W5168: Environmental and Genetic Determinants of Seed Quality and Performance

(Multistate Research Project)

Status: Active

Project Menu

SAES-422 Reports

Annual/Termination Reports:

[12/14/2024] [12/15/2025]

Date of Annual Report: 12/14/2024

Report Information

Annual Meeting Dates: 10/03/2024 - 10/05/2024
Period the Report Covers: 10/01/2023 - 09/30/2024

Participants

Brief Summary of Minutes

Accomplishments

Accomplishments OR (Elias): Oregon State University (OSU) conducts studies exploring and adopting new technologies to assess and manipulate traits to enhance seed quality of various crops. This is agreeing with the second objective of the W5168 project. Currently, Dr. Sabry Elias is only seed scientist conducting seed research in Oregon, after the retirement of two colleagues, Dr. Thomas Chastain, and Dr. Hiro Nonogaki.  The following projects have been conducted in 2023/2024: <ol> <li>Development of qPCR test to detect and quantify annual contamination in perennial ryegrass.</li> <li>Development of glyphosate bioassay test for annual ryegrass.</li> <li>The use of thermogradient table in screening cover crops for cold and heat tolerance.</li> <li>Development of two tolerance tables for native species to compare purity test results of two subsamples from the same or different submitted samples.</li> <li>Sabry is also working on the 5th of the “Principles of Seed Science and Technology” book.</li> </ol> FL (Pérez): Coastal dune restoration programs are essential for protecting natural areas and human created infrastructure. Such programs rely on a mix of engineering and nature-based solutions to re-establish or stabilize dune systems. Dune stabilizing plants such as Uniola paniculata (sea oats) represent an essential component of nature-based solutions. However, the supply and quality of seeds from genetically appropriate source material can be problematic. Lack of information regarding factors associated with sea oats seed quality are lacking. This knowledge gap is magnified by the highly fragmented yet wide (> 1300 km) spatial distribution of sea oats along the US Atlantic and Gulf coasts.  Objective 1.1 Understand how developmental and environmental mechanisms affect seed quality – We worked with five state agencies to collects seeds of sea oats from 18 populations over a two-year period. We then investigated biochemical, physiological, and physical seed traits associated with seed quality and how these traits varied over a large latitudinal gradient. We discovered that higher seed antioxidant concentrations were common in parts of the distribution with extreme environmental conditions. This correlates with sea oats populations growing at latitudinal extremes that experienced relatively warmer or colder temperatures. However, germination capacity was not coupled with baseline antioxidant concentrations. Higher antioxidant concentrations evident after imbibition were associated with poor seed germination in warmer conditions. We also found that seed traits such as surface area and surface-to-volume ratio were positively correlated with aging stress tolerance. Similarly, the initial respiratory capacity and baseline antioxidant concentrations were positively correlated with aging stress survival. Alternatively, a spike in antioxidant concentrations at 36 hours after imbibition was negatively correlated with aging stress survival. Our results indicate that climate conditions and environmental components associated with temperature and precipitation may largely influence the initial pool of antioxidants in sea oats seeds. For example, a high concentration of antioxidants following seed imbibition could be indicative of seed damage or poor viability that may be influenced by environmental stress. Moreover, stable levels of antioxidants through the early imbibition process were typical of seeds with extended aging stress survival while unstable levels corresponded to reduced aging stress survival. Seed traits including surface-to-volume ratio and increased metabolism time were better positive predictors of extended aging stress survival. CA (Khanday): Research at UC Davis focuses on understanding the complexities of seed development and germination to create clonal and high-quality seeds. The research enhances our understanding of plant reproductive development and seed biology. Key findings from this year include: 1) The identification of a gene regulatory module involving male-expressed BABY BOOM (BBM) transcription factors that activate the expression from female alleles of auxin biosynthesis, YUCCA genes to initiate embryogenesis. This demonstrates a pivotal male-female genomic partnership during early seed development. This breakthrough provides new insights into plant reproductive biology and paves the way for engineering superior seeds. 2) In collaboration with international partners, we have significantly advanced our synthetic apomixis technology, achieving over 95% clonal seed formation in commercial hybrid rice. This advancement paves the way for the field application of this groundbreaking breeding technology, ensuring the preservation of hybrid vigor and revolutionizing crop propagation. 3) We explored the regulation of ABA biosynthesis during tomato seed development, identified critical ABA biosynthesis genes involved in seed dormancy and created mutants through targeted gene editing and development seed with high quality, enhanced vigor and climate resilience.  