Tissue-specific transcriptomics reveal functional differences in maize floral development

Flowers are produced by floral meristems, groups of stem cells that give rise to floral organs. In grasses, including the major cereal crops, flowers (florets) are contained in spikelets, which contain one to many florets, depending on the species. Importantly, not all grass florets are developmentally equivalent, and one or more florets are often sterile or abort in each spikelet. Members of the Andropogoneae tribe, including maize, produce spikelets with two florets; the upper and lower florets are usually dimorphic and the lower floret greatly reduced compared to the upper floret. In maize ears, early development appears identical in both florets but the lower floret ultimately aborts. To gain insight into the functional differences between florets of different fates, we used laser capture microdissection coupled with RNA-seq to globally examine gene expression in upper and lower floral meristems in maize. Differentially expressed genes were involved in hormone regulation, cell wall, sugar and energy homeostasis. Furthermore, cell wall modifications and sugar accumulation differed between the upper and lower florets. Finally, we identified a novel boundary domain between upper and lower florets, which we hypothesize is important for floral meristem activity. We propose a model in which growth is suppressed in the lower floret by limiting sugar availability and upregulating genes involved in growth repression. This growth repression module may also regulate floret fertility in other grasses and potentially be modulated to engineer more productive cereal crops.

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Transcriptional landscapes of floral meristems in barley

Science Advances ◽

10.1126/sciadv.abf0832 ◽

2021 ◽

Vol 7 (18) ◽

pp. eabf0832

Author(s):

J. Thiel ◽

R. Koppolu ◽

C. Trautewig ◽

C. Hertig ◽

S. M. Kale ◽

...

Keyword(s):

High Resolution ◽

Hordeum Vulgare ◽

Reproductive Success ◽

Regulatory Networks ◽

Cereal Crops ◽

Organ Development ◽

Rna Seq ◽

Floral Meristems ◽

Laser Capture ◽

Laser Capture Microdissected

Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.

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Impacts of Nitrogen Deficiency on Wheat (Triticum aestivum L.) Grain During the Medium Filling Stage: Transcriptomic and Metabolomic Comparisons

Frontiers in Plant Science ◽

10.3389/fpls.2021.674433 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yanjie Wang ◽

Demei Wang ◽

Zhiqiang Tao ◽

Yushuang Yang ◽

Zhenxian Gao ◽

...

Keyword(s):

Triticum Aestivum ◽

Cell Wall ◽

Grain Yield ◽

Seedling Stage ◽

Sugar Accumulation ◽

Grain Protein ◽

Rna Seq ◽

Filling Stage ◽

N Deficiency ◽

The Impact

Nitrogen (N) supplementation is essential to the yield and quality of bread wheat (Triticum aestivum L.). The impact of N-deficiency on wheat at the seedling stage has been previously reported, but the impact of distinct N regimes applied at the seedling stage with continuous application on filling and maturing wheat grains is lesser known, despite the filling stage being critical for final grain yield and flour quality. Here, we compared phenotype characteristics such as grain yield, grain protein and sugar quality, plant growth, leaf photosynthesis of wheat under N-deficient and N-sufficient conditions imposed prior to sowing (120 kg/hm2) and in the jointing stage (120 kg/hm2), and then evaluated the effects of this continued stress through RNA-seq and GC-MS metabolomics profiling of grain at the mid-filling stage. The results showed that except for an increase in grain size and weight, and in the content of total sugar, starch, and fiber in bran fraction and white flour, the other metrics were all decreased under N-deficiency conditions. A total of 761 differentially expressed genes (DEGs) and 77 differentially accumulated metabolites (DAMs) were identified. Under N-deficiency, 51 down-regulated DEGs were involved in the process of impeding chlorophyll synthesis, chloroplast development, light harvesting, and electron transfer functions of photosystem, which resulted in the SPAD and Pn value decreased by 32 and 15.2% compared with N-sufficiency, inhibited photosynthesis. Twenty-four DEGs implicated the inhibition of amino acids synthesis and protein transport, in agreement with a 17–42% reduction in ornithine, cysteine, aspartate, and tyrosine from metabolome, and an 18.6% reduction in grain protein content. However, 14 DEGs were implicated in promoting sugar accumulation in the cell wall and another six DEGs also enhanced cell wall synthesis, which significantly increased fiber content in the endosperm and likely contributed to increasing the thousands-grain weight (TGW). Moreover, RNA-seq profiling suggested that wheat grain can improve the capacity of DNA repair, iron uptake, disease and abiotic stress resistance, and oxidative stress scavenging through increasing the content levels of anthocyanin, flavonoid, GABA, galactose, and glucose under N-deficiency condition. This study identified candidate genes and metabolites related to low N adaption and tolerance that may provide new insights into a comprehensive understanding of the genotype-specific differences in performance under N-deficiency conditions.

