants13131873.

Chávez Montes, R.A., Mary, M.A, Rashel, R.H., Fokar, M., Herrera-Estrella, L., Lopez-Arredondo, D., Patiño, R. Hormetic and transcriptomic responses of the toxic alga Prymnesium parvum to glyphosate. (2024). Science of The Total Environment, Volume 954, 176451. https://doi.org/10.1016/j.scitotenv.2024.176451.

Flores-Tinoco, V, Brito-Bello, A.A. Le, V.P., Lopez-Arredondo, D. (2024) Chapter 18 - Control of Biological Contamination in Microalgae Cultures, In Woodhead Series in Bioenergy, Algal Bioreactors, Elsevier Science Ltd, 239-262. https://doi.org/10.1016/B978-0-443-14058-7.00005-1.

Study of plant and microalgae responses to abiotic and biotic stresses.

Elucidation and rewiring of regulatory networks controlling stress responses.

Plant and microalgae molecular improvement.

Discovery of microalgae metabolites with herbicidal and nematocidal effects.

Domestication of microalgae to optimize production of biofuels and bioproducts.

Major discoveries We discovered alternative mechanisms of gene architecture and expression in higher plants and microalgae, which may play an important role in stress adaptation.

We identified sets of transcription factors that orchestrate cell growth and neutral lipid biosynthesis/accumulation in green algae.

We generated high-quality genome sequences of the NemX (G. hirsutum) cotton, which is resistant to root-knot nematode.

Effects of phosphite (Phi) on Arabidopsis thaliana on different levels of Phosphate (Pi). (a) Representative photographs of 10 dag Arabidopsis plants under different phosphite and phosphate treatments.

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Jiao Lab

The Jiao Lab is dedicated to advancing the field of sorghum genetics and genomics with the overarching goal of identifying and utilizing beneficial genes to drive innovations in sorghum breeding. Our research emphasizes agronomic traits critical to grain quality, addressing key challenges in enhancing nutritional value, productivity, and environmental adaptability. Beyond gene discovery, the lab develops and curates an extensive sorghum mutant population, providing a foundational resource for functional genomics studies in sorghum and other grass crops. By employing state-of-the-art genomic tools and interdisciplinary approaches, the Jiao Lab strives to uncover novel insights and practical solutions that promote the sustainable development of sorghum as a robust, highyielding, and climate-resilient crop for the future.

The Jiao Lab focuses on sorghum seed development, particularly pathways related to grain quality, including starch, protein, and lysine biosynthesis.

Additionally, the lab develops and maintains sorghum mutant resources, providing valuable tools to support functional genomics studies and advance research within the broader scientific community.

Major discoveries A novel gene that enhances protein digestibility in sorghum grain.

The transcriptome and metabolome landscape during sorghum seed development.

A new gene involved in the regulation of cuticular wax biosynthesis in sorghum.

Image in high definitions with image captions Caption: the structure of starch granules of sorghum grain.

Relevant publications Tian, R., Nájera-González, H.R., Nigam, D., Khan, A., Chen, J., Xin, Z., HerreraEstrella, L., Jiao, Y. (2024). A leucine-rich repeat receptor kinase as a regulator in the cuticular wax deposition in sorghum. Journal of Experimental Botany, 2024; erae319,https://doi.org/10.1093/jxb/erae319.

Khan, A., Tian, R., Bean, S.R., Yerka M., Jiao Y. (2024). Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 7, 841.https://doi.org/10.1038/s42003-024-06525-7.

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Liu Lab

Global climate change, caused mainly by the rising CO 2 concentration in the Earth’s atmosphere, presents challenges to agricultural production systems.

Plants are linchpins in global carbon cycling, with a unique capacity to capture CO2 via photosynthesis. Application of gene-editing for crop improvement has been slow, due to inefficient methods of reagent delivery and the reliance on tissue culture to create gene-edited plants. Our research program is dedicated to advancing high-throughput genome editing and synthetic biology technologies.

By leveraging these innovative approaches, we aim to redesign photosynthesis to contribute to the sustainable fulfillment of global food, fiber, bioenergy, and carbon sequestration needs in response to the climate crisis.

Hu, R., Zhang, J., Jawdy, S., Sreedasyam, A., Lipzen, A., Wang, M., Ng, V., Daum, C., Keymanesh, K., Liu, D., Hu, A., Chen, J. -G., Tuskan, G. A., Schmutz, J., & Yang, X. (2024). Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes. Plants, 13(23), 3444. https://doi.org/10.3390/plants13233444.

Research subjects Development of cutting-edge genome editing and synthetic biology technologies.

Establishment of transgene-free, tissue culture-independent genome editing methods in crop plants.

Engineering photosynthesis to improve water use efficiency and abiotic stress tolerances in plants.

Investigation into the molecular and cellular mechanisms that underlie plant responses to abiotic stresses.

Major discoveries Development of transgene-free, tissue culture-independent genome editing methods in plants.

Establishment of a viral vector with large cargo capacity for gene function studies and genome editing in sorghum and Setaria.

Relevant publications Gene-edited tomatoes developed using tissue culture-independent genome editing methods.

Liu, D. Ellison, E.E., Myers, E.A., Donahue, L.I., Xuan, S., Swanson, R., Qi, S., Prichard, L.E., Starker, C.G., Voytas, D.F. (2024). Heritable gene editing in tomato through viral delivery of isopentenyl transferase and singleguide RNAs to latent axillary meristematic cells. Proceedings of the National Academy of Sciences of the United States of America. 121 (39) e2406486121https://doi.org/10.1073/pnas.2406486121.

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Janga Lab

Our lab focuses on understanding gene functions to enhance crop performance, sustainability, and resilience. Targeting key crops like soybean, cotton, and peanut, we aim to improve stress tolerance, yields, and nutritional quality. We generate stable transgenic plants using Agrobacterium-mediated transformation for gene overexpression studies and employ CRISPR/Cas9 for precise gene knockouts. Additionally, we utilize virus-induced gene silencing (VIGS) and Agrobacterium rhizogenes-mediated hairy root transformation for rapid gene function characterization. To advance crop improvement, we are pioneering prime editing in cotton, soybean, and peanut for precise gene modifications and leveraging developmental regulators to enhance transformation efficiency. Our lab also provides collaborative plant transformation services, contributing to a deeper understanding of crop genetics and innovation in agriculture.