KY (Downie): LATE EMBRYOGENESIS ABUNDANT PROTEINs (LEAPs), intrinsically disordered proteins found in most organisms that can withstand desiccation at some stage of their life-cycle) are hypothesized to provide protection to stressed cells. So too are non-reducing sugars (NRS; trehalose, sucrose, raffinose) thought to provide desiccation tolerance. Furthermore, the two PROTEIN ISOASPARTYL METHYLTRANSFERASE (PIMT) paralogs in plants are very active following seed rehydration to repair the deleterious and non-enzymatic conversion of asparagine and aspartic acid into iso-aspartate back into aspartic acid. Together, these molecules are components of the natural protection and repair (NPR) mechanism in orthodox seeds, the focus of our studies. Using two orthologous dehydrin LEAPs, one from Arabidopsis (At2G21490; LEA14; (Hundertmark and Hincha 2008)), its soybean (Glycine max) orthologous protein (GmPM12; Glyma.04G009900.1) we have demonstrated their interaction with ABSCISIC ACID INSENSITIVE3 (ABI3; At3g24650). The bioinformatic pipeline used to recover LEAP interacting protein partners (client proteins; CtPs) from paired end reads of recovered phage and the validation of LEAP:CtP binding use temperature related intensity change (TRIC) and split-YFP visualization is now published (Uneda-Trevisoli et al 2024). Three undergraduate researchers from the Agricultural and Medical BioTechnology program are co-authors. Also published are results demonstrating that raffinose or its hydrolysis products (galactose and/or sucrose) play a major role in promoting adventitious root formation during severe water logging in Maize (Yan et al. 2024). We have additionally demonstrated the role one of the two maize paralogous PIMTs plays in repairing select mitochondrial CtPs to safeguard seed vigor (Zhang, Song, et al. 2024). In particular, this study linked maize seed vigor to the repair of the CtP, 3-METHYLCROTONYL COA CARBOXYLASE. In a project unrelated to the natural protection and repair mechanism, an investigation into a QTL influencing the embryo weight relative to the whole maize seed was identified as COMPACT PLANT2. The maize embryo contains much more oil than the maize endosperm which is predominately starch and storage proteins. High oil content is viewed favorably by the poultry feed industry (Zang, Zhen, et al. 2024). I continue to seek funds from the department of defense to purchase instrumentation to permit automated assessments of cell densities. I continue to gather preliminary data to permit a resubmission of an NSF proposal for funds to pursue LEA14’s involvement in mitigating the capacity of ABI3 to alter the transcriptome during maturation desiccation and early germination. Preliminary data are also being gathered to demonstrate the consequences of a LEA_3 family LEAP, SEED MATURATION PROTEIN1 (SMP1) BARENTZS2 (BTZ2) one of two paralogous BTZ proteins in plants. BTZ2 is one protein that comprises the exon junction complex of proteins responsible for optimal translation as well as nonsense mediated mRNA decay (NMD) of transcripts that have had a 3’ untranslated region (UTR) intron, situated more than 50 nts distal to the stop codon, spliced from them. Based on mutant, over-expressor, and biochemical data, SMP1 binds to, and interferes with, BTZ2’s capacity to induce NMD. KY (Kawashima): A greenhouse study using soybean cultivars with varying seed weights (two small-seeded and two large-seeded) showed a significant positive correlation between seed weight and the duration of lag phase (flowering to 3 mm seed in diameter), suggesting a genetic link between the early-stage seed development and the final seed size. The large-seed cultivars exhibited more pavement cells on the ventral cotyledon surface compared to smaller-seeded ones, implying that a longer lag phase allows for more cell division in the cotyledons. To further explore these findings, we analyzed publicly available RNA-seq data of the cotyledon-stage (the final stage of the lag phase) seeds from large- and small-seed soybeans. Differential gene expression analysis revealed transcripts that were enriched in either the large- or small-seed cultivars although no significant Gene Ontology term enrichment was observed to understand molecular differences among small and large seeded cultivar seed development. However, mapping these transcripts to specific seed compartments using a seed compartment-specific RNA-seq dataset showed a higher representation of genes promoting cell division in the large-seeded cultivar developing seed. These physiological and molecular data suggest that seed growth is collaboratively regulated across different seed compartments, with prolonged development in large seeds - characterized by a longer lag phase - resulting in more cotyledon cells and increased seed size. SD (Gu): Research was continued to improve germinability of hybrid varieties of rice using mapped seed dormancy genes, to develop a genetic strategy to mitigate the risk of transgene flow into weedy relatives using a tandem construct with a CRIPSR/Cas9-based multiplex against seed adaptive traits, to identify regulatory mechanisms of the gibberellin signaling pathway for the development or release of seed dormancy and germination velocity, or to evaluate effects of seed dormancy genes on soil seedbank longevity.  MI (Isaacs): Dr. Isaacs has just joined this group and there is no report on accomplishment.

