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1. The transcriptome landscape of developing barley seeds

   https://doi.org/10.1093/plcell/koae095  

   Kovacik, Martin; Nowicka, Anna; Zwyrtková, Jana; Strejčková, Beáta; Vardanega, Isaia; Esteban, Eddi; Pasha, Asher; Kaduchová, Kateřina; Krautsova, Maryna; Červenková, Marie; et al (April 2024, The Plant Cell)

   Abstract Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4–32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains. 

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2. Spatially Resolved Transcriptomic Analysis of the Germinating Barley Grain

   https://doi.org/10.1101/2023.01.24.525109  

   Marta Peirats-Llobet, Changyu Yi (January 2023, bioRxiv)

   Seeds, which provide a major source of calories for humans, are a unique stage of a flowering plant’s lifecycle. During seed germination the embryo reactivates rapidly and goes through major developmental transitions to become a seedling. This requires extensive and complex spatiotemporal coordination of cell and tissue activity. Existing gene expression profiling methods, such as laser capture microdissection followed by RNA-seq and single-cell RNA7 seq, suffer from either low throughput or the loss of spatial information about the cells analysed. Spatial transcriptomics methods couple high throughput analysis of gene expression simultaneously with the ability to record the spatial location of each individual region analysed. We developed a spatial transcriptomics workflow for germinating barley grain to better understand the spatiotemporal control of gene expression within individual seed cell types. More than 14,000 genes were differentially regulated across 0, 1, 3, 6 and 24 hours after imbibition. This approach enabled us to observe that many functional categories displayed specific spatial expression patterns that could be resolved at a sub-tissue level. Individual aquaporin gene family members, important for water and ion transport, had specific spatial expression patterns over time, as well as genes related to cell wall modification, membrane transport and transcription factors. Using spatial autocorrelation algorithms, we were able to identify auxin transport genes that had increasingly focused expression within subdomains of the embryo over germination time, suggestive of a role in establishment of the embryo axis. Together, our data provides an unprecedented spatially resolved cellular map for barley grain germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination. The data can be viewed at https://spatial.latrobe.edu.au/. 

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3. Regulation of the plastochron by three many-noded dwarf genes in barley

   https://doi.org/10.1371/journal.pgen.1009292  

   Hibara, Ken-ichiro; Miya, Masayuki; Benvenuto, Sean Akira; Hibara-Matsuo, Naoko; Mimura, Manaki; Yoshikawa, Takanori; Suzuki, Masaharu; Kusaba, Makoto; Taketa, Shin; Itoh, Jun-ichi (May 2021, PLOS Genetics)

   Hake, Sarah (Ed.)

   The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf ( mnd ) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plastochron1 ( pla1 ), pla2 , and pla3 mutants in rice. In addition, the maturation of mnd leaves was accelerated, similar to pla mutants in rice. Several barley mnd alleles were derived from three genes— MND1 , MND4 , and MND8 . Although MND4 coincided with a cytochrome P450 family gene that is a homolog of rice PLA1 , we clarified that MND1 and MND8 encode an N-acetyltransferase-like protein and a MATE transporter-family protein, which are respectively orthologs of rice GW6a and maize BIGE1 and unrelated to PLA2 or PLA3 . Expression analyses of the three MND genes revealed that MND1 and MND4 were expressed in limited regions of the shoot apical meristem and leaf primordia, but MND8 did not exhibit a specific expression pattern around the shoot apex. In addition, the expression levels of the three genes were interdependent among the various mutant backgrounds. Genetic analyses using the double mutants mnd4mnd8 and mnd1mnd8 indicated that MND1 and MND4 regulate the plastochron independently of MND8 , suggesting that the plastochron in barley is controlled by multiple genetic pathways involving MND1 , MND4 , and MND8 . Correlation analysis between leaf number and leaf blade length indicated that both traits exhibited a strong negative association among different genetic backgrounds but not in the same genetic background. We propose that MND genes function in the regulation of the plastochron and leaf growth and revealed conserved and diverse aspects of plastochron regulation via comparative analysis of barley and rice. 

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4. Genomic signatures of barley breeding for environmental adaptation to the new continents

   https://doi.org/10.1111/pbi.14077  

   Hu, Haifei; Wang, Penghao; Angessa, Tefera Tolera; Zhang, Xiao‐Qi; Chalmers, Kenneth J; Zhou, Gaofeng; Hill, Camilla Beate; Jia, Yong; Simpson, Craig; Fuller, John; et al (September 2023, Plant Biotechnology Journal)
5. Measuring hidden phenotype: quantifying the shape of barley seeds using the Euler characteristic transform

   https://doi.org/10.1093/insilicoplants/diab033  

   Amézquita, Erik J; Quigley, Michelle Y; Ophelders, Tim; Landis, Jacob B; Koenig, Daniel; Munch, Elizabeth; Chitwood, Daniel H (January 2022, in silico Plants)

   Chen, Tsu-Wei; Long, Stephen P (Ed.)

   Abstract Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare and analyse this information embedded in a robust and concise way, we turn to topological data analysis (TDA), specifically the Euler characteristic transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray computed tomography (CT) technology at 127 μm resolution. The Euler characteristic transform measures shape by analysing topological features of an object at thresholds across a number of directional axes. A Kruskal–Wallis analysis of the information encoded by the topological signature reveals that the Euler characteristic transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of ‘hidden’ shape nuances which are otherwise not detected. 

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