Brief Summary of Minutes of Annual Meeting

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:

1. Development of qPCR test to detect and quantify annual contamination in perennial ryegrass.
2. Development of glyphosate bioassay test for annual ryegrass.
3. The use of thermogradient table in screening cover crops for cold and heat tolerance.
4. Development of two tolerance tables for native species to compare purity test results of two subsamples from the same or different submitted samples.
5. Sabry is also working on the 5^th of the “Principles of Seed Science and Technology” book.

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.

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. DOI: 10.1002/csc2.21103 - Search (bing.com).

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 https://doi.org/10.1038/s41477-024-01848-z

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. https://doi.org/10.1094/PHYTO-05-22-0164-FI

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: https://doi.org/10.1111/nph.18774

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: 10.1016/j.jgg.2024.09.012

 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) https://doi.org/10.1016/j.pbi.2024.102566

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 8^th International Hybrid Rice Symposium. Edited by Ali J. International Rice Research Institute, Los Banos, Laguna, Philippines (Impress).