Karen A. Sanguinet

Pennycress ( Thlaspi arvense ) is an intermediate oilseed bioenergy crop under development for growth over winter in the Midwest. Crucial work remains to domesticate and optimize pennycress for incorporation into cropping systems and to increase its resilience to stresses. We found that increased planting density reduces biomass and hastens time to flowering and maturity in field‐grown pennycress, both of which are associated with plant shade avoidance responses (SAR). We confirmed that pennycress elongates when exposed to foliar shade and elevated ambient temperatures (28°C), physiological responses controlled by the red‐light photoreceptor PHYTOCHROME B. We applied knowledge of the PHYTOCHROME B signalling pathway from Arabidopsis thaliana to identify target genes to mutate to suppress shade‐avoidance responses during interseeding and to alter tissue responses to elevated temperatures. Mutating PHYTOCHROME INTERACTING FACTOR 7 reduced organ elongation to competition and heat cues and retained a compact rosette when exposed to shade and/or elevated temperature. Crucially, yield and oil content were unaltered in pif7 . Furthermore, indicators of plant health, including hue, chlorophyll indices, and root system architecture, were improved in the pif7 mutant compared with the wild type. This showed that plant architecture and physiological health can be uncoupled under competition and heat stress, supporting our efforts to attenuate morphological responses to environmental cues. We propose that mutating PIF7 is a strategy to reduce SAR, improve pennycress performance at high densities during interseeding establishment in standing crops, and address the impacts of a warming climate on plant architecture.

Pennycress ( Thlaspi arvense ) is being developed as a winter annual intermediate oilseed bioenergy crop in the Midwest during typical fallow periods. Crucial work remains to domesticate and optimize pennycress for incorporation into cropping systems and increasing resilience to rising temperatures. We found that increased planting density reduces biomass and hastens time to flowering and maturity, which are associated with shade avoidance responses. In controlled conditions, we found that pennycress elongates in response to foliar shade and increased ambient temperatures (28 °C). We applied the knowledge base from Arabidopsis thaliana to manipulate genes in the PHYB signaling pathway to simultaneously decrease the shade avoidance response during interseeding and tissue responses to elevated temperatures. Evaluation of CRISPR alleles of PIF7 shows that pif7 reduces organ elongation to competition and heat cues and retains a compact rosette when exposed to shade or elevated temperature and their combination. Crucially, yield and oil content were unaltered in pif7 and plants maintained earlier flowering in stress conditions. Furthermore, indicators of plant health, such as hue, chlorophyll indices, and root system architecture, were improved between wild type and pif7 . This is evidence that plant architecture and physiological health can be uncoupled under competition and heat conditions, supporting our efforts to attenuate morphological responses to environmental cues. We propose this strategy for reducing SAR, improving pennycress performance at high densities, for during interseeding establishment in standing crops, and in a warming climate.

Summary: Root hair (RH) cells can elongate to several hundred times their initial size, and are an ideal model system for investigating cell size control. Their development is influenced by both endogenous and external signals, which are combined to form an integrative response. Surprisingly, a low‐temperature condition of 10°C causes increased RH growth in Arabidopsis and in several monocots, even when the development of the rest of the plant is halted. Previously, we demonstrated a strong correlation between RH growth response and a significant decrease in nutrient availability in the growth medium under low‐temperature conditions. However, the molecular basis responsible for receiving and transmitting signals related to the availability of nutrients in the soil, and their relation to plant development, remain largely unknown. We have discovered two antagonic gene regulatory networks (GRNs) controlling RH early transcriptome responses to low temperature. One GNR enhances RH growth and it is commanded by the transcription factors (TFs) ROOT HAIR DEFECTIVE 6 (RHD6), HAIR DEFECTIVE 6‐LIKE 2 and 4 (RSL2‐RSL4) and a member of the homeodomain leucine zipper (HD‐Zip I) group I 16 (AtHB16). On the other hand, a second GRN was identified as a negative regulator of RH growth at low temperature and it is composed by the trihelix TF GT2‐LIKE1 (GTL1) and the associated DF1, a previously unidentified MYB‐like TF (AT2G01060) and several members of HD‐Zip I group (AtHB3, AtHB13, AtHB20, AtHB23). Functional analysis of both GRNs highlights a complex regulation of RH growth response to low temperature, and more importantly, these discoveries enhance our comprehension of how plants synchronize RH growth in response to variations in temperature at the cellular level.