Publications

Colette M. Richter, Sabry G. Elias, & Robert S. Zemetra. (2023). Evaluation of bioassay methods to screen winter wheat for quizalofop herbicide tolerance. Crop Sci.1-11. <a href="https://www.bing.com/search?pglt=41&q=DOI%3A+10.1002%2Fcsc2.21103&cvid=a23fab9746264d08bcb716062338a041&gs_lcrp=EgZjaHJvbWUyBggAEEUYOTIGCAEQRRg6MgYIAhBFGEAyBwgDEEUY_FXSAQgyMTA0ajBqMagCALACAA&FORM=ANNAB1&PC=U531">DOI: 10.1002/csc2.21103 - Search (bing.com)</a>. The manuscript of the use of thermogradient table in screening cover crops for cold and heat tolerance was submitted to the Seed Science & Technology Journal. Egesa AO, Pérez HE, Begcy K. 2023. Environmental conditions predetermine quality, germination, and innate antioxidants pool in sea oat (Uniola paniculata L.) seeds. Frontiers in Environmental Science. 11:1263300. Doi: 10.3389/fenvs.2023.1263300 Egesa AO, Davidson MT, Pérez HE, Begcy K. 2024. Biochemical and physical screening using optical oxygen-sensing and multispectral imaging in sea oats seeds. Agriculture. 14:875. Doi: 10.3390/agriculture14060875 Ren, H., Shankle, K., Cho, M.-J., Tjahjadi, M., Khanday, I., and Sundaresan, V. (2024). Synergistic induction of fertilization-independent embryogenesis in rice egg cells by paternal-genome-expressed transcription factors. Nature Plants <a href="https://doi.org/10.1038/s41477-024-01848-z">https://doi.org/10.1038/s41477-024-01848-z</a> Rasool, B., Summuna, B., Djalovic, I., Shah, T.A., Sheikh, P.A., Gupta, S., Tyagi, S., Bilal, S., Varshney, R.K., Abidi, I., Kumar, J., Penmetsa, R.V., Khanday, I., Kumar, U., Sofi, P.A., Khan, M.A., Bhat, M.A., Wani, Fahim J., Thudi, M., and Mir, R.R. (2023). Delineating Marker-Trait Associations for Fusarium Wilt in Chickpea Using the Axiom® CicerSNP Array. Phytopathology® 113, 836-846. <a href="https://doi.org/10.1094/PHYTO-05-22-0164-FI">https://doi.org/10.1094/PHYTO-05-22-0164-FI</a> Khanday, I., Santos-Medellín, C., and Sundaresan, V. (2023). Somatic embryo initiation by rice BABY BOOM1 involves activation of zygote-expressed auxin biosynthesis genes. New Phytologist 238, 673-687. doi: <a href="https://doi.org/10.1111/nph.18774">https://doi.org/10.1111/nph.18774</a> Unêda-Trevisoli, SH, Dirk, LMA, Carlos Bezerra Pereira FE, Chakrabarti, M, Hao, G, Campbell, JM, Bassetti Nayakwadi, SD, Morrison, A, Joshi, S, Perry, SE, Sharma, V, Mensah, C, Willard, B, de Lorenzo, L, Afroza, B, Hunt, AG, Kawashima, T, Vaillancourt, L, Pinheiro, DG, Downie, AB. 2024. Dehydrin client proteins identified using phage display affinity selected libraries processed with Paired-End PhAge Sequencing (PEPA-Seq), Molecular & Cellular Proteomics, doi: https://doi.org/10.1016/j.mcpro.2024.100867. DOI: <a href="http://dx.doi.org/10.1016/j.jgg.2024.09.012">10.1016/j.jgg.2024.09.012</a>  Yan, Dong, Gao, Yu, Zhang, Yumin, Li, Dan, Dirk, Lynnette M.A., Downie, A. Bruce, Zhao, Tianyong. 2024. Raffinose catabolism enhances maize waterlogging tolerance by stimulating adventitious root growth and development. Journal of Experimental Botany. 75: (18) 5955–5970. DOI: 10.1093/jxb/erae284 Zhang, Yumin, Song, Xianbo, Zhang, Wenli, Liu, Feijun, Wang, Chunmei, Liu, Ying, Dirk, Lynnette, Downie, Bruce, Zhao, Tianyong. 2023. Maize PIMT2 repairs the damaged 3-METHYLCROTONYL COA CARBOXYLASE in mitochondria controlling seed vigor. The Plant Journal. 115(1):220-235. doi: 10.1111/tpj.16225 Zhang, Yumin, Zhen, Sihan, Zhang, Chunxia, Shangguan, Xiaoqing, Lu, Jiawen, Bao, Runhao, Dirk, Lynnette M.A., Downie, A. Bruce, Wang, Guoying, Zhao, Tianyong, Fu, Junjie. 2024. Natural variation of CT2 affects the embryo/kernel weight ratio in maize. Journal of Genetics and Genomics.  Sugi, N., et al., The peri-germ cell membrane: poorly characterized but key interface for plant reproduction. Nature Plants 10:1607–1609 (2024) Sharma, V., Ali, M.F., Kawashima, T. Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity. Current Opinion in Plant Biology 81:102566 (2024) <a href="https://doi.org/10.1016/j.pbi.2024.102566">https://doi.org/10.1016/j.pbi.2024.102566</a> Gu X-Y, Guo M, Bhattarai K, Batth BS, Feng J. Genetic Improvement of Hybrid Rice for Germinability using Linked Genes Controlling Embryo Dormancy. Proceedings of the 8th International Hybrid Rice Symposium. Edited by Ali J. International Rice Research Institute, Los Banos, Laguna, Philippines (Impress).