Research subjects Identification of commercial cotton varieties response for cotton transformation.

Prime editing in cotton, soybean, and peanut.

Development of genotype-independent transformation using developmental regulatory genes in soybean and cotton.

Understanding gossypol biosynthesis in glanded and glandless cotton.

Dissecting resistance mechanisms to S. rolfsii in peanut through comparative RNA-seq profiling of resistant and susceptible genotypes.

First report of CLRDV in samples collected from a cotton field in Lubbock, Texas.

Identified the S. rolfsii resistance genes in peanut using transcriptome analysis of resistant and susceptible cultivars.

Successful identification and sequencing of mid-region of CLRDV. Relevant publications Kim, W-S., Gillman, J.D., Kim, S., Liu J., Janga, M.R., Stupar, R.M., Krishnan, H.B. (2024). Bowman–Birk Inhibitor Mutants of Soybean Generated by CRISPR-Cas9 Reveal Drastic Reductions in Trypsin and Chymotrypsin Inhibitor Activities. International Journal of Molecular Sciences.

25(11):5578. https://doi.org/10.3390/ijms25115578.

Phogat, S., Lankireddy, S.V., Lekkala, S., Anche, V.C., Sripathi, R.V., Patil, G.B., Puppala N., Janga, M.R. (2024). Progress in genetic engineering and genome editing of peanuts: revealing the future of crop improvement. Physiol Mol Biol Plants. https://doi.org/10.1007/s12298024-01534-6.

Major discoveries Identification of genes involved in gossypol biosynthesis pathway in cotton.

Overexpression of IPT significantly improved soybean transformation efficiency by enhancing shoot regeneration, but excessive expression caused undesirable bushy phenotypes, highlighting the need for controlled expression.

STM and WUS had effects similar to the control, indicating their less impact on shoot development compared to IPT. Spectinomycin proved most effective followed by phosphinothricin in selecting transformed shoots in soybean.

A hypothetical prime editing strategy to reduce/eliminate allergenicity in peanuts. The process of prime editing to reduce peanut allergenicity by targeting the Ara h 2 protein, one of the major allergenic storage proteins. A Peanut Allergens: Displays common peanut allergens, including Ara h 1, Ara h 2, Ara h 3, Ara h 5, Ara h 6, and Ara h 8. B Prime editing: Illustrates the Prime editing process, where alterations are made at the active site of Ara h 2's DNA sequence, leading to modified mRNA and subsequently altered protein structure. C Response of the immune system in the body: This section depicts the response of immune cells to an unmodified peanut allergen (Ara h 2), showing how sensitization leads to histamine release and allergic responses. Prime-edited peanuts, with altered allergenic protein, can potentially evade immune recognition, thus preventing allergic reactions.

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Patil Lab

Patil lab integrates genome engineering and genomics tools to (1) discover novel traits to improve disease resistance, nutrient uptake, and seed composition and (2) develop high-throughput technologies to improve genetic transformation and gene-editing platforms in recalcitrant crop species.

Relevant publications Kshetry, A. Ghose, K., Alok, A., Devkar, V., Raman, V., Stupar, R.M., HerreraEstrella, L., Zhang, F., Patil, G.B. Shoot at Site: Advancing in planta transformation, regeneration and gene-editing through a cascade of wounding-mediated developmental regulators. bioRxiv. 2025:2025-02.

Dhingra, A., Shinde S., D’Agostino, L., Devkar V., Shinde, H., Rajurkar, A.B., Sonah, H., Vuong,T.D., Siebecker, M.G., Jiao, Y., Hancock, C.N., Nguyen, H.T., Deshmukh, R., Patil, G.B. (2024). Identification of novel germplasm and genetic loci for enhancing mineral element uptake in soybean.

Environmental and Experimental Botany, Volume 219, 105643. https://doi.org/10.1016/j.envexpbot.2023.105643.

In planta transformation and de novo shoot regeneration in tomato (Kshetry et al. 2025).

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FUNDING

Herrera-Estrella Lab Grants USDA-NIFA NSF United Sorghum Checkoff

USDA-NIFA

Lopez-Arredondo Lab Grants Texas Tech Start-up USDA-NIFA United Soybean Board The Texas State Support Committee Cotton Incorporated Jiao Lab Grants

UNITED SORGHUM CHECKOFF

2024

TEXAS TECH START-UP

UNITED SOYBEAN BOARD

THE TEXAS STATE SUPPORT COMMITTEE

COTTON INCORPORATED

USDA NIFAAFR

USDA-ARS

USDA NIFA-AFRI USDA-ARS Liu Lab Grants Texas Tech start up Davis College-Bayer Challenge Grant Partnership for Research and Innovation Patil Lab Grants United Soybean Board USDA-NIFA BASF Cotton Incorporated United Sorghum Checkoff USDA-ARS Tran Lab Grants Texas Tech Start-up USDA-NIFA United Soybean Board The Texas State Support Committee Cotton Incorporated United Sorghum Checkoff

NSF

SMITHBUCKLIN CORPORATION

DAVIS COLLEGEBAYER CHALLENGE

BASF

$6,612,774 11

Reinforcing Institutional Collaborations Early last year (February 2024), collaborators from the University of Nevada (Reno), Virginia Tech, and the University of Missouri visited IGCAST facilities and laboratories. Texas Tech hosted the annual meeting for the team participating in the NSF grant 2243690: “Unraveling the origin of vegetative desiccation tolerance in vascular plants” (VDT). The main objective of this collaborative project is to identify the mechanisms that plants evolved to activate extreme dehydration tolerance in both vegetative and reproductive tissues. Specifically, this study seeks to identify key genes and pathways of desiccation tolerance using genomics, transcriptomics, metabolomics, and machine learning algorithms to integrate all these data. This kind of activity reinforces scientific collaborations between different institutions, making it possible to integrate research teams with diverse backgrounds. During their visit, a couple of talks were presented: one about how plants survive extreme water loss by Prof. Melvin Oliver (University of Missouri), and another on computational biology and bioinformatics research by Prof. Lenwood Heath (Virginia Tech).

