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1. Wide‐ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum

   https://doi.org/10.1111/tpj.14671  

   Chakrabarti, Manohar ; de Lorenzo, Laura ; Abdel‐Ghany, Salah E. ; Reddy, Anireddy S. N. ; Hunt, Arthur G. ( January 2020 , The Plant Journal)

   Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport.Sorghumis a major cereal crop in the world and, despite its importance, not much is known about the role of post‐transcriptional regulation in mediating responses to abiotic stresses inSorghum. A genome‐wide APA analysis unveiled widespread occurrence of APA inSorghumin response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re‐directing of transcriptional output into non‐productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response ofSorghumto abiotic stresses that involves the re‐direction of transcriptional output into non‐productive transcriptional and translational pathways. Large numbers of stress‐inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress‐specificcis‐element in intronic poly(A) sites used in drought‐ and heat‐stressed plants that might play an important role in non‐canonical poly(A) site choice in response to abiotic stresses.
2. Genetic Perturbation of the Starch Biosynthesis in Maize Endosperm Reveals Sugar-Responsive Gene Networks

   https://doi.org/10.3389/fpls.2021.800326  

   Finegan, Christina ; Boehlein, Susan K. ; Leach, Kristen A. ; Madrid, Gabriela ; Hannah, L. Curtis ; Koch, Karen E. ; Tracy, William F. ; Resende, Marcio F. ( February 2022 , Frontiers in Plant Science)

   In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such as large subunit of AGPase Shrunken2 ( Sh2 ) and isoamylase type DBE Sugary1 ( Su1 ). While many starch biosynthesis enzymes have been characterized, the mechanisms of certain genes (including Sugary enhancer1 ) are yet undefined, and very little is understood about the regulation of starch biosynthesis. As a model, we utilize commercially important sweet corn mutations, sh2 and su1 , to genetically perturb starch production in the endosperm. To characterize the transcriptomic response to starch mutations and identify potential regulators of this pathway, differential expression and coexpression network analysis was performed on near-isogenic lines (NILs) (wildtype, sh2 , and su1 ) in six genetic backgrounds. Lines were grown in field conditions and kernels were sampled in consecutive developmental stages (blister stage at 14 days after pollination (DAP), milk stage at 21 DAP, and dent stage at 28 DAP). Kernels were dissected to separate embryo and pericarp from the endosperm tissue and 3′ RNA-seq libraries were prepared. Mutation of the Su1 gene led to minimal changes in the endosperm transcriptome. Responses to loss of sh2 function include increased expression of sugar (SWEET) transportersmore »and of genes for ABA signaling. Key regulators of starch biosynthesis and grain filling were identified. Notably, this includes Class II trehalose 6-phosphate synthases, Hexokinase1 , and Apetala2 transcription factor-like (AP2/ERF) transcription factors. Additionally, our results provide insight into the mechanism of Sugary enhancer1 , suggesting a potential role in regulating GA signaling via GRAS transcription factor Scarecrow-like1 .« less
3. Overexpression of a Plant-Specific Gγ Protein, AGG3 , in the Model Monocot Setaria viridis Confers Tolerance to Heat Stress

   https://doi.org/10.1093/pcp/pcad093  

   Torres Rodríguez, María Daniela ; Bhatnagar, Nikita ; Pandey, Sona ( August 2023 , Plant And Cell Physiology)

   The vascular plant-specific, cysteine-rich type III Gγ proteins, which are integral components of the heterotrimeric G-protein complex, play crucial roles in regulating a multitude of plant processes, including those related to crop yield and responses to abiotic stresses. The presence of multiple copies of type III Gγ proteins in most plants and a propensity of the presence of specific truncated alleles in many cultivated crops present an ambiguous picture of their roles in modulating specific responses. AGG3 is a canonical type III Gγ protein of Arabidopsis, and its overexpression in additional model crops offers the opportunity to directly evaluate the effects of protein expression levels on plant phenotypes. We have shown that AGG3 overexpression in the monocot model Setaria viridis leads to an increase in seed yield. In this study, we have investigated the response of the S. viridis plants overexpressing AGG3 to heat stress (HS), one of the most important abiotic stresses affecting crops worldwide. We show that a short span of HS at a crucial developmental time point has a significant effect on plant yield in the later stages. We also show that plants with higher levels of AGG3 are more tolerant to HS. This is attributedmore »to an altered regulation of stress-responsive genes and improved modulation of the photosynthetic efficiency during the stress. Overall, our results confirm that AGG3 plays a crucial role in regulating plant responses to unfavorable environmental conditions and may contribute positively to avoiding crop yield losses.

