Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans-regulation architectures.

Common wheat is an allohexaploid, where it is difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3' RNA-seq, is technology efficient at obtaining homoeolog-distinguished transcriptomes. Here, we applied Lasy-Seq to obtain transcriptome data from the seedlings, second leaves, and root tips of 25 common wheat lines mainly from East Asia.

A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat.

Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) is to be developed for large-scale transcriptomic studies such as time-series analysis and genome-wide association studies in allopolyploids. In this study, we employed a 3' RNA-seq utilizing 3' untranslated regions (UTRs) containing frequent mutations among homeologous genes, compared to coding sequence.

WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus.

Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition.

Targeted single-cell gene induction by optimizing the dually regulated CRE/ system by a newly defined heat-shock promoter and the steroid hormone in .

Multicellular organisms rely on intercellular communication systems to organize their cellular functions. In studies focusing on intercellular communication, the key experimental techniques include the generation of chimeric tissue using transgenic DNA recombination systems represented by the CRE/ system. If an experimental system enables the induction of chimeras at highly targeted cell(s), it will facilitate the reproducibility and precision of experiments.

Auxin-Induced WUSCHEL-RELATED HOMEOBOX13 Mediates Asymmetric Activity of Callus Formation upon Cutting.

Plants have the regenerative ability to reconnect cut organs, which is physiologically important to survive severe tissue damage. The ability to reconnect organs is utilized as grafting to combine two different individuals. Callus formation at the graft junction facilitates organ attachment and vascular reconnection.

Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware.

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, high-throughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field.

Corrigendum: An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation.

[This corrects the article DOI: 10.3389/fpls.2021.

The boundary-expressed gene encoding a signaling peptide promotes cotyledon growth during embryogenesis.

The shoot organ boundaries have important roles in plant growth and morphogenesis. It has been reported that a gene encoding a cysteine-rich secreted peptide of the EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family, , is expressed in the boundary domain between the two cotyledon primordia of embryo. However, its developmental functions remain unknown.

Wound-inducible WUSCHEL-RELATED HOMEOBOX 13 is required for callus growth and organ reconnection.

Highly efficient tissue repair is pivotal for surviving damage-associated stress. Plants generate callus upon injury to heal wound sites, yet regulatory mechanisms of tissue repair remain elusive. Here, we identified WUSCHEL-RELATED HOMEOBOX 13 (WOX13) as a key regulator of callus formation and organ adhesion in Arabidopsis (Arabidopsis thaliana).

An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation.

Recent technical advances in the computer-vision domain have facilitated the development of various methods for achieving image-based quantification of stomata-related traits. However, the installation cost of such a system and the difficulties of operating it on-site have been hurdles for experimental biologists. Here, we present a platform that allows real-time stomata detection during microscopic observation.

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes.

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars.

Multiple wheat genomes reveal global variation in modern breeding.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome, and the lack of genome-assembly data for multiple wheat lines.

Homeolog expression quantification methods for allopolyploids.

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately.

The functional balance between the gene and the phytohormone auxin is a key factor for cell proliferation in Arabidopsis seedlings.

The WUSCHEL-RELATED HOMEOBOX1 (WOX1) transcription factor and its homolog PRESSED FLOWER (PRS) are multifunctional regulators of leaf development that act as transcriptional repressors. These genes promote cell proliferation under certain conditions, but the related molecular mechanisms are not well understood. Here, we present a new function for WOX1 in cell proliferation.

Stem development through vascular tissues: EPFL-ERECTA family signaling that bounces in and out of phloem.

Plant cells communicate with each other using a variety of signaling molecules. Recent studies have revealed that various types of secreted peptides, as well as phytohormones known since long ago, mediate cell-cell communication in diverse contexts of plant life. These peptides affect cellular activities, such as proliferation and cell fate decisions, through their perception by cell surface receptors located on the plasma membrane of target cells.

Impact of erecta mutation on leaf serration differs between Arabidopsis accessions.

Serrations or teeth of plant leaves are a morphological trait regulated genetically and environmentally. Very recently, it has been reported that the receptor kinases encoded by three ERECTA (ER)-family genes, ER, ER-LIKE1 (ERL1) and ERL2, redundantly play a role in tooth growth in Arabidopsis thaliana. In the report, Columbia (Col) accession was used for analyses, where none of the signal mutant of the ER-family genes exhibited serration defects.

A Secreted Peptide and Its Receptors Shape the Auxin Response Pattern and Leaf Margin Morphogenesis.

Secreted peptides mediate intercellular communication [1, 2]. Several secreted peptides in the EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family regulate morphogenesis of tissues, such as stomata and inflorescences in plants [3-15]. The biological functions of other EPFL family members remain unknown.

Cell walls as a stage for intercellular communication regulating shoot meristem development.

Aboveground organs of plants are ultimately derived/generated from the shoot apical meristem (SAM), which is a proliferative tissue located at the apex of the stem. The SAM contains a population of stem cells that provide new cells for organ/tissue formation. The SAM is composed of distinct cell layers and zones with different properties.

Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development.

The maintenance and reformation of gene expression domains are the basis for the morphogenic processes of multicellular systems. In a leaf primordium of Arabidopsis thaliana, the expression of FILAMENTOUS FLOWER (FIL) and the activity of the microRNA miR165/166 are specific to the abaxial side. This miR165/166 activity restricts the target gene expression to the adaxial side.

Succinic semialdehyde dehydrogenase is involved in the robust patterning of Arabidopsis leaves along the adaxial-abaxial axis.

Polarity along the adaxial-abaxial axis of the leaf is essential for leaf development and morphogenesis. One of the genes that encodes a putative transcription factor regulating adaxial-abaxial polarity, FILAMENTOUS FLOWER (FIL), is expressed in the abaxial region of the leaf primordia. However, the molecular mechanisms controlling the polarized expression of FIL remain unclear.