By Gerardo Alejo

VDT Team

Prof. Lenwood Heath

Prof. Melvin Oliver

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Institutional Collaborations Collaboration among researchers and institutions is essential for addressing the complex challenges that require diverse strategies, expertise, and resources. At the Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), we continually partner with experts worldwide to remain at the forefront of agricultural innovation. In February, Dr. Guohua Xu from Nanjing Agricultural University delivered a lecture on “The regulation of nitrogen (N) and phosphorus (P) on flowering time, crop architecture, and nutrient use efficiency in food crops.

He shared valuable insights and approaches being implemented in China.

Additionally, Hanfang Ni, a student from Dr. Xu’s lab, had the opportunity to further her studies in Dr. Herrera-Estrella’s lab for three months.

Dr. Herrera-Estrella's research began with fieldwork in Antarctica, focusing on various studies involving seeds, plants, lichens, and algae. During his trip, he collected several samples for analysis at IGCAST. Building on this work, we collaborated with Dr. Angélica Casanova-Katny from Universidad Católica de Temuco in Chile. Dr. Casanova-Katny delivered a lecture titled “Why do cryptogams colonize extreme environments, and how do they respond to climate change?” She worked in Dr. Herrera-Estrella's lab during her visit to Texas Tech University.

Antarctic facilities

Prof. Herrera-Estrella Prof. Xu Seminar

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Institutional Collaborations This research relates to a project investigating the physiological, biochemical, and molecular mechanisms contributing to salinity tolerance in populations of Colobanthus quitensis. This native Antarctic plant species thrives in contrasting habitats. The project also includes the sequencing the Colobanthus quitensis Genome. This initiative is supported by Chile’s National Agency for Research and Development. It involves collaboration between researchers from Universidad de Concepción, Universidad Autónoma de Chile, Universidad de La Frontera, and Texas Tech University. This collaborative effort enhances our understanding of Antarctic vascular plants by leveraging cutting-edge biotechnological tools, including advanced bioinformatics analyses.

Prof. Olman Gomez-Espinoza

Prof. Casanova-Katny Seminar

Prof. Cuba-Diaz Prof. Casanova-Katny

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Advanced agricultural science through highthroughput phenotyping system Advanced phenotyping technologies have transformed agricultural sciences by providing innovative solutions to tackle challenges presented by environmental and biological factors. Recent advancements in high-throughput phenotyping, such as imaging, robotics, machine learning, and artificial intelligence, enable rapid, non-destructive, and large-scale assessment of plant traits. These technologies aid in identifying stress-resistant genotypes, enhancing crop management, and accelerating breeding programs. At Texas Tech University, installing the 1000-carrier high-throughput plant phenotyping system in the Phytotron at the Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST) exemplifies these cutting-edge developments. The newly customized LemnaTec system is set to revolutionize agricultural science research at Texas Tech University and in the South Plains area. This phenotyping system enables researchers to examine plant growth and development, plant-microbe interactions, soil biology, and environmental stress responses through nondestructive, large-scale, and seamless workflows. Equipped with a series of sensors, including thermal, top and side visible (RGB), multispectral, hyperspectral, and chlorophyll fluorescence sensors, the system allows for comprehensive measurement of plant growth and development, shape, biomass, water content, water consumption and evaporation, leaf and plant temperature, soil and pot temperature, biochemical properties, yield, and photosynthetic performance. This versatility supports research on plants subjected to various conditions such as water deficit, nutrient deficiency, salinity, or herbicide treatment. Plants will be automatically and continuously scheduled for watering, weighing, and imaging. In addition, the high-throughput phenotyping system is designed to minimize noise in data caused by microclimates within the greenhouse.

Experiments can be loaded into the system from within the headhouse, and plants are transferred to the greenhouse via a conveyor system. Each plant is monitored as it travels from the greenhouse through a high-speed automatic door to the imaging cabinets, where all morphological, biochemical, and physiological measurements are taken. To ensure consistent exposure to similar microclimates, plants are rotated through different positions within the greenhouse throughout the experiment. The system also automatically controls watering and treatments (such as nutrient or salt solutions) at the watering and weighing station. This automated process reduces the chances of inconsistencies due to human errors. All image data is analyzed and interpreted during and after the experiment, offering valuable insights. By addressing current limitations through interdisciplinary efforts and investments in scalable and accessible solutions, our phenotyping system can be fully utilized to tackle critical challenges. These include managing data efficiently, ensuring cost accessibility, and achieving standardization. The system supports advancements in scalable agricultural solutions and contributes to creating a sustainable and resilient global food supply, which is crucial in facing environmental uncertainties.

By Chien Ha

Phenotyping System

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Dissertation Defenses

This year, four IGCAST students successfully defended their PhD exams and graduated. These academic achievements are the result of their students’ dedication, professors’ guidance, and the support of their peers.

In March, Nasir Khan from Dr. Jiao's laboratory successfully defended his master's exam on the topic “Characterization of the Roles of Kafirin Genes in Sorghum Grain Quality.” Similarly, Anik Touhidur Rahman from Dr. Tran's laboratory presented his master's exam on “ Improvement of Cotton Growth Performance Under Drought Stress Using Zinc Fertilizer.”

In October, Arjun Ojha Kshetry from Dr. Patil's laboratory defended his doctoral research, “Advancing Planta Transformation and Gene Editing in Plants: Deciphering the Molecular Complexities of Somatic Cell Regeneration.” Adil Khan, from Dr. Jiao’s lab, presented his Ph.D. research on “A Multi-Omic Resource of Sorghum Seed Tissues for Understanding Nutrient Synthesis and Heat Stress Tolerance.” These two students are the first to receive a PhD as part of the IGCAST project.

Interdisciplinary workgroups of undergraduate and graduate students and postdoctoral fellows are crucial in advancing the Institute's mission as a leading research center. The collaboration of diverse perspectives enhances both education and research.

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Engagement and Outreach Programs At IGCAST, we are committed to expanding our outreach efforts as part of our mission to share scientific knowledge with not just the research community, but also with children, schools, and the public at large. By combining in-person activities and social media platforms, we strive to create more opportunities to highlight our discoveries and demonstrate their real-world relevance.

