Restructuring plant types for developing tailor-made crops

The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba

Schima superba is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in S. superba growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 S. superba individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including Ss4CL2, SsCSL1, and SsCSL2, and transcription factors, including SsDELLA2 (SsSLR), SsDELLA3 (SsSLN), SsDELLA5 (SsGAI-like2), and SsNAM1, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of S. superba. The results not merely provide candidate functional genes related to S. superba growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.

Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton

Introduction

Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity.

Methods

Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants.

Results

Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.

Roles of auxin pathways in maize biology

Phytohormones play a central role in plant development and environmental responses. Auxin is a classical hormone that is required for organ formation, tissue patterning, and defense responses. Auxin pathways have been extensively studied across numerous land plant lineages, including bryophytes and eudicots. In contrast, our understanding of the roles of auxin in maize morphogenesis and immune responses is limited. Here, we review evidence for auxin-mediated processes in maize and describe promising areas for future research in the auxin field. Several recent transcriptomic and genetic studies have demonstrated that auxin is a key influencer of both vegetative and reproductive development in maize (namely roots, leaves, and kernels). Auxin signaling has been implicated in both maize shoot architecture and immune responses through genetic and molecular analyses of the conserved co-repressor RAMOSA ENHANCER LOCUS2. Polar auxin transport is linked to maize drought responses, root growth, shoot formation, and leaf morphogenesis. Notably, maize has been a key system for delineating auxin biosynthetic pathways and offers many opportunities for future investigations on auxin metabolism. In addition, crosstalk between auxin and other phytohormones has been uncovered through gene expression studies and is important for leaf and root development in maize. Collectively these studies point to auxin as a cornerstone for maize biology that could be leveraged for improved crop resilience and yield.

Genome-wide identification of peanut IGT family genes and their potential roles in the development of plant architecture

IGT family genes play essential roles in shaping plant architecture. However, limited amount of information is available about IGT family genes in peanuts (Arachis hypogaea). In the current study, 13 AhIGT genes were identified and classified into three groups based on their phylogenetic relationship. Gene structure, conserved domain analyses indicated all AhIGTs were observed to share a similar exon-intron distribution pattern. AhIGTs within the same subfamily maintained a consistent motif composition. Chromosomal localization and synteny analyses showed that AhIGTs were unevenly localized on 9 chromosomes and that segmental duplication and purifying selection may have played important roles in the evolution of AhIGT genes. The analysis of conserved motifs, GO annotation, and transcript profile suggested that AhLAZY1-3 may play roles in gravity sensing and shaping peanut plant architecture. Transcript profile analysis suggested that AhTAC1 could potentially be involved gynophore ('peg') penetration into the soil. The cis-element analysis revealed that the light-responsive elements accounted for most of all cis-acting elements. Furthermore, qRT-PCR analysis showed that the expression of several AhIGT genes, like AhTAC1-2/4, was light-dependent, indicating that these genes may regulate plant architecture in response to light signals. This study may facilitate functional studies of the IGT genes in peanut.

CRISPR/Cas Technology Revolutionizes Crop Breeding

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed.

Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture

KEY MESSAGE

TAC1 is involved in photoperiodic and gravitropic responses to modulate rice dynamic plant architecture likely by affecting endogenous auxin distribution, which could explain TAC1 widespread distribution in indica rice. Plants experience a changing environment throughout their growth, which requires dynamic adjustments of plant architecture in response to these environmental cues. Our previous study demonstrated that Tiller Angle Control 1 (TAC1) modulates dynamic changes in plant architecture in rice; however, the underlying regulatory mechanisms remain largely unknown. In this study, we show that TAC1 regulates plant architecture in an expression dose-dependent manner, is highly expressed in stems, and exhibits dynamic expression in tiller bases during the growth period. Photoperiodic treatments revealed that TAC1 expression shows circadian rhythm and is more abundant during the dark period than during the light period and under short-day conditions than under long-day conditions. Therefore, it contributes to dynamic plant architecture under long-day conditions and loose plant architecture under short-day conditions. Gravity treatments showed that TAC1 is induced by gravistimulation and negatively regulates shoot gravitropism, likely by affecting auxin distribution. Notably, the tested indica rice containing TAC1 displayed dynamic plant architecture under natural long-day conditions, likely explaining the widespread distribution of TAC1 in indica rice. Our results provide new insights into TAC1-mediated regulatory mechanisms for dynamic changes in rice plant architecture.

Blocking Rice Shoot Gravitropism by Altering One Amino Acid in LAZY1

Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In this study, we identified and characterized a new allele of LA1 based on analysis of a rice (Oryza sativa L.) spreading-tiller mutant la1^G74V, which harbors a non-synonymous mutation in the predicted transmembrane (TM) domain-encoding region of this gene. The mutation causes complete loss of shoot gravitropism, leading to prostrate growth of plants. Our results showed that LA1 localizes not only to the nucleus and plasma membrane but also to the endoplasmic reticulum. Removal of the TM domain in LA1 showed spreading-tiller phenotype of plants similar to la1^G74V but did not affect the plasma membrane localization; thus, making it distinct from its ortholog ZmLA1 in Zea mays. Therefore, we propose that the TM domain is indispensable for the biological function of LA1, but this domain does not determine the localization of the protein to the plasma membrane. Our study provides new insights into the LA1-mediated regulation of shoot gravitropism.

Tiller Angle Control 1 Is Essential for the Dynamic Changes in Plant Architecture in Rice

Plant architecture is dynamic as plants develop. Although many genes associated with specific plant architecture components have been identified in rice, genes related to underlying dynamic changes in plant architecture remain largely unknown. Here, we identified two highly similar recombinant inbred lines (RILs) with different plant architecture: RIL-Dynamic (D) and RIL-Compact (C). The dynamic plant architecture of RIL-D is characterized by ‘loose^{tiller angle} (tillering stage)–compact (heading stage)–loose^{curved stem} (maturing stage)’ under natural long-day (NLD) conditions, and ‘loose^{tiller angle} (tillering and heading stages)–loose^{tiller angle and curved stem} (maturing stage)’ under natural short-day (NSD) conditions, while RIL-C exhibits a compact plant architecture both under NLD and NSD conditions throughout growth. The candidate locus was mapped to the chromosome 9 tail via the rice 8K chip assay and map-based cloning. Sequencing, complementary tests, and gene knockout tests demonstrated that Tiller Angle Control 1 (TAC1) is responsible for dynamic plant architecture in RIL-D. Moreover, TAC1 positively regulates loose plant architecture, and high TAC1 expression cannot influence the expression of tested tiller-angle-related genes. Our results reveal that TAC1 is necessary for the dynamic changes in plant architecture, which can guide improvements in plant architecture during the modern super rice breeding.