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4. CYTOKININ RESPONSE FACTOR 2 is involved in modulating the salt stress response

   https://doi.org/10.1111/tpj.15726  

   Keshishian, Erika A. ; Cliver, Brannan R. ; McLaughlin, William F. ; Hallmark, H. Tucker ; Plačková, Lenka ; Goertzen, Leslie R. ; Novák, Ondřej ; Cobine, Paul A. ; Leisner, Courtney P. ; Rashotte, Aaron M. ( March 2022 , The Plant Journal)

   Cytokinin has strong connections to development and a growing role in the abiotic stress response. Here we show that CYTOKININ RESPONSE FACTOR 2 (CRF2) is additionally involved in the salt (NaCl) stress response. CRF2 promoter‐GUS expression indicates CRF2 involvement in the response to salt stress as well as the previously known cytokinin response. Interestingly, CRF2 mutant seedlings are quite similar to the wild type (WT) under non‐stressed conditions yet have many distinct changes in response to salt stress. Cytokinin levels measured by liquid chromatography–tandem mass spectrometry (LC‐MS/MS) that increased in the WT after salt stress are decreased incrf2, potentially from CRF2 regulation of cytokinin biosynthesis genes. Ion content measured by inductively coupled plasma optical emission spectrometry (ICP‐OES) was increased in the WT for Na, K, Mn, Ca and Mg after salt stress, whereas the corresponding Ca and Mg increases are lacking incrf2. Many genes examined by RNA‐seq analysis were altered transcriptionally by salt stress in both the WT andcrf2, yet interestingly approximately one‐third of salt‐modifiedcrf2transcripts (2655) showed unique regulation. Different transcript profiles for salt stress incrf2compared with the WT background was further supported through an examination of co‐expressed genes by weighted gene correlation network analysis (WGCMA) and principal component analysismore »(PCA). Additionally, Gene Ontology (GO) enrichment terms found from salt‐treated transcripts revealed most photosynthesis‐related terms as only being affected incrf2, leading to an examination of chlorophyll levels and the efficiency of photosystem II (via the ratio of variable fluorescence to maximum fluorescence,F_v/F_m) as well as physiology after salt treatment. Salt stress‐treatedcrf2plants had both reduced chlorophyll levels and lowerF_v/F_mvalues compared with the WT, suggesting that CRF2 plays a role in the modulation of salt stress responses linked to photosynthesis.

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5. Genome wide study of cysteine rich receptor like proteins in Gossypium sp.

   https://doi.org/10.1038/s41598-022-08943-1  

   Hussain, Athar ; Asif, Naila ; Pirzada, Abdul Rafay ; Noureen, Azka ; Shaukat, Javeria ; Burhan, Akif ; Zaynab, Madiha ; Ali, Ejaz ; Imran, Koukab ; Ameen, Ayesha ; et al ( March 2022 , Scientific Reports)

   Cysteine-rich receptor-like-kinases (CRKs), a transmembrane subfamily of receptor-like kinase, play crucial roles in plant adaptation. As such cotton is the major source of fiber for the textile industry, but environmental stresses are limiting its growth and production. Here, we have performed a deep computational analysis ofCRKsin fiveGossypiumspecies, includingG. arboreum(60 genes), G. raimondii(74 genes), G. herbaceum(65 genes), G. hirsutum(118 genes), andG. barbadense(120 genes). All identified CRKs were classified into 11 major classes and 43 subclasses with the finding of several novel CRK-associated domains includingALMT, FUSC_2, Cript, FYVE,andPkinase. Of these,DUF26_DUF26_Pkinase_Tyrwas common and had elevated expression under different biotic and abiotic stresses. Moreover, the 35 land plants comparison identified several newCRKsdomain-architectures. Likewise, several SNPs and InDels were observed in CLCuD resistantG. hirsutum. The miRNA target side prediction and their expression profiling in different tissues predictedmiR172as a major CRK regulating miR. The expression profiling ofCRKsidentified multiple clusters with co-expression under certain stress conditions. The expression analysis under CLCuD highlighted the role ofGhCRK057, GhCRK059, GhCRK058, and GhCRK081in resistant accession. Overall, these results provided primary data for future potential functional analysis as well as a reference study for other agronomically important crops.