This year, we launched a series of short, accessible videos to share key findings from our specialists' research, much of which has been published in prestigious journals. These videos are designed to simplify complex topics in an engaging way, making scientific information more accessible on social media. In addition, we produced in-depth research videos aimed at students and researchers, focusing on protocols, equipment, and strategies for addressing diverse biological questions. One notable success is our video on 'Isolation of Protoplasts from Nicotiana benthamiana leaves,' which has become a widely used resource on our campus and beyond, sparking greater interest in the field and supporting the broader scientific community.

We also recognize the importance of engaging with children to inspire the next generation of scientists. Through hands-on activities, we aim to spark curiosity, connect classroom learning to real-world applications, and foster a lifelong interest in STEM careers. IGCAST continued its outreach this year by visiting local schools and participating in community events. For example, during STEM Family Night at Legacy Elementary School in the Frenship District, we demonstrated how plants absorb water and highlighted key plant structures, giving children and their families a firsthand look at the wonders of plant biology.

The Lopez-Arredondo Lab also maintained its longstanding partnership with Lubbock Cooper Central Elementary School’s Dual Language Program (English/Spanish), marking its fourth consecutive year of participation. These visits remain a cornerstone of our outreach efforts, providing interactive, bilingual science experiences that engage and inspire students.

Through these initiatives, IGCAST is dedicated to bridging the gap between science and the community, fostering a deeper understanding of the natural world, and nurturing a passion for discovery in people of all ages.

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2024 IGCAST SYMPOSIUM The conference program offered an engaging and dynamic agenda, showcasing cutting-edge research and stimulating discussions on a variety of agricultural science and biotechnology topics. Dr. Luis Herrera-Estrella, IGCAST Director, welcomed attendees, followed by remarks from Dr. Clint Krehbiel, Dean of the Davis College of Agricultural Sciences, who delivered a compelling speech about the collaborative efforts at TTU. In its third edition, the Symposium expanded to include two full days of conferences, additional guest speakers, and a large poster contest. The program was organized into six thematic sessions, promoting deeper connections between diverse research areas and discoveries.

Session 1: Nutrient Stress and Improvement Strategies Moderated by Dr. Yinping Jiao, this session explored plant responses to nutrient stress and innovative improvement strategies. Dr. Kashchandra G. Raghothama, Professor of Horticulture and Landscape Architecture at Purdue University, kicked off the session with a fascinating talk on phosphorus acquisition strategies in plants. Following his presentation, Ph.D. students Rogelio NajeraGonzalez and Matteo Tosoni shared their research on chemical screenings and microalgae adaptations under nutrient stress. Moises Frausto wrapped up the session with an insightful discussion on using CRISPRa circuits to address phosphate stress in plant roots.

Clint Krehbiel, Dean

Session 2: Developmental Processes and Metabolic Pathways Led by Dr. Degao Liu, this session began with Dr. Matt Olson from the Department of Biological Sciences at TTU, who discussed the evolution of sex chromosomes in poplars and willows. The audience was captivated by cuttingedge methodologies, such as single-nucleus RNA sequencing in cotton fibers, presented by Lenin Yong-Villalobos, and an analysis of cuticular wax production in sorghum, shared by Ran Tian. Contributions from students Valeria Flores-Tinoco and Sai Krishna Lekkala further enriched the session with insights into polycistrons and gossypol biosynthesis.

Session 3: Novel Tools for Plant Transformation Moderated by Dr. Madhusudhana Janga, this session highlighted advancements in plant transformation technologies. Manman Hu introduced a breakthrough in tissue culture-free genome editing via viral delivery of CRISPR/Cas12f. Presentations by Sri Harsha Vardhan Reddy Lankireddy and Pallavi showcased genotype-independent transformation systems for soybean and sorghum.

Prof. Lopez-Arredondo

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The second day began with Session 4: Agricultural Technologies and Crop Stress Resilience, moderated by Dr. Son Tran. Dr. Stephen O. Duke from the National Center for Natural Products Research at the University of Mississippi opened the session with an exploration of natural herbicides and their molecular targets. Postdoctoral associates Francisco Perez-Zavala and Lingran Zhang followed with innovative approaches to improve soybean cultivation and abiotic stress tolerance in cereal crops. Dr. Chien Ha and Zhiyuan Liu concluded the session with talks on genetic strategies to enhance drought and heat tolerance in plants.

Session 5: Drought and Desiccation Tolerance Moderated by Dr. Wenxuan Guo, Associate Professor of the Department of Plant and Soil Science at TTU, this session began with an in-depth look at using data science to understand crops and their environmental interactions. Ph.D. students Chidinma Nwoko, Micayla Lamb, and Mezanur Rahman presented research on cellular mechanisms in desiccation tolerance, chemical signals for drought management, and plant stress responses. The session closed with Dr. Olman José Gómez Espinoza from Universidad Autónoma de Chile, who shared his fascinating study on the resilience of Antarctic plants.

Session 6: Biotic Interactions Moderated by Dr. Gunvant Patil, this session focused on plant-microbe interactions and crop resilience. Dr. Gözde S. Demirer, Assistant Professor at the California Institute of Technology, delivered a keynote on engineering rhizosphere interactions. Students Sanjida Keya, Leonidas Dagostino, and Pankaj Verma presented studies on salinity resilience, soybean-AMF symbiosis, and fungal resistance, respectively.

Scientific Poster Contest Winners

The event concluded with a poster awards ceremony, recognizing outstanding contributions from the seven IGCAST labs and students from related classes.

The winners of the poster competition of the IGCAST symposium were: Postdoc category First Place. Francisco Perez-Zavala Second Place. Alfonso Carlos Barragan-Rosillo Third Place. Vikas Devkar M. SC. and Ph. D category First Place. Himanshu Yadav Second Place. Alethia Brito Third Place. Pradeep Kumar

Scientific Poster Contest Session

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Symposium assistants

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2024 Recognitions The Grand Challenges Catalyst Grant Program The Grand Challenges Catalyst Grant Program 2024 awarded Dr. Yinping Jiao for the project titled "Developing Sorghum with Dual Benefits for ClimateSmart Sustainable Agriculture and Human Health."

