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Abstract Abscission, known as shattering in crop species, is a highly regulated process by which plants shed parts. Although shattering has been studied extensively in cereals and a number of regulatory genes have been identified, much diversity in the process remains to be discovered. Teff (Eragrostis tef) is a crop native to Ethiopia that is potentially highly valuable worldwide for its nutritious grain and drought tolerance. Previous work has suggested that grain shattering in Eragrostis might have little in common with other cereals. In this study, we characterize the anatomy, cellular structure, and gene regulatory control of the abscission zone (AZ) in E. tef. We show that the AZ of E. tef is a narrow stalk below the caryopsis, which is common in Eragrostis species. X-ray microscopy, scanning electron microscopy, transmission electron microscopy, and immunolocalization of cell wall components showed that the AZ cells are thin walled and break open along with programmed cell death (PCD) at seed maturity, rather than separating between cells as in other studied species. Knockout of YABBY2/SHATTERING1, documented to control abscission in several cereals, had no effect on abscission or AZ structure in E. tef. RNA sequencing analysis showed that genes related to PCD and cell wall modification are enriched in the AZ at the early seed maturity stage. These data show that E. tef drops its seeds using a unique mechanism. Our results provide the groundwork for understanding grain shattering in Eragrostis and further improvement of shattering in E. tef.more » « less
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Abstract Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.more » « less
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In this work, we sequenced and annotated the genome of Streptochaeta angustifolia , one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.more » « less
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Abstract Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (
Setaria viridis ), a model species for studies of C4grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica ). We produced a platinum-quality genome assembly ofS. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validatedLess Shattering1 (SvLes1 ) as a gene whose product controls seed shattering. InS. italica , this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering alleleSiLes1-TE (transposable element). This resource will enhance the utility ofS. viridis for dissection of complex traits and biotechnological improvement of panicoid crops. -
Abstract Plant heterotrimeric G proteins modulate numerous developmental stress responses. Recently, receptor‐like kinases (RLKs) have been implicated as functioning with G proteins and may serve as plant G‐protein‐coupled‐receptors. The RLK FERONIA (FER), in the
Catharantus roseus RLK1‐like subfamily, is activated by a family of polypeptides called rapid alkalinization factors (RALFs). We previously showed that the Arabidopsis G protein β subunit, AGB1, physically interacts with FER, and that RALF1 regulation of stomatal movement through FER requires AGB1. Here, we investigated genetic interactions of AGB1 and FER in plant salinity response by comparing salt responses in the single and double mutants ofagb1 andfer . We show that AGB1 and FER act additively or synergistically depending on the conditions of the NaCl treatments. We further show that the synergism likely occurs through salt‐induced ROS production. In addition, we show that RALF1 enhances salt toxicity through increasing Na+accumulation and decreasing K+accumulation rather than by inducing ROS production, and that the RALF1 effect on salt response occurs in an AGB1‐independent manner. Our results indicate that RLK epistatic relationships are not fixed, as AGB1 and FER display different genetic relationships to RALF1 in stomatal versus salinity responses. -
Summary Abscission is a process in which plants shed their parts, and is mediated by a particular set of cells, the abscission zone (AZ). In grasses (Poaceae), the position of the AZ differs among species, raising the question of whether its anatomical structure and genetic control are conserved.
The ancestral position of the AZ was reconstructed. A combination of light microscopy, transmission electron microscopy, RNA‐Seq analyses and RNA
in situ hybridisation were used to compare three species, two (weedy rice andBrachypodium distachyon ) with the AZ in the ancestral position and one (Setaria viridis ) with the AZ in a derived position below a cluster of flowers (spikelet).Rice and
Brachypodium are more similar anatomically thanSetaria . However, the cell wall properties and the transcriptome of rice andBrachypodium are no more similar to each other than either is toSetaria . The set of genes expressed in the studied tissues is generally conserved across species, but the precise developmental and positional patterns of expression and gene networks are almost entirely different.Transcriptional regulation of AZ development appears to be extensively rewired among the three species, leading to distinct anatomical and morphological outcomes.
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Premise Abscission zones (
AZ ) are specialized cell layers that separate plant parts at the organ junction upon developmental or environmental signals. Fruit or seed abscission has been well studied in model species because of its crucial role for seed dispersal. Previous work showed thatAZ localization differs among species of Poaceae and thatAZ formation is histologically and genetically distinct in three distantly related grass species, refuting the idea of a broadly conserved module. However, whetherAZ structure is consistent within subfamilies is unknown.Methods Eleven species were selected from six subfamilies of Poaceae, and their
AZ was investigated using paraffin‐embedded, stained material. Observations were added from the literature for an additional six species. Data were recorded onAZ location and whether cells in theAZ were distinguishable by size or lignification. Characteristics of theAZ were mapped on the phylogeny using maximum likelihood.Results Abscission zone anatomy and histology vary among species, and characteristics of the
AZ do not correlate with phylogeny. Twelve of the seventeen studied species have anAZ in which the cells are significantly smaller than surrounding cells. Of these, eight have differential lignification. Differential lignification is often associated with differential cell size, but not vice versa.Conclusions Neither smaller cells in the
AZ nor differential lignification between theAZ and surrounding cells is required for abscission, although differential cell size and lignification are often correlated. Abscission zone anatomy does not correlate with phylogeny, suggesting its rapid change over evolutionary time.