Impact Statements

OR (Elias): The seed research at Oregon State University focuses on solving actual problems that face growers, answering their buzzling questions, contributing to their welfare, and increasing crop productivity and quality. For example, study 1 (above) aimed to solve the problem of contamination of annual ryegrass in perennial seed lots which has been one of the major problems in Oregon seed industry, the largest producer of ryegrass in the USA, and the 2nd in the world. Study 2 (above) will help avoiding unfounded claims of the presence of resistant ARG seeds to glyphosate, and subsequent stopping potential lawsuits and disputes between seed buyers and producers. Study 3 (above) will help screening for cold/heat tolerances using the thermogradient germination test, which help growers and seed companies to make quick decisions on selecting the best varieties for cold or warm regions to warrant a successful stand establishment. Study 4 (above) will increase the uniformity of purity seed testing of native species among labs.
FL (Pérez): A change in knowledge related to the importance of environmental signaling in accumulation of key secondary metabolites (i.e., antioxidants) associated with seed quality occurred. This can be helpful in guiding the collection and post-harvest management of genetic resources necessary for nature-based dune restoration programs. Also, we now know the potential of using physical and biochemical screening via various scanning technologies to predict seed quality. This type of knowledge contributes to uncovering key seed traits that contribute to viability and longevity.
CA (Khanday): Research at UC Davis addresses critical challenges in seed biology, including understanding seed development, enhancing seed vigor, and creating technologies to improve seed quality. This year, work at UC Davis advanced the understanding of embryogenesis during seed development and led to improvements in synthetic apomixis technology that was developed previously. Previously, research at UC Davis uncovered that in rice, male-expressed BABY BOOM (BBM) transcription factors initiate embryogenesis. We have now revealed that the male-expressed BBMs activate maternal auxin biosynthesis, YUCCA genes, demonstrating a pivotal male-female genomic partnership during early seed development. This breakthrough provides new insights into plant reproductive biology and paves the way for engineering superior seeds. In collaboration with international partners, significant strides in synthetic apomixis technology have been made, achieving over 95% clonal seed formation in commercial hybrid rice lines. This represents a big step toward preserving hybrid vigor and offers immense potential for revolutionizing crop breeding and propagation. This is also a big step forward towards the field application of this technology. Additionally, efforts at UC Davis to enhance seed vigor have shown promising results. By modulating abscisic acid (ABA) biosynthesis pathways in tomato seeds through targeted gene editing, seeds have been developed that germinate faster, more synchronously, and exhibit greater thermotolerance. These traits are crucial for improving crop performance under stress conditions, ensuring resilience in diverse agricultural systems and possibly mitigate some of the effects of climate change on crop production. Research at UC Davis not only deepens the fundamental understanding of seed biology but also contributes to practical innovations to secure sustainable food production.
KY (Kawashima): received an NSF award ($870,396, 1/15/2024 – 1/14/2027) to investigate the molecular and cellular mechanism of plant fertilization.
SD (Gu): About 300 hybrid populations, progeny lines, or induced mutants were developed in greenhouse or field experiments, more than 500 plants were genotyped using regular or high-throughput techniques, some of the lines/plants were sequenced to decode the mutations, and one of the seed burial experiments were advanced to the third year.
MI (Isaacs): Dr. Isaacs has just joined this group and there is no report on Impacts.

Date of Annual Report: 12/15/2025

Report Information

Annual Meeting Dates: 07/17/2025 - 07/20/2025
Period the Report Covers: 10/01/2024 - 09/30/2025

Participants

Please see attached pdf with participant names.