SUMMARY: Root systems are uniquely adapted to fluctuations in external nutrient availability. In response to suboptimal nitrogen conditions, plants adopt a root foraging strategy that favors a deeper and more branched root architecture, enabling them to explore and acquire soil resources. This response is gradually suppressed as nitrogen conditions improve. However, the root hairless mutant buzz in Brachypodium distachyon shows a constitutive nitrogen‐foraging phenotype with increased root growth and root branching under nitrate‐rich conditions. To investigate how this unique root structure and root hair morphology in the buzz mutant affects nitrate metabolism, we measured the expression of nitrate‐responsive genes, nitrate uptake and accumulation, nitrate reductase activity, and nitrogen use efficiency. We found that nitrate responses were upregulated by low nitrate conditions in buzz relative to wild type and correlated with increased expression of nitrate transport genes. In addition, buzz mutants showed increased nitrate uptake and a higher accumulation of nitrate in shoots. The buzz mutant also showed increased nitrate reductase activity in the shoots under low nitrate conditions. However, developmentally mature wild‐type and buzz plants grown under low nitrate had similar nitrogen use efficiencies. These findings suggest that BUZZ influences nitrate signaling and that enhanced responsiveness to nitrate is required in buzz seedlings to compensate for the lack of root hairs. These data question the importance of root hairs in enhancing nitrate uptake and expand our understanding of how root hairs in grasses affect physiological responses to low nitrate availability.

Background: CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance. Results: In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs. Conclusions: Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.

Conventional farming practices have negatively impacted micronutrient fertility and overall soil health. Metal lactates are an organic micronutrient amendment that provide both a labile carbon substrate as well as mineral nutrition for plant and microbial growth. To determine the ability of metal lactates to provide readily available micronutrients, Zn, Cu, Mn, Ni, and Co in lactate and chloride salt form were amended to soils and incubated for 28 days. Operationally defined speciation was determined using sequential extraction on samples incubated for 1, 5, or 28 days. The results show a comparable distribution of metals in chloride and lactate form; however, differences were detected in water‐soluble and exchangeable Ni and Zn at each timepoint. For example, in the water exchangeable fraction, there was 2.6%–2.9% less Ni and 0.2%–0.3% less Zn in the metal lactate‐treated soil compared to soil treated with metal chlorides. Furthermore, carbonate‐bound Ni averaged 4.1% and 4% less in metal lactate‐treated soils as compared to metal chloride‐treated soils on days 1 and 5, and Cu decreased 2.9%–3.3% during the treatment period for the lactate‐bound form. Additionally, microbial phospholipid fatty acid (PLFA) was performed and found a stimulatory effect of metal lactates on bacterial biomass with an increase of 12%–18% relative to the metal chloride treatment. Results from this study support the use of metal lactates as a sustainable alternative to conventional fertilizers by providing bioavailable micronutrients for plant nutrition in addition to a labile carbon source to support the growth of microbial populations.

Background: Alfalfa (Medicago sativa L.) is the most cultivated forage legume around the world. Under a variety of growing conditions, forage yield in alfalfa is stymied by biotic and abiotic stresses including heat, salt, drought, and disease. Given the sessile nature of plants, they use strategies including, but not limited to, differential gene expression to respond to environmental cues. Transcription factors control the expression of genes that contribute to or enable tolerance and survival during periods of stress. Basic-leucine zipper (bZIP) transcription factors have been demonstrated to play a critical role in regulating plant growth and development as well as mediate the responses to abiotic stress in several species, including Arabidopsis thaliana, Oryza sativa, Lotus japonicus and Medicago truncatula. However, there is little information about bZIP transcription factors in cultivated alfalfa. Result: In the present study, 237 bZIP genes were identified in alfalfa from publicly available sequencing data. Multiple sequence alignments showed the presence of intact bZIP motifs in the identified sequences. Based on previous phylogenetic analyses in A. thaliana, alfalfa bZIPs were similarly divided and fell into 10 groups. The physico-chemical properties, motif analysis and phylogenetic study of the alfalfa bZIPs revealed high specificity within groups. The differential expression of alfalfa bZIPs in a suite of tissues indicates that bZIP genes are specifically expressed at different developmental stages in alfalfa. Similarly, expression analysis in response to ABA, cold, drought and salt stresses, indicates that a subset of bZIP genes are also differentially expressed and likely play a role in abiotic stress signaling and/or tolerance. RT-qPCR analysis on selected genes further verified these differential expression patterns. Conclusions: Taken together, this work provides a framework for the future study of bZIPs in alfalfa and presents candidate bZIPs involved in stress-response signaling.

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Summary: Here, we discover a player in root development. Recovered from a forward‐genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild‐type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole‐genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin‐dependent kinase (CDK)‐like gene. The buzz mutant phenotypes are rescued by the wild‐type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T‐DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA‐Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX‐1 and ‐2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.