Length of Service Awards On April 5, 2024, Davis College faculty and staff recognized those for their length of service, including: Dr. Luis Herrera-Estrella Dr. Damar Lopez-Arredondo M.S Mylea C. Lovell

On May 9, 2024, Texas Tech University's Davis College of Agricultural Sciences and Natural Resources concluded its 2024 Faculty Fellows Program. This yearlong program, led by Associate Dean Noureddine Abidi, supports new faculty with monthly sessions on research excellence, teaching, mentoring, work-life balance, and communication training. The program aims to help new faculty integrate into Davis College and Texas Tech while advancing their careers.

Participants included: Highly Cited Researchers 2024 For the second consecutive year, Texas Tech professors Dr. Son Tran and Dr. Herrera-Estrella have earned the recognition of Highly Cited Researchers from Clarivate. This honor underscores their exceptional scientific research achievements and significant contributions to their respective fields. Tran has appeared on the list for seven years, 2016 and 2018-2023, while Herrera-Estrella has been recognized in 2022, 2023, and 2024. Their groundbreaking publications rank in the top 1% of citations in at least one of the 21 research fields assessed in the "Essential Science Indicators," reinforcing their status as highly influential figures in the scientific community.

Madhusudhana Janga: An assistant professor focusing on gene-editing technologies, highlighted the program's assistance in navigating university resources.

Degao Liu: An assistant professor working on genome editing and synthetic biology, valued the program’s professional growth opportunities.

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2024 Recognitions

Global Exchange Research Seed Award, TTU International Affairs Dr. Patil is working on a project focused on developing sustainable solutions to reduce the use of chemical fertilizers through advanced genomics and genome engineering technologies. This project is supported by up to four One-Way Seed grants and two Faculty Exchange grants, both aimed at fostering long-term initiatives. The Faculty Exchange grants facilitate visits by TTU faculty to international partners, allowing for reciprocal visits to TTU.

European Molecular Biology Organization Dr. Luis Rafael Herrera-Estrella, the President's Distinguished Professor of Plant Genomics within Texas Tech's Department of Plant & Soil Science, was elected a member of the European Molecular Biology Organization (EMBO). The group touts a community of 1,900 leading scientists from various fields, including cell biology, cancer, vaccine development, and machine learning.

Dr. Herrera-Estrella also received recognition from Governor of Texas Greg Abbot as a recipient of a grant from “The Governor's University Research Initiative” program.

International Award for Environmental Botany, Eurasian Academy of Environmental Sciences (EAES).

Dr. Patil received the prestigious International Award for Environmental Botany from the Eurasian Academy of Environmental Sciences (EAES) in 2023, recognizing contributions to environmental research and botany.

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Awards to IGCAST students Alethia Brito from LopezArredondo Lab won the Spring 2024 Graduate Student Research Support Award Recipients.

Claudio Barrera from LopezArredondo’s Lab won The Algal BBB 2024 poster competition award at the International Conference on Algal Biomass, Biofuels & Bioproducts.

Pradeep Kumar won at the 3rd Oral and poster presentation of the 2024 ASA, CSSA, SSSA International Annual Meeting (Graduate Student Competition)

Pallavi from Jiao’s Lab won the 3rd place in the student oral presentation at The Sorghum Improvement Conference of North America (SICNA 2024).

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2024 TTU Department of Plant & Soil Science Student Research Symposium.

The Texas Tech University Department of Plant & Soil Science’s 2024 Student Research Symposium is a premier annual event that provides students with an invaluable platform to showcase their research and refine critical skills in presenting scientific work through conferences and posters. This year, IGCAST students made remarkable contributions, excelling in both oral and poster presentations and highlighting the depth and diversity of their research.

Several Ph.D. students delivered outstanding oral presentations: Leonidas D'Agostino (Patil Lab) earned second place for his presentation, “Symphony of Symbiosis: A Single-Cell Transcriptomic Exploration of Soybean-Microbe Interactions.”

Matteo Tosoni (Lopez-Arredondo Lab) presented “Transcriptomic Profiling of a Hatching Defective Mutant of Chlamydomonas reinhardtii,” showcasing his pioneering work in algal genetics.

Pallavi (Jiao and Patil Lab) shared her insights in “Impact of the Knockout of Amylose Synthesis on Grain Quality in Sorghum: A Step Towards Comprehensive Understanding.”

The Poster Session also featured contributions from three Ph.D. students: Claudio Barrera Duarte (Lopez-Arredondo Lab) presented “Exploring Gene Regulation of Triacylglycerol Accumulation in Chlorella sorokiniana Under Nitrogen and Phosphorus Deprivation.”

Micayla Lamb (Patil Lab) showcased her work, “Optimizing Cotton's Root System Architecture to Improve Adaptive Response to Water-Deficit Stress.”

Zhiyuan Liu (Jiao Lab) introduced his study, “Characterization of hs1 as a Key Regulator of Heat and Drought Tolerance in Sorghum.”

These presentations reflect our students' dedication and innovative spirit, highlighting the importance of collaborative research and interdisciplinary learning. IGCAST students continue to demonstrate excellence in advancing agricultural sciences, making significant contributions to both their fields and the broader scientific community.

Leonidas D'Agostino

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IGCAST MEMBERS 2024 Herrera-Estrella Lab Luis Herrera-Estrella (Professor) Rozalynne Samira (Assistant Professor) Gerardo Alejo Jacuinde (Postdoc) Carlos Barragan Rosillo (Postdoc) Gabriela Cabrales Orona (Postdoc) Shumayla (Postdoc) Lenin Yong-Villalobos (Postdoc) Moises Frausto (Ph.D. Student) Hector Rogelio Najera Gonzales (Ph.D. Student) Lois Nwoko (Ph.D. student) Benjamin Perez-Sanchez (Ph.D. Student) Pablo Silva Villatoro (Ph.D. Student)

Tran Lab Lam-Son Phan Tran (Professor) Chien Ha (Research Assistant Professor) Mostafa Abdelrahman (Research Scientist) Aarti Gupta (Research Scientist) Md. Arifur Rahman Khan (Research Scientist) Huong Nguyen (Visiting Scientist) Anket Sharma (Visiting Scientist) Md. Mezanur Rahman (PhD student) Sanjida Sultana Keya (PhD student) Vy Le (PhD student) Touhidur Rahman Anik (Ph.D. student)

