CSNet: A Count-Supervised Network via Multiscale MLP-Mixer for Wheat Ear Counting.

Wheat is the most widely grown crop in the world, and its yield is closely related to global food security. The number of ears is important for wheat breeding and yield estimation. Therefore, automated wheat ear counting techniques are essential for breeding high-yield varieties and increasing grain yield. However, all existing methods require position-level annotation for training, implying that a large amount of labor is required for annotation, limiting the application and development of deep learning technology in the agricultural field. To address this problem, we propose a count-supervised multiscale perceptive wheat counting network (CSNet, count-supervised network), which aims to achieve accurate counting of wheat ears using quantity information. In particular, in the absence of location information, CSNet adopts MLP-Mixer to construct a multiscale perception module with a global receptive field that implements the learning of small target attention maps between wheat ear features. We conduct comparative experiments on a publicly available global wheat head detection dataset, showing that the proposed count-supervised strategy outperforms existing position-supervised methods in terms of mean absolute error (MAE) and root mean square error (RMSE). This superior performance indicates that the proposed approach has a positive impact on improving ear counts and reducing labeling costs, demonstrating its great potential for agricultural counting tasks. The code is available at http://csnet.samlab.cn.

Effect of potato flour on quality and staling properties of wheat-potato flour bread.

To elucidate the impact of potato flour (PF) on quality changes and staling characteristics of the composite bread from wheat-potato flour (WPF), the physicochemical (specific volume, colority, sensory value, texture, and viscosity) properties, and staling (X-ray diffraction and water migration) properties of bread were investigated. The quality of composite bread was comparable to wheat bread when addition level of PF at 20%, but decreased when the addition level increased to 30% or more, and became unacceptable at 50%. A chewy mouthfeel and an elastic and none-crumbly texture were observed on composite bread, which had higher hardness than wheat bread, and could keep on both longer linear distance and higher linear force during compression test. It indicated that such new parameters other than hardness should be introduced to coordinate with the texture quality of composite bread. During storage, the higher addition level of PF significantly decreased crystallinity of composite bread and slowed water migration rate from the crumb to crust, suggesting that PF had antistaling effect on composite bread, which was further emphasized by the fact that the setback value of the WPF decreased with the increase of PF addition.

The effects of extruded corn flour on rheological properties of wheat-based composite dough and the bread quality.

The effects of extruded corn flour (ECF) on the rheological properties of the wheat-based composite dough and quality of the bread were investigated. The RVA results of the composite flour with ECF showed weak thermal viscosity and resistance to starch retrogradation. Mixolab tests revealed that the water absorption capacity increased with the increasing amount of ECF, while dough development time (DT) and dough stability (ST) showed a downward trend, and the composite dough became more resistant to retrogradation. The microstructure of the composite dough showed that the presence of both ECF and unextruded corn flour (UECF) resulted in a more broken gluten matrix. The breads made from the composite flour with ECF had significantly softer texture, lower hardening percentage with storage time, darker crust color, larger specific volume, and higher sensory scores than the UECF ones. It is concluded that the extrusion of corn flour is an effective way to improve the quality of the composite bread and retard staling during storage.

Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes.

An important component of cellular biochemistry is the concentration of proteins and nucleic acids in non-membranous compartments1,2. These biomolecular condensates are formed from processes that include liquid-liquid phase separation. The multivalent interactions necessary for liquid-liquid phase separation have been extensively studied in vitro1,3. However, the regulation of this process in vivo is poorly understood. Here we identify an in vivo regulator of liquid-liquid phase separation through a genetic screen targeting factors required for Arabidopsis RNA-binding protein FCA function. FCA contains prion-like domains that phase-separate in vitro, and exhibits behaviour in vivo that is consistent with phase separation. The mutant screen identified a functional requirement for FLL2, a coiled-coil protein, in the formation of FCA nuclear bodies. FCA reduces transcriptional read-through by promoting proximal polyadenylation at many sites in the Arabidopsis genome3,4. FLL2 was required to promote this proximal polyadenylation, but not the binding of FCA to target RNA. Ectopic expression of FLL2 increased the size and number of FCA nuclear bodies. Crosslinking with formaldehyde captured in vivo interactions between FLL2, FCA and the polymerase and nuclease modules of the RNA 3'-end processing machinery. These 3' RNA-processing components colocalized with FCA in the nuclear bodies in vivo, which indicates that FCA nuclear bodies compartmentalize 3'-end processing factors to enhance polyadenylation at specific sites. Our findings show that coiled-coil proteins can promote liquid-liquid phase separation, which expands our understanding of the principles that govern the in vivo dynamics of liquid-like bodies.

Chloroplast-to-Nucleus Signaling Regulates MicroRNA Biogenesis in Arabidopsis.

As integral regulators in plant development and stress response, microRNAs (miRNAs) themselves need to be tightly regulated. Here, we show that tocopherols (vitamin E), lipid-soluble antioxidants synthesized from tyrosine in chloroplasts, positively regulate the biogenesis of miRNAs. Tocopherols are required for the accumulation of 3'-phosphoadenosine 5'-phosphate (PAP), a retrograde inhibitor of the nuclear exoribonucleases (XRN), which may protect primary miRNAs from being degraded and promote mature miRNA production. Such regulation is involved in heat-induced accumulation of miR398 and plant acquisition of heat tolerance. Our study reveals a chloroplast-to-nucleus signaling mechanism that favors miRNA biogenesis under heat and possibly other environmental perturbations.

A Role for MINIYO and QUATRE-QUART2 in the Assembly of RNA Polymerases II, IV, and V in Arabidopsis.

RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of MINIYO (IYO), QUATRE-QUART2 (QQT2), and NUCLEAR RNA POLYMERASE B11/D11/E11 (NRPB/D/E11) that cause defects in RdDM in Arabidopsis thaliana We found that Pol IV-dependent small interfering RNAs and Pol V-dependent transcripts were greatly reduced in the mutants. NRPE1, the largest subunit of Pol V, failed to associate with other Pol V subunits in the iyo and qqt2 mutants, suggesting the involvement of IYO and QQT2 in Pol V assembly. In addition, we found that IYO and QQT2 were mutually dependent for their association with the NRPE3 subassembly prior to the assembly of Pol V holoenzyme. Finally, we show that IYO and QQT2 are similarly required for the assembly of Pol II and Pol IV. Our findings reveal IYO and QQT2 as cofactors for the assembly of Pol II, Pol IV, and Pol V and provide mechanistic insights into how RNA polymerases are assembled in plants.

Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis.

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in gene expression in plants and animals. The biogenesis of miRNAs involves the transcription of primary miRNAs (pri-miRNAs) by RNA polymerase II (RNAPII) and subsequent processing by Dicer or Dicer-like (DCL) proteins. Here we show that the Elongator complex is involved in miRNA biogenesis in Arabidopsis. Disruption of Elongator reduces RNAPII occupancy at miRNA loci and pri-miRNA transcription. We also show that Elongator interacts with the DCL1-containing Dicing complex and lack of Elongator impairs DCL1 localization in the nuclear Dicing body. Finally, we show that pri-miRNA transcripts as well as DCL1 associate with the chromatin of miRNA genes and the chromatin association of DCL1 is compromised in the absence of Elongator. Our results suggest that Elongator functions in both transcription and processing of pri-miRNAs and probably couples these two processes.