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Spaceflight Induces Novel Regulatory Responses in Arabidopsis Seedling as Revealed by Combined Proteomic and Transcriptomic Analyses

10.21203/rs.2.21481/v2 ◽

2020 ◽

Author(s):

Colin Peter Singer Kruse ◽

Alexander D Meyers ◽

Proma Basu ◽

Sarahann Hutchinson ◽

Darron R Luesse ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Membrane Proteins ◽

Plant Growth ◽

Gene Transcription ◽

Space Station ◽

Growth Efficiency ◽

Rna Seq ◽

Plastid Gene ◽

The Impact

Abstract Background: Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated. Results: Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4,. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-a 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription. Conclusions: The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What’s more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.

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Transcripts repressed at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit.

10.1101/2021.01.19.427234 ◽

2021 ◽

Author(s):

Stefania Savoi ◽

Laurent Torregrosa ◽

Charles Romieu

Keyword(s):

Cell Wall ◽

Regulatory Elements ◽

Solute Concentration ◽

Growth Patterns ◽

Individual Growth ◽

Sugar Accumulation ◽

Minor Role ◽

Phloem Unloading ◽

Sugar Transporters ◽

A Minor

AbstractTranscriptomic changes at the cessation of sugar accumulation in the pericarp of Vitis vinifera were addressed on single berries re-synchronized according to their individual growth patterns. The net rates of water, sugars and K+ accumulation inferred from individual growth and solute concentration confirmed that these inflows stopped simultaneously in the ripe berry, while the small amount of malic acid remaining at this stage was still being oxidized at a low rate. Resynchronized individual berries displayed negligible variations in gene expression among triplicates. RNA-Seq studies revealed sharp reprogramming of cell wall enzymes and structural proteins, associated with an 80% repression of specific sugar transporters and aquaporins on the plasma or tonoplast membranes, at the stop of phloem unloading in the three genotypes and two environments investigated. The prevalence of SWEET transporters suggests that electrogenic transporters would just play a minor role on the plasma membrane of SE/CC complex, and the one of the flesh, while sucrose/H+ exchangers dominate on its tonoplast. Cis-regulatory elements present in their promoters allowed to sort these transporters in different groups, also including specific TIPs and PIPs paralogs, and cohorts of cell wall related genes. These results lead us to propose which structural, developmental and energy adaptations would give this fruit such a power of attraction for water and photoassimilates.

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The Antifungal Effects of Citral on Magnaporthe oryzae Occur via Modulation of Chitin Content as Revealed by RNA-Seq Analysis

Journal of Fungi ◽

10.3390/jof7121023 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1023

Author(s):

Xingchen Song ◽

Qijun Zhao ◽

Aiai Zhou ◽

Xiaodong Wen ◽

Ming Li ◽

...