Lopez-Arredondo Lab Damar Lopez-Arredondo (Assistant Professor) Puneet Mangat (Postdoc) Francisco Perez-Zavala (Postdoc) Alethia Alejandra Brito Bello (Ph.D. Student) Claudio Barrera Duarte (Ph.D. Student) Valeria Flores Tinoco (Ph.D. Student) Vy Le Phuong (Ph.D. Student) Matteo Tosoni (Ph.D. Student) Himanshu Yadav (Ph.D. Student)

Patil Lab Gunvant Patil (Assistant Professor) Vikas Devkar (Research Scientist) Wuzi Xie (Research Scientist) Kaushik Ghose (Research Scientist) Mallesham Bulle (Postdoc) Ramkumar Rajaram (Postdoc) Gaurav Raturi (Postdoc) Micayla Lamb (Graduate Research Assistant) Leonidas D’Agostino (Ph.D. student) Arjun Ojha (Ph.D. student) Pallavi (Ph.D. Student) Durgeshwari Prabhakar Gadpayale (Research Intern)

Jiao Lab Yinping Jiao (Assistant Professor) Deepti Singh (Postdoc) Ran Tian (Postdoc) Guanyuan Cheng (Ph.D. student) Adil Khan (Ph.D. student) Pradeep Kumar (Ph.D. student) Zhiyuan Liu (Ph.D. student) Pallavi (Ph.D. student) Shejal Soumen (Ph.D. student) Nasir Khan (M.S. student)

Janga Lab Madhusudhana Janga (Professor) Pankaj Kumar Verma (Ph.D. student) Archana Khadgi (Ph.D. student) Sai Krishna Lekkala (M.S. student) Sri Harsha Vardhan Reddy Lankireddy (M.S. student)

Liu Lab Degao Liu (Assistant Professor) Lingran Zhang (Postdoc) Manman Hu (Ph.D. Student) Vishal (M.S. Student)

Staff Deanna Galvan (Lead Administrator) Gabriela Castillo-Estrada (Lab Manager LHE/DLLA) Gabriela Prieto Soriano (Multimedia Specialists) Mylea Lovell (Phytotron Manager)

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IGCAST PUBLICATION LIST 2024

Alyammahi, O., Kappachery, S., Sasi, S., Ghosh, R., Venkatesh, J., Varghese, N., Abdelrahman, M., Tran, L.-S. P., Gururani, M.A. (2024). Ectopic Expression of the Potato StD26 Encoding a Ribosomal Protein S27 Enhances Salt Tolerance in Arabidopsis thaliana. Journal of Plant Growth Regulation. https://doi.org/10.1007/s00344-023-11175-w Alejo-Jacuinde, G., Chávez Montes, R.A., Gutierrez Reyes, C.D., Yong-Villalobos, L., Simpson, J., Herrera-Estrella, L. (2024). Gene family rearrangements and transcriptional priming drive the evolution of vegetative desiccation tolerance in Selaginella. The Plant Journal, (2024), doi: 10.1111/tpj.17169 Anik, T.R., Chu, H.D., Ahmed, M.S., Ha, C.V., Gangurde, S.S., Khan, M.A.R., Le, T.D., Le, D.T., Abdelrahman, M., Tran, L.-S. P. (2024). Genome-wide characterization of the glutathione S-transferase gene family in Phaseolus vulgaris reveals insight into the roles of their members in responses to multiple abiotic stresses. Plant Stress, Volume 12, 100489. https://doi.org/10.1016/j.stress.2024.100489 Bawa, G., Liu, Z., Yu, X., Tran, L.-S. P., Sun, X. Introducing single cell stereosequencing technology to transform the plant transcriptome landscape.

(2024). Trends in Plant Science, Volume 29, Issue 2. https://doi.org/10.1016/j.tplants.2023.10.002 Bello-Bello, E., Herrera-Estrella, L. (2024). Breaking new ground: Decoding the root’s molecular circuits to penetrate compacted soil. Developmental Cell, Vol.59, Issue 4, page 431-433. https://doi.org/10.1016/j.devcel.2024.01.028 Chávez Montes, R.A., Mary, M.A, Rashel, R.H., Fokar, M., Herrera-Estrella, L., Lopez-Arredondo, D., Patiño, R. Hormetic and transcriptomic responses of the toxic alga Prymnesium parvum to glyphosate. (2024). Science of The Total Environment, Volume 954, 176451. https://doi.org/10.1016/j.scitotenv.2024.176451 De Jesús-Campos, D., García-Ortega, L.F., Fimbres-Olivarría, D., Herrera-Estrella, L., López-Elías, J.A., Hayano-Kanashiro, C. (2024). Transcriptomic analysis of Chaetoceros muelleri in response to different nitrogen concentrations reveals the activation of pathways to enable efficient nitrogen uptake.

Gene, Volume 924,2024, 148589. https://doi.org/10.1016/j.gene.2024.148589

Dhingra, A., Shinde S., D’Agostino, L., Devkar V., Shinde, H., Rajurkar, A.B., Sonah, H., Vuong,T.D., Siebecker, M.G., Jiao, Y., Hancock, C.N., Nguyen, H.T., Deshmukh, R., Patil, G.B. (2024). Identification of novel germplasm and genetic loci for enhancing mineral element uptake in soybean.

Environmental and Experimental Botany, Volume 219, 105643. https://doi.org/10.1016/j.envexpbot.2023.105643 Gupta, A., Kumar, M., Zhang, B., Tomar, M., Walia, A.K., Choyal, P., Saini, R.P., Potkule, J., Burritt, D.J., Sheri, Verma, P., Chandran, D., Tran, L.-S. P. (2024).

Improvement of qualitative and quantitative traits in cotton under normal and stressed environments using genomics and biotechnological tools: A review. Plant Science, Volume 340,111937. https://doi.org/10.1016/j.plantsci.2023.111937 Gupta, A., Li, L., Zhu, C., Kun, K.,Jia, K.,Miao, Y., Li, W.,Tran, L.-S. P. (2024).