Brief Summary of Minutes

Accomplishments

Accomplishments   CA (Khanday): Research at UC Davis focuses on understanding plant reproductive development and seed biology. The research enhances our understanding of seed development and germination to improve seed quality and vigor. This year, progress was made in identifying genetic and molecular mechanisms that regulate various seed quality traits. Key findings from this year include: <ul> <li>A comprehensive developmental, physiological, and transcriptomic analysis of tomato seed development revealed key transition points associated with the acquisition of seed quality traits such as germinability, desiccation tolerance, reduced primary dormancy, and rapid germination. Several gene modules and candidate genes regulating these transitions during seed development were identified.</li> <li>To investigate the role of ABA biosynthesis in regulating seed dormancy and germination, expression of 9-cis-epoxycarotenoid dioxygenase (NCED) genes was examined. NCED enzymes regulate a key rate-limiting step in ABA biosynthesis pathway. Of the 11 NCED genes encoded in the tomato genome, five (SlNCED1, SlNCED2, SlNCED4, SlNCED5A, and SlNCED5B) were found to be expressed in seeds, each showing a distinct expression patterns during seed development.</li> <li>Loss-of-function mutants created in some of these seed-expressed NCED genes, demonstrated significantly enhanced vigor and stress-tolerance. These seeds show higher germination percentages, more rapid and synchronous germination compared to wild-type controls. They also show higher thermotolerance for germination than controls.</li> </ul>   TX (Leskovar): Research at Texas A&M University, Texas A&M AgriLife Research Objective 2: Capitalize on new technologies to assess and manipulate traits to enhance seedling quality This year we focused on gaining more understanding on how selective strategies regulate or induce key morpho-physiological traits involved in seedling and grafted transplant adaptation. We also evaluated grafting as a tool to mitigate abiotic stress when exposed to different management strategies, under protected environments and organic systems.  We conducted four studies: 1) Pant biostimulants to enhance seedling and plant growth in seedless watermelon, 2) Role of microbial consortia and rootstocks for organic pepper production, 3) Heat stress responses of tomato genotypes across vegetative and reproductive stages, and 4) Grafted tomato rootstock screening under heat stress. 1) Plant biostimulants to enhance seedling and plant growth in seedless watermelon The seedless watermelon study was conducted to evaluate microbial and seaweed extract biostimulants for their ability to enhance seed germination, seedling vigor, and canopy growth. A follow up trial evaluated seedlings treated with the same biostimulants at seeding, transplanting, and a day before moisture stress was initiated. Overall seaweed extracts significantly enhanced germination and emergence while no effect was observed for mycorrhizae treated seeds. Transplants treated with seaweed also had higher canopy and CO2 assimilation under water deficit conditions.  These studies showed potential of microbial and seaweed biostimulant in seed germination, and enhanced seedling tolerance and growth in watermelon under moisture deficit stress. 2) Role of microbial consortia and rootstocks for organic pepper production The grafted pepper study conducted in a high tunnel environment evaluated the performance of two Phytophthora-resistant rootstocks, CM-334 and YC-207, grafted with a common scion (Mama Mia Giallo), and the application of a mycorrhizal and bacterial mix consortium under two organic fertilization rates (optimal and reduced rate). The hypothesis explored whether the synergy of microbial inoculation and grafting could compensate for the reduced growth of the low rate by improving nutrient use efficiency.  Overall chlorophyll content was higher (~10 %) in inoculated plants compared to non-inoculated plants under low fertilization. Leaf net photosynthesis was similar at both fertilization rates, while inoculated plants had an increase in plant water use efficiency (~12 %). Microbial inoculation and low fertilization induced early flowering compared to non-inoculated plants grown at optimal fertilization rate. Under low fertilization, inoculated YC-grafted plants exhibited higher electron transport rate, stomatal conductance, and transpiration rate than other inoculated plants.  Our follow up studies will evaluate the correlation of these physiological traits with fruit yield, quality, and soil health to provide further understanding applicable to rootstock selection and microbial inoculation to optimize pepper production, particularly in resource-limited conditions. 3) Heat stress responses of tomato genotypes across vegetative and reproductive stages We evaluated heat stress responses of ten tomato genotypes across the vegetative and reproductive stages over two seasons. Across all cultivars, ‘Big Beef’ showed larger declines in shoot and root biomass (74.1% and 70.4%), canopy leaf area (59.4%), stigma receptivity (82.1%), and pollen viability (60.3%) compared to the average genotype, but its pollen and ovule numbers (14.6% and 3.1%) were less reduced than the average. In contrast, ‘Cherokee Purple’ demonstrated similar thermotolerance levels during the vegetative and flowering stages to those of genotypes with tolerant yield responses. From that study we concluded that heat-tolerant or heat-sensitive responses in the vegetative or flowering stages did not always correlate with fruit yield reductions in tomato under heat stress. 4) Grafted tomato rootstock screening under heat stress   This study assessed the productivity of novel rootstock-grafted tomato plants against the industry standard (Maxifort rootstock). A total of 27 scion/rootstock combinations, using two processing tomato industry scions (H1996 and H1015), and including non-grafted and self-grafted controls were compared under field conditions during summer 2025.  Based on yield performance and canopy growth, a set of four rootstocks (diploids) were selected for further studies.  Based on yield performance, best rootstock genotypes in combination were: X20-07 (1st), X21-02 (3rd), X20-06 (4th), X21-09 (10th). Genotypes that exhibited higher shoot biomass than non-grafted, self-grafted and Maxifort were also X20-07 and X21-09.     