Keyword(s):

Cell Wall ◽

Magnaporthe Oryzae ◽

Amino Sugar ◽

Cell Wall Integrity ◽

Rna Seq ◽

Chitin Synthesis ◽

Nucleotide Sugar ◽

Qpcr Analysis ◽

Antifungal Effects ◽

Glucose Synthesis

The natural product citral has previously been demonstrated to possess antifungal activity against Magnaporthe oryzae. The purpose of this study was to screen and annotate genes that were differentially expressed (DEGs) in M. oryzae after treatment with citral using RNA sequencing (RNA-seq). Thereafter, samples were reprepared for quantitative real-time PCR (RT-qPCR) analysis verification of RNA-seq data. The results showed that 649 DEGs in M. oryzae were significantly affected after treatment with citral (100 μg/mL) for 24 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) and a gene ontology (GO) analysis showed that DEGs were mainly enriched in amino sugar and nucleotide sugar metabolic pathways, including the chitin synthesis pathway and UDP sugar synthesis pathway. The results of the RT-qPCR analysis also showed that the chitin present in M. oryzae might be degraded to chitosan, chitobiose, N-acetyl-D-glucosamine, and β-D-fructose-6-phosphate following treatment with citral. Chitin degradation was indicated by damaged cell-wall integrity. Moreover, the UDP glucose synthesis pathway was involved in glycolysis and gluconeogenesis, providing precursors for the synthesis of polysaccharides. Galactose-1-phosphate uridylyltransferase, which is involved in the regulation of UDP-α-D-galactose and α-D-galactose-1-phosphate, was downregulated. This would result in the inhibition of UDP glucose (UDP-Glc) synthesis, a reduction in cell-wall glucan content, and the destruction of cell-wall integrity.

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Fertility of Pedicellate Spikelets in Sorghum is Controlled by a Jasmonic Acid Regulatory Module

10.1101/773564 ◽

2019 ◽

Author(s):

Nicholas Gladman ◽

Yinping Jiao ◽

Young Koung Lee ◽

Lifang Zhang ◽

Ratan Chopra ◽

...

Keyword(s):

Transcription Factor ◽

Jasmonic Acid ◽

Sorghum Bicolor ◽

Spikelet Fertility ◽

Cereal Crops ◽

Grain Number ◽

Regulatory Module ◽

Induced Module ◽

Acid Pathway ◽

Floral Meristems

AbstractAs in other cereal crops, the panicles of sorghum (Sorghum bicolor (L.) Moench) comprise two types of floral spikelets (grass flowers). Only sessile spikelets (SSs) are capable of producing viable grains, whereas pedicellate spikelets (PSs) cease development after initiation and eventually abort. Consequently, grain number per panicle (GNP) is lower than the total number of flowers produced per panicle. The mechanism underlying this differential fertility is not well understood. To investigate this issue, we isolated a series of EMS-induced multiseeded (msd) mutants that result in full spikelet fertility, effectively doubling GNP. Previously, we showed that MSD1 is a TCP (Teosinte branched/Cycloidea/PCF) transcription factor that regulates jasmonic acid (JA) biosynthesis, and ultimately floral sex organ development. Here, we show that MSD2 encodes a lipoxygenase (LOX) that catalyzes the first committed step of JA biosynthesis. Further, we demonstrate that MSD1 binds to the promoters of MSD2 and other JA pathway genes. Together, these results show that a JA-induced module regulates sorghum panicle development and spikelet fertility. The findings advance our understanding of inflorescence development and could lead to new strategies for increasing GNP and grain yield in sorghum and other cereal crops.SignificanceThrough a single base pair mutation, grain number can be increased by ~200% in the globally important crop Sorghum bicolor. This mutation affects the expression of an enzyme, MSD2, that catalyzes the jasmonic acid pathway in developing floral meristems. The global gene expression profile in this enzymatic mutant is similar to that of a transcription factor mutant, msd1, indicating that disturbing any component of this regulatory module disrupts a positive feedback loop that occurs normally due to regular developmental perception of jasmonic acid. Additionally, the MSD1 transcription factor is able to regulate MSD2 in addition to other jasmonic acid pathway genes, suggesting that it is a primary transcriptional regulator of this hormone signaling pathway in floral meristems.

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