Differential modulation of hormonal pathways by strigolactone and karrikin signaling. Plant Growth Regul 104, 1197–1205. https://doi.org/10.1007/s10725-024-01227-w Gupta, A., Watanabe, Y., Ha, C., Abdelrahman, M., Li, W., Rahman,Md. M., Sultana, S., Nigam, D., Jiao,Y., Anik, T.R., Saha,G., Kojima, M., Sakakibara,H., Mochida, K., Tran, L.-S. P. (20204).Disruption in Jasmonic Acid Biosynthesis Influences Metabolism of Other Hormones in Arabidopsis. J Plant Growth Regul. https://doi.org/10.1007/s00344-024-11446-0 Hu, R., Zhang, J., Jawdy, S., Sreedasyam, A., Lipzen, A., Wang, M., Ng, V., Daum, C., Keymanesh, K., Liu, D., Hu, A., Chen, J. -G., Tuskan, G. A., Schmutz, J., & Yang, X. (2024). Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes. Plants, 13(23), 3444. https://doi.org/10.3390/plants13233444 Hossain, M.M., Sultana, F., Khan, S. Nayeema, J., Mostafa, M., Fer, H., Tran, L.-S. P., Mostofa, M.G., (2024). Carrageenans as biostimulants and bio-elicitors: plant growth and defense responses. Stress Biology 4, 3. https://doi.org/10.1007/s44154-023-00143-9 Khalil, M.I., Hassan, M.M., Samanta, S.C., Chowdhury, A.K., Hassan, M.Z., Ahmed, N.U., Somaddar, U., Ghosal, S., Robin, A.H.K., Nath, U.K., Mostofa, M.G., Burritt, D.J., Ha, C.V., Gupta, A., Tran, L.-S. P., Saha, G. (2024). Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1. Plant Physiology

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and Biochemistry, Volume 206, 108224. https://doi.org/10.1016/j.plaphy.2023.108224 Khan, A., Tian, R., Bean, S.R., Yerka M., Jiao Y. (2024). Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 7, 841. https://doi.org/10.1038/s42003-024-06525-7 Kandhol, N., Pandey, S., Pratap Singh, V. Herrera-Estrella, L., Tran, L.-S.P., And Kumar Tripathi, D. (2024). Link between plant phosphate and drought stress responses. Science Pater Journal. https://spj.science.org/doi/10.34133/research.0405 Kean-Galeno, T., Lopez-Arredondo, D., Herrera-Estrella, L. (2024). The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants. Int. J. Mol. Sci. 2024, 25, 1519. https://doi.org/10.3390/ijms25031519 Kim, W-S., Gillman, J.D., Kim, S., Liu J., Janga, M.R., Stupar, R.M., Krishnan, H.B. (2024). Bowman–Birk Inhibitor Mutants of Soybean Generated by CRISPRCas9 Reveal Drastic Reductions in Trypsin and Chymotrypsin Inhibitor Activities. International Journal of Molecular Sciences. 25(11):5578. https://doi.org/10.3390/ijms25115578 Le, D.T., Ha, C.V., Nguyen, K.H., Chu,H.D., Zhu, C., Li, W., Watanabe, Y., Kojima, M., Takebayashi, Y., Sakakibara, H., Mochida, K., Tran, L.-S. P. (2024). Altering endogenous cytokinin content by GmCKX13 as a strategy to develop drought-tolerant plants. Plant Stress, Volume 14,100678. https://doi.org/10.1016/j.stress.2024.100678 Liu, D. Ellison, E.E., Myers, E.A., Donahue, L.I., Xuan, S., Swanson, R., Qi, S., Prichard, L.E., Starker, C.G., Voytas, D.F. (2024). Heritable gene editing in tomato through viral delivery of isopentenyl transferase and single-guide RNAs to latent axillary meristematic cells. Proceedings of the National Academy of Sciences of the United States of America. 121 (39) e2406486121 https://doi.org/10.1073/pnas.2406486121 Ma, X., Zhang, B., Xiang, X., Li, W., Li, J., Li, Y., Tran, L. -S. P., Yin, H. (2024).

Characterization of Bacillus pacificus G124 and Its Promoting Role in Plant Growth and Drought Tolerance. Plants, 13(20), 2864. https://doi.org/10.3390/plants13202864

Mahmud, A., Islam, M.N., Islam, A.K.M.A., Islam, M.M., Ghosh, U.K., Hossain, M.S., Sheikh, A., Rahman, M.H.S., Tran, L.-S. P., Khan, M.A.R. (2024). Evaluation of yield-attributing parameters in Aus rice for enhancing productivity.

Plant Genetic Resources: Characterization and Utilization. 2024;22(6):368-377. doi:10.1017/S1479262124000364 Mostafa, A., Gorafi, Y., Sulieman, S., Jogaiah, S., Gupta, A., Tsujimoto, H., Nguyen, H.T., Herrera-Estrella, L., Tran, L.-S. P., (2024). Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. The Plant Journal, (2024). https://doi.org/10.1111/tpj.16887 Nguyen, K. H., Li, Z., Wang, C., Ha, C.V., Tran, C.D., Abdelrahman, M., Pham, H.X., Trung, K.H., Khanh, T.D., Chu, H.D., Mostofa, M.G., Watanabe, Y., Wang, Y., Miao, Y., Mochida, K., Pal, S., Li, W., Tran, L.-S.P. (2024). Cytokinin and MAX2 signaling pathways act antagonistically in drought adaptation of Arabidopsis thaliana. Plant Stress,100484. https://doi.org/10.1016/j.stress.2024.100484 Ojeda-Rivera, J., Ulloa, M., Pérez-Zavala, F., Nájera-González, H., Roberts, P., Yong-Villalobos, L., Yadav H., Chávez Montes, R., Herrera-Estrella, L., LopezArredondo, D. (2024). Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum f. sp. vasinfectum race 4 infection in the cotton cultivar Pima-S6 (Gossypium barbadense L.) Front. Genet.