FL ( Pérez): Coastal dune restoration programs are essential for protecting natural areas and human created infrastructure. Such programs rely on a mix of engineering and nature-based solutions to re-establish or stabilize dune systems. Dune stabilizing plants such as Uniola paniculata (sea oats) represent an essential component of nature-based solutions. However, the supply and quality of seeds from genetically appropriate source material can be problematic. Lack of information regarding factors associated with sea oats seed quality are lacking. This knowledge gap is magnified by the highly fragmented yet wide (> 1300 km) spatial distribution of sea oats along the US Atlantic and Gulf coasts. Likewise, knowledge of environmental and management factors that influence wiregrass (Aristida beyrichiana) seed quality is lacking. Wiregrass is a foundational species due to its ability to carry regenerative fires and occurs in the critically endangered longleaf pine ecosystem throughout the southeastern US. Seed production is stimulated almost exclusively by growing season burns. Wiregrass is a key species used in long leaf pine ecosystem restoration to re-establish the vegetation-fire feedback system. But wiregrass seed quality is highly variable. The gap in wiregrass seed biology knowledge therefore limits restoration activities.  Objective 1.1 Understand how developmental and environmental mechanisms affect seed quality – We worked with five state agencies to collects seeds of sea oats from 18 populations over a two-year period. We then investigated biochemical, physiological, and physical seed traits associated with seed quality and how these traits varied over a large latitudinal gradient. We discovered that higher seed antioxidant concentrations were common in parts of the distribution with extreme environmental conditions. This correlates with sea oats populations growing at latitudinal extremes that experienced relatively warmer or colder temperatures. However, germination capacity was not coupled with baseline antioxidant concentrations. Higher antioxidant concentrations evident after imbibition were associated with poor seed germination in warmer conditions. We also found that seed traits such as surface area and surface-to-volume ratio were positively correlated with aging stress tolerance. Similarly, the initial respiratory capacity and baseline antioxidant concentrations were positively correlated with aging stress survival. Alternatively, a spike in antioxidant concentrations at 36 hours after imbibition was negatively correlated with aging stress survival. We also ascertained that panicle density had the largest effects on seed production throughout the sea oats distribution. Our results indicate that climate conditions and environmental components associated with temperature and precipitation may largely influence the initial pool of antioxidants in sea oats seeds. For example, a high concentration of antioxidants following seed imbibition could be indicative of seed damage or poor viability that may be influenced by environmental stress. Moreover, stable levels of antioxidants through the early imbibition process were typical of seeds with extended aging stress survival while unstable levels corresponded to reduced aging stress survival. Seed traits including surface-to-volume ratio and increased metabolism time were better positive predictors of extended aging stress survival. We studied wiregrass seed quality in terms of seed fill and pathogen presence across 19 wiregrass populations throughout Florida. Seeds were collected from these sites over multiple seasons. We also studied factors that influence seedling emergence. We found that wiregrass seeds while desiccation tolerant also expressed a short lifespan when confronted with ageing stress. We discovered that the type of habitat (e.g., xeric vs. mesic) and burn timing displayed the largest effects on the production of filled versus empty seeds. However, the type of habitat and rainfall amount during the seed developmental period were the strongest predictors of filled and infected seeds. Additionally, we uncovered that wiregrass seedling production was most strongly influenced by seasonal temperatures. Wiregrass seeds tend to avoid transitioning to seedlings during winter conditions. But there may be strong interannual differences in this response. The type of habitat where wiregrass occurred had a small effect on the seed to seedling transition. KY (Finneseth): Joined group February 10, 2025. Established field plots of 60 native perennial species at the University of Kentucky Horticulture Research Farm (Lexington, KY) to explore seed production protocols and commercial feasibility. Preliminary data collected include mortality ratings, in-season performance ratings, and flowering interval. Seed harvest is underway and laboratory quality studies will be conducted over the winter. KY (Kawashima): This year, we investigated how plants utilize actin filaments (F-actin) in the coenocytic endosperm to regulate final seed size, using Arabidopsis thaliana as a model. Our lab demonstrated that F-actin forms aster-shaped structures around each nucleus in the coenocytic endosperm, and that enhancing F-actin function by overexpressing actin genes increases seed size. Conversely, reducing F-actin function by expressing a dominant-negative form of actin results in smaller seeds. Through transcriptomic analyses, we identified a unique actin gene specifically expressed in the coenocytic endosperm. Interestingly, the mutant of this gene produces enlarged seeds, while its overexpression in the endosperm leads to smaller seeds. Biochemical assays further revealed that this actin isoform possesses distinct properties compared to conventional, ubiquitously expressed actins: faster polymerization and reduced bundling. We hypothesize that this endosperm-specific actin regulates nuclear movement and determines the number of nuclei retained in the endosperm, thereby controlling endosperm size and ultimately final seed size. KY (Downie): The Natural Protection and repair mechanism in orthodox seeds encompasses a host of molecules and pathways put in place to permit survival of maturation desiccation and repair of essential entities following the reintroduction of water. In the first category are protective molecules including the LATE EMBRYOGENESIS ABUNDANT PROTEINs (LEAPs), intrinsically disordered proteins found in most organisms that can withstand desiccation at some stage of their life-cycle) that are hypothesized to provide protection to stressed cells. So too are non-reducing sugars (NRS; trehalose, sucrose, raffinose) which are thought to provide protection to membranes and proteins during desiccation tolerance as well as to mitigate the negative influence of reactive oxygen species. Following imbibition, one protein repair mechanism is the activity of PROTEIN ISOASPARTYL METHYLTRANSFERASE (PIMT) that acts to change isoAspartic acid (isoAsp, an abnormal amino acid formed non-enzymatically in proteins from either Asparagine [Asn] or Aspartic acid [Asp]) back to Asp. Together, these molecules are components of the natural protection and repair (NPR) mechanism in orthodox seeds, the focus of our studies. We found that the pathway providing precursors to raffinose production also contributes to the vigor of Zea mays (maize) seeds during germination at sub-optimal temperatures (Li et al. 2025). Additionally, we ascertained that raffinose or one of its degradation products, galactose, contributes to flooding tolerance in maize (Yan et al. 2024). This is apparently through the stimulation of adventitious