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1. Biggest of tinies: natural variation in seed size and mineral distribution in the ancient crop tef [Eragrostis tef (Zucc.) Trotter]

   https://doi.org/10.3389/fpls.2024.1485819  

   Whisnant, Eric D; Keith, Christian; Smieska, Louisa; Chia, Ju-Chen; Bekele-Alemu, Abreham; Vatamaniuk, Olena K; VanBuren, Robert; Ligaba-Osena, Ayalew (December 2024, Frontiers in plant science)

   Jain, Shri_Mohan (Ed.)

   Tef Eragrostis tef(Zucc.) Trotter] is the major staple crop for millions of people in Ethiopia and Eritrea and is believed to have been domesticated several thousand years ago. Tef has the smallest grains of all the cereals, which directly impacts its productivity and presents numerous challenges to its cultivation. In this study, we assessed the natural variation in seed size of 189 tef and 11 accessions of its wild progenitor Indian lovegrass (Eragrostis pilosa (L.) P. Beauv.) and explored the mineral distribution of representative accessions. Our findings revealed significant natural variation in seed size and mineral concentration among both the tef and E. pilosa accessions. We observed significant variation in seed length, seed width, and seed area among the accessions of both Eragrostis spp. we analyzed. Using representative accessions of both species, we also found significant variation in 1000-grain weight. The observed variation in seed size attributes prompted us to use comparative genomics to identify seed size regulating genes based on the well-studied and closely related monocot cereal rice (Oryza sativa L.]. Using this approach, we identified putative orthologous genes in the tef genome that belong to a number of key pathways known to regulate seed size in rice. Phylogenetic analysis of putative tef orthologs of ubiquitin-proteasome, G-protein, MAPK, and brassinosteroid (BR)-family genes indicate significant similarity to seed size regulating genes in rice and other cereals. Because tef is known to be more nutrient-dense than other more common cereals such as rice, wheat, and maize, we also studied the mineral concentration of selected accessions using ICP-OES and explored their distribution within the seeds using synchrotron-based X-ray fluorescence (SXRF) microscopy. The findings showed significant variation in seed mineral concentration and mineral distribution among the selected accessions of both Eragrostis spp. This study highlights the natural variation in seed size attributes, mineral concentration, and distribution, while establishing the basis for understanding the genetic mechanisms regulating these traits. We hope our findings will lead to a better understanding of the evolution of tef at the genetic level and for the development of elite tef cultivars to improve seed size, yield, and quality of the grains. 

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2. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds

   https://doi.org/10.1111/pce.14103  

   Sandhu, Jaspreet; Irvin, Larissa; Liu, Kan; Staswick, Paul; Zhang, Chi; Walia, Harkamal (June 2021, Plant, Cell & Environment)

   Abstract A transient heat stress occurring during early seed development in rice (Oryza sativa) reduces seed size by altering endosperm development. However, the relationship between the timing of the stress and specific developmental stage on heat sensitivity is not well‐understood. To address this, we imposed a series of non‐overlapping heat stress treatments and found that young seeds are most sensitive during the first two days after flowering. Temporal transcriptome analysis of developing, heat stressed (35°C) seeds during this window shows thatInositol‐requiring enzyme 1 (IRE1)‐mediated endoplasmic reticulum (ER) stress response and jasmonic acid (JA) pathways are the early (1–3 h) drivers of heat stress response. We propose that increased JA levels under heat stress may precede ER stress response as JA application promotes the spliced form ofOsbZIP50,an ER response marker gene linked to IRE1‐specific pathway. This study presents temporal and mechanistic insights into the role of JA and ER stress signalling during early heat stress response of rice seeds that impact both grain size and quality. Modulating the heat sensitivity of the early sensing pathways and downstream endosperm development genes can enhance rice resilience to transient heat stress events. 

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3. A Deep Learning Framework for Processing and Classification of Hyperspectral Rice Seed Images Grown under High Day and Night Temperatures

   https://doi.org/10.3390/s23094370  

   Díaz-Martínez, Víctor; Orozco-Sandoval, Jairo; Manian, Vidya; Dhatt, Balpreet K; Walia, Harkamal (May 2023, Sensors)

   A framework combining two powerful tools of hyperspectral imaging and deep learning for the processing and classification of hyperspectral images (HSI) of rice seeds is presented. A seed-based approach that trains a three-dimensional convolutional neural network (3D-CNN) using the full seed spectral hypercube for classifying the seed images from high day and high night temperatures, both including a control group, is developed. A pixel-based seed classification approach is implemented using a deep neural network (DNN). The seed and pixel-based deep learning architectures are validated and tested using hyperspectral images from five different rice seed treatments with six different high temperature exposure durations during day, night, and both day and night. A stand-alone application with Graphical User Interfaces (GUI) for calibrating, preprocessing, and classification of hyperspectral rice seed images is presented. The software application can be used for training two deep learning architectures for the classification of any type of hyperspectral seed images. The average overall classification accuracy of 91.33% and 89.50% is obtained for seed-based classification using 3D-CNN for five different treatments at each exposure duration and six different high temperature exposure durations for each treatment, respectively. The DNN gives an average accuracy of 94.83% and 91% for five different treatments at each exposure duration and six different high temperature exposure durations for each treatment, respectively. The accuracies obtained are higher than those presented in the literature for hyperspectral rice seed image classification. The HSI analysis presented here is on the Kitaake cultivar, which can be extended to study the temperature tolerance of other rice cultivars. 

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4. Endomembrane mediated-trafficking of seed storage proteins: from Arabidopsis to cereal crops

   https://doi.org/10.1093/jxb/erab519  

   Zheng, Ping; Zheng, Chunyan; Otegui, Marisa S; Li, Faqiang (November 2021, Journal of Experimental Botany)

   Penfield, Steve (Ed.)

   Abstract Seed storage proteins (SSPs) are of great importance in plant science and agriculture, particularly in cereal crops, due to their nutritional value and their impact on food properties. During seed maturation, massive amounts of SSPs are synthesized and deposited either within protein bodies derived from the endoplasmic reticulum, or into specialized protein storage vacuoles (PSVs). The processing and trafficking of SSPs vary among plant species, tissues, and even developmental stages, as well as being influenced by SSP composition. The different trafficking routes, which affect the amount of SSPs that seeds accumulate and their composition and modifications, rely on a highly dynamic and functionally specialized endomembrane system. Although the general steps in SSP trafficking have been studied in various plants, including cereals, the detailed underlying molecular and regulatory mechanisms are still elusive. In this review, we discuss the main endomembrane routes involved in SSP trafficking to the PSV in Arabidopsis and other eudicots, and compare and contrast the SSP trafficking pathways in major cereal crops, particularly in rice and maize. In addition, we explore the challenges and strategies for analyzing the endomembrane system in cereal crops. 

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5. Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance

   https://doi.org/10.3390/plants12152850  

   Osakina, Aron; Jia, Yulin (August 2023, Plants)

   Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders. 

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