14:1271200. https://doi.org/10.3389/fgene.2023.1271200 Pérez-Zavala, F.G., Ojeda-Rivera, J.O., Herrera-Estrella, L., López-Arredondo, D. (2024). Beneficial Effects of Phosphite in Arabidopsis thaliana Mediated by Activation of ABA, SA, and JA Biosynthesis and Signaling Pathways. Plants 2024, Volume 13, Issue 13, 1873. https://doi.org/10.3390/plants13131873 Phogat, S., Lankireddy, S.V., Lekkala, S., Anche, V.C., Sripathi, R.V., Patil, G.B., Puppala N., Janga, M.R. (2024). Progress in genetic engineering and genome editing of peanuts: revealing the future of crop improvement. Physiol Mol Biol Plants. https://doi.org/10.1007/s12298-024-01534-6 Rahman, M.M., Mostofa, M.G., Keya, S.S., Ghosh, P.K., Abdelrahman, M., Anik, T.R., Gupta, A., Tran, L.-S.P. (2024). Jasmonic acid priming augments antioxidant defense and photosynthesis in soybean to alleviate combined heat and drought stress effects. Plant Physiology and Biochemistry, Volume 206. https://doi.org/10.1016/j.plaphy.2023.108193

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Tian, L., Wang, J., Chen, H., Li, W., Tran, L.-S. P., Tian, C. (2024). Integrative multiomics approaches reveal that Asian cultivated rice domestication influences its symbiotic relationship with arbuscular mycorrhizal fungi.

Pedosphere, Volume 34, Issue 2. https://doi.org/10.1016/j.pedsph.2023.09.007

Tian, R., Nájera-González, H.R., Nigam, D., Khan, A., Chen, J., Xin, Z., HerreraEstrella, L., Jiao, Y. (2024). A leucine-rich repeat receptor kinase as a regulator in the cuticular wax deposition in sorghum. Journal of Experimental Botany, 2024; erae319, https://doi.org/10.1093/jxb/erae319

Shefali, M., Ashish Kumar, S., Aamir, W.K., Tran, L.-S. P., Henry, T. N. (2024). The era of panomics-driven gene discovery in plants. Trends in Plant Science. 995, VL - 29. https://doi.org/10.1016/j.tplants.2024.03.007

Wu, R., Liu, Z., Sun, S., Qin, A., Liu, H., Zhou, Y., Li, W., Liu, Y., Hu, M., Yang, J., Rochaix, J-D., An, G., Herrera-Estrella L., Tran, L.-S. P., Sun X. (2024).

Identification of bZIP Transcription Factors That Regulate the Development of Leaf Epidermal Cells in Arabidopsis thaliana by SingleCell RNA Sequencing. Int. J. Mol. Sci. 2024, 25, 2553. https://doi.org/10.3390/ijms25052553

Sudhakaran, S., Mandlik, R., Kumawat, S., Raturi, G., Gupta, S.K., Shivaraj, S.M.,Patil, G.B., Deshmukh, R., Sharma, T.J., Sonah, H. (2024). Evolutionary analysis of tonoplast intrinsic proteins (TIPs) unraveling the role of TIP3s in plant seed development. Plant Physiology and Biochemistry, Volume 215,109022. https://doi.org/10.1016/j.plaphy.2024.109022 Sulieman, S., Ha, C.V., Le, D.T., Abdelrahman, M., Tran, C.D., Watanabe, Y., Tanaka, M., Ulhassan, Z., Sheteiwy, M.S., Gangurde, S.S., Mochida, K., Seki, M., Tran, L.-S. P. (2024). Comparative transcriptome analysis of respirationrelated genes in nodules of phosphate-deficient soybean (Glycine max cv.

Williams 82). Plant Stress, Volume 11,100368. https://doi.org/10.1016/j.stress.2024.100368 Sulieman, S., Sheteiwy, M.S.,Abdelrahman, M., Tran, L.-S. P. (2024). γAminobutyric acid (GABA) in N2-fixing-legume symbiosis: Metabolic flux and carbon/nitrogen homeostasis in responses to abiotic constraints. Plant Physiology and Biochemistry, Volume 207,108362. https://doi.org/10.1016/j.plaphy.2024.108362 Sultana, S., Rahman, M.M., Das, A.K., Haque, M.A., Rahman, M.A., Islam, S.M.N., Ghosh, P.K., Keya, S.S., Tran, L.-S. P., Mostofa, M.G. (2024). Role of salicylic acid in improving the yield of two mung bean genotypes under waterlogging stress through the modulation of antioxidant defense and osmoprotectant levels. Plant Physiology and Biochemistry. Volume 206, 108230, https://doi.org/10.1016/j.plaphy.2023.108230 Tan, W., Nian, H., Tran, L.-S. P., Jin, J., Lian, T. (2024). Small peptides: novel targets for modulating plant–rhizosphere microbe interactions. Trends in Microbiology. Vol. 32, Issue 11. https://doi.org/10.1016/j.tim.2024.03.011

Xie, X., Liu, Y., Chen, G., Turatsinze, A. N., Yue, L., Ye, A., Zhou, Q., Wang, Y., Zhang, M., Zhang, Y., Li, Z., Tran, L.-S. P., Wang, R. (2024). Granular bacterial inoculant alters the rhizosphere microbiome and soil aggregate fractionation to affect phosphorus fractions and maize growth. Science of The Total Environment, Volume 912,169371. https://doi.org/10.1016/j.scitotenv.2023.169371 Yi, F., Li, Y., Song, A., Shi, X., Hu, S., Wu, S., Shao, L., Chu, Z., Xu, K., Li, L., Tran, L.-S. P., Li, W., Cai, Y. (2024). Positive roles of the Ca2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance. Molecular Plant Pathology, 25, e13483. https://doi.org/10.1111/mpp.13483 Yuli, D., Heng, Z., Kunpeng, J., Zongyan, C., Shican, X., Tran, L.-S. P., Jinggong, G., Weiqiang, L., Kun, L. (2024). Role of abscisic acid-mediated stomatal closure in responses to pathogens in plants. Physiologia Plantarum.

Volume 176, Issue 1, e14135. https://doi.org/10.1111/ppl.14135 Zhang, P., Liu, F., Abdelrahman, M., Song, Q., Wu, F., Li, R., Wu, M., HerreraEstrella, L., Tran, L.-S.P., Xu, J. (2024). ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1. Plant J. https://doi.org/10.1111/tpj.17065 Zhao, Y., Liu, S., Liu, H., Wang, F., Dong, Y., Wu, G., Li, Y., Wang, W., Tran, L.-S. P., Li, W., (2024). Multi-objective ecological restoration priority in China: Cost-benefit optimization in different ecological performance regimes based on planetary boundaries. Journal of Environmental Management, Vol., 356,120701. https://doi.org/10.1016/j.jenvman.2024.120701

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