root formation close to the surface where oxygen availability in flooded soils is greater. LEAPs have been thought to act as simple shield molecules, physically separating two otherwise reactive molecules from each other as water is removed from the system. The evidence for this is convincing but it does not illustrate the entire mode of action of the LEAPs. They, or at least some of them, have preferred client proteins to which they physically bind, including the formation of homodimers that can influence subcellular localization, or rapidly render the LEAPs innocuous upon the return of homeostasis to the cell. We have documented the preferred client proteins of one such LEAP in the dehydrin family (Unêda-Trevisoli, Dirk et al. 2024). Ms. Deepshikha Sai Bassetti, Ms. Ashley Morrison, and Mr. James Campbell, all University of Kentucky Agriculture and Medical Biotechnology students at the time, were co-authors on this publication (Unêda-Trevisoli, Dirk, et al. 2024.) We have published a review of one mechanism of action of some LEAPs in forming biomolecular condensates (Elder et al. 2025). All proteins containing Asn or Asp (if not at the end of the peptide or immediately followed by proline) are susceptible to isoAsp formation and susceptibility (likelihood of forming isoAsp) is protein dependent. Upon dehydration the non-enzymatic, water independent, conversion of Asn and Asp to the intermediate succinimide is un-repairable. Succinimide in the stored proteome builds up over time. Upon imbibition the entire population of succinimide, unstable and highly reactive in water, converts to isoAsp (75%) or Asp (25%). The formation of isoAsp adds an additional carbon in the peptide chain of the protein misaligning important regulatory and catalytic domains. Fortunately, the protein repair PIMT recognizes isoAsp and, using S-Adenosyl methionine (SAM), methylates the alpha carbon, destabilizing it, which results in the conversion of isoAsp back to succinimide. The entire process repeats until the isoAsp is stoiciometrically converted back to Asp. Plants have two PIMTs. Previously, we have examined the prefered client protein repertoire of ZmPIMT2, unveiling a propensity to repair mitochondrial proteins without which the seed is of poor vigor. We have now unveiled the client proteins of ZmPIMT1 which includes many proteins involved in translation. Gratifyingly, client proteins identified using protein pull-down assays with ZmPIMT1 included a DEAD-box RNA HELICASE ortholog previously identified as a PIMT1 target in Arabidopsis! Additionally, many POLY-A BINDING PROTEINs (PABPs) were ZmPIMT1 targets. In addition to enhancing seed longevity, these PABPs are instrumental for alleviating seed dormancy in Arabidopsis (Zhang et al. 2025, in press). This article will be introduced in an In Brief summary. SD (GU): 1. Completed a multi-year project to identify adaptive mechanisms of seed pigment traits. Seeds are coated with red or dark pigments presumably to promote plant adaptation. Allelic variants of the red (Rc/rc) and purple (Pb/pb) pericarp color genes were assembled into the same genetic background of rice. Genotypic differences in the developmental and histological patterns of pigment traits, seed flavonoid chemicals, seed dormancy, and germination velocity were detected. The biochemical and physiological data were used to model genetic component effects and genotype-by-environmental effects of the two genes. OR (Sabry): Oregon State University (OSU) conducts studies in both basic and applied research, focusing on the application of new technologies to assess and manipulate traits to enhance seed quality. In 2025, our project addressed the following issues: <ol> <li>Development of digital PCR test to detect and quantify annual contamination in perennial ryegrass samples. This project is the fruit of collaboration with scientists from the USDA-ARS FRRL in Logan, UT and Oregon state University. The same research group developed KASP and qPCR tests to distinguish between annual and perennial ryegrass.</li> <li>Determine the reliability of fluorescence and growout tests in detecting annual ryegrass in perennial samples.</li> <li>Developing a short grow-out method to differentiate between annual and perennial ryegrass by using morphological traits of seedlings.</li> <li>Elias collaborated with international researchers in two projects: 1) Enhancing salt tolerance in rye (Secale cereale) through ZnO and SiO2 nanoparticles and mycorrhizal fungi: Insights into antioxidant activation and physiological responses; and 2) Develop a novel approach in using insect-based spinach-food waste for gene targeting to cancer tissues.</li> <li>Elias is also working on the 5th ed. of the “Principles of Seed Science and Technology”.</li> </ol> The seed research at Oregon State University focuses on solving actual problems that are facing growers in Oregon and the US, answering their buzzling questions, increasing crop productivity and quality, and contributing to farmers welfare. For example, project 1 (above) aimed to solve the problem of contamination of annual ryegrass in perennial seed lots which has been one of the major problems in grass seed industry, especially in Oregon, the largest producer of ryegrass in the USA, and the 2nd in the world. Project 2 (above) will help determine the reliability of the fluorescence test as a fast, economic test to detect annual ryegrass in perennial types. Project 3 (above) will provide US grass seed growers with an effective tool to differentiate between annual and perennial ryegrass when the fluorescence test over estimates the contamination of perennial ryegrass samples with annual types. Project 4 (above) aimed to explore methods for enhancing salt tolerance in rye (Secale cereale). Collaborated with scientists from the USDA-ARS and from other universities help expand the usefulness of our studies beyond only one state (Oregon) of even one country (the US). Sabry is also a Co-PI in a project that has been submitted to NIFA on turfgrass genomics, with Texas A&M. MI (Isaacs): Started a 3-year project to collaboratively build seed systems with midwestern Native American communities. Developed and distributed surveys to partner tribal communities to learn about their seed keeping practices, reasons for growing, and challenges with access to appropriate seed. Designed and facilitated 3 Native Seed Workshops with Winnebago, Santee, Ponca, and Omaha Nations: Creating A Shared Vision for Seed Saving, Seed Production, And Access to Native Foods (Total 60 participants). These workshops were in collaboration with Center for Rural Affairs and two branches of Nebraska Indian College, and Ponca Tribe of Nebraska, and Iowa State University. We determined future goals related to improving seed production and storage of native seed and identified seed training needs. At MSU, 30 students completed Isaacs’ course in Spring 2025, Grain Grading and Seed Quality. They learned the principles of seed quality and important factors for testing and regulating seed.

Publications

Impact Statements

CA (Khanday): Research at UC Davis addresses critical challenges in seed biology and agriculture by generating both new knowledge and applied innovations. Current work advances the understanding of seed development while also creating technologies to enhance seed vigor and improve seed quality. To understand the relationship between developmental stage, acquisition of seed quality traits, and their molecular regulation, several gene modules were identified that are associated with germinability, desiccation tolerance, reduced primary dormancy, and rapid germination. These studies revealed multiple potential genetic targets that can be modulated to improve seed quality. Through targeted editing of ABA biosynthesis pathway genes, tomato seeds with enhanced vigor, high germination rates, rapid and synchronous germination, and enhanced thermotolerance were developed. These traits are particularly valuable for crop establishment under temperature fluctuations and other stress conditions commonly encountered in the field. Enhanced seed vigor directly translates into more uniform seedling emergence and improved crop establishment. By working at the interface of fundamental discovery and translational outcomes, UC Davis research is contributing to sustainable food production systems and strengthening the U.S. seed and agricultural industry.
TX (Leskovar): These results provide evidence that specific plant biostimulants can be selected for improving seedling and plant growth performance. However, the observed genotype-specific responses and the absence of consistent additive effects call for additional research aimed at customized inoculation protocols focusing on optimizing timing, dosage, and microbial consortium composition for diverse crop varieties and environmental conditions. This targeted approach will be crucial for maximizing the benefits of microbial inoculants, fostering sustainable agricultural practices, and ensuring long-term ecological and economic viability. The results for the tomato screening for heat stress tolerance and grafting are attractive for developing more resilient and sustainable methods to maintain or improve productivity of fresh market Texas crops growing in harsh environments. We expect findings from these studies will provide recommendations to small- to large-scale growers to enhance their profits and contribute to the sustainable production of high value vegetable crops.
FL (Perez): A change in knowledge related to the importance of environmental signaling in accumulation of key secondary metabolites (i.e., antioxidants) associated with seed quality occurred. This can be helpful in guiding the collection and post-harvest management of genetic resources necessary for nature-based dune restoration programs. Also, we now know the potential of using physical and biochemical screening via various scanning technologies to predict seed quality. This type of knowledge contributes to uncovering key seed traits that contribute to viability and longevity. Knowledge regarding factors affecting seed production, like panicle density, serves as the foundation to quantify the panicle density-seed production relationship. Modelling this relationship can lead to tools that help sea oats farmers develop more efficient, sustainable, and profitable seed harvesting methods. A change in knowledge regarding wiregrass seed quality and factors that influence plant regeneration from seeds provides key information for proper post-harvest seed handling and optimizing actions that limit deterioration. Moreover, this information can support stakeholder decision-making related to matching seeding activities in the field or simulating appropriate seedling establishment activities in the greenhouse. Recognizing a definition of seed quality that includes seed fill and health components can ensure that restoration efforts are based on seeds that can produce seedlings. This is amplified by understanding how collection sites and environmental conditions during seed development may influence seed quality thus improving seed collection.
KY (Finneseth): Two field days sharing results with local growers (about 150 in total). Extension agent training is planned for November at 4 sites with 60 agents signed up for the training. Through the group connection, Krista Isaacs and I are applying for 2 grants together! The UK Sustainability Challenge Grant (due tomorrow) and an ARC POWER grant (due Oct. 22), looking at motivations for saving heritage seed kinds in Appalachia and development of production/business resources to help entrepreneurs improve practices.
KY (Kawashima): Understanding how plants regulate seed size is critical for ensuring a stable food supply, as seeds account for more than seventy percent of human calorie intake, either directly or indirectly. While many pathways have been identified that control seed size, the pathway involving F-actin–mediated nuclear organization in the coenocytic endosperm represents a novel mechanism. The coenocytic phase of endosperm development is conserved across plants, including major crops such as soybean, maize, rice, and wheat. Further characterization of the underlying molecular and cellular mechanisms will provide a foundation for integrating this pathway as a new strategy to promote larger seeds and strengthen food security.
KY (Downie): The catabolism of raffinose in the basal internode assists maize to generate more and longer adventitious roots and this greatly increases the capacity of maize seedlings to withstand waterlogging. One possible mechanism by which this physical alteration is orchestrated is that the galactose released upon localized raffinose hydrolysis may promote localized intracellular increases in auxin, stimulating adventitious root production. With this revelation we have provided those colleagues interested in such diverse abiotic stresses as drought and flood with one means by which maize protects itself from these diametrically opposed stresses. The capacity of raffinose, or the galactose derived from its catabolism, to promote adventitious root formation when stimulated by flooding was hitherto unreported. The variety of roles raffinose, and its precursors, play in mitigating all manner of abiotic perturbations continues to increase. The maize embryo contains far more storage lipid than does the maize endosperm. This is a trait with practical meaning to poultry farmers whose livestock benefit more from the lipid than they do from the starch in the endosperm. Hence, our discovery of CT2 as a marker for the ratio between the embryo and endosperm weight (Zhang et al. 2024) serves as a molecular marker for breeders attempting to produce maize for feed.
SD (GU): Continued to advance the project “genetic improvement of the resistance to pre-harvest sprouting in rice”. A major allele at the major quantitative trait locus (QTL) qSD12 was introduced into the genetic background of an elite variety of rice by generations of marker-assisted selection and phenotypic identification for seed dormancy (SD) and agronomic traits, such as flowering time (FT) and plant height (PH). Additional QTLs for SD, FT and PH were identified in the background. Genomic selection is being used to accelerate the project. Two publications developed based on the data from the project are in press or under review.
OR (Sabry): Our research and projects’ activities have been benefiting our seed growers in Oregon and across the US through addressing problems and finding solutions to challenges that are facing the seed industry. For example, developing qPCR tests will make ryegrass growers in the US more competitive in the world market through making fast science-based decisions about marketing their crops and delivering high quality seeds to the end users. Other projects’ activities will have similar benefits and impact on a wide range of farmers and the seed industry in general. Most of our studies contribute to increasing crop productivity and quality, which benefits the seed industry and the agricultural sector not only in the US but also worldwide. It is worth to note that currently Dr. Sabry Elias is only seed scientist conducting seed research in Oregon, after the retirement of two colleagues, Dr. Thomas Chastain, and Dr. Hiro Nonogaki.
MI (Isaacs): Funding secured to support seed selection and production activities with Native American growers in Nebraska and workshops have commenced. Data collected from 60 respondents on Native Seed Survey. Seed sovereignty workshops completed with 60 seed keepers and community members. Our research and engagement activities have been benefiting growers and seed keepers in Nebraska and Michigan by addressing access to desired seeds and increasing resources available for seed production and seed selection.