Developmental role and auxin responsiveness of Class III homeodomain leucine zipper gene family members in rice

Mutation of rice SM1 enhances solid leaf midrib formation and increases methane emissions

The leaf midrib system is essential for plant growth and development, facilitating nutrient transport, providing structural support, enabling gas exchange, and enhancing resilience to environmental stresses. However, the molecular mechanism regulating leaf midrib development is still unclear.In this study, we reported a rice solid midrib 1 (sm1) mutant, exhibiting solid leaf aerenchyma and abaxial rolling leaves due to abnormal development of parenchyma and bulliform cells. Map-based cloning revealed that SM1 encodes a litter zipper protein (ZPR). SM1 was mainly expressed in the sheaths and basal midrib and was associated with the nucleus. Further experiments indicated that SM1 can interact with OSHB1, preventing the formation of OSHB:OSHB dimers and subsequently repressing the expression of OSH1 involved in the regulation and maintenance of apical stem meristem formation. The sm1 mutant reduced long-distance oxygen transport ability from shoot to root. The impaired oxygen transport in the sm1 mutant may have contributed to the increase in methanogens and elevated methane emissions. Collectively, our findings revealed that the SM1-OSHB1-OSH1 modules regulate leaf aerenchyma development in rice. These modules not only enhance our understanding of the molecular mechanism of rice leaf aerenchyma development but also offer insights for reducing methane emissions through genetic modification.

DWARF TILLER1 regulates apical-basal pattern formation and proper orientation of rice embryos

Body axis establishment is one of the earliest patterning events in plant embryogenesis. Asymmetric zygote division is critical for apical-basal axis formation in Arabidopsis (Arabidopsis thaliana). However, how the orientation of the cell division plane is regulated and its relation to apical-basal axis establishment and proper position of embryos in grasses remain poorly understood. By characterizing mutants of 3 rice (Oryza sativa) WUSCHEL HOMEOBOX9 (WOX9) genes, whose paralogs in Arabidopsis play essential roles in zygotic asymmetric cell division and cell fate determination, we found 2 kinds of independent embryonic defects: topsy-turvy embryos, in which apical-basal axis twists from being parallel to the longitudinal axis of the seed to being perpendicular; and organ-less embryos. In contrast to their Arabidopsis orthologs, OsWOX9s displayed dynamic distribution during embryo development. Both DWT1/OsWOX9A and DWL2/WOX9C play major roles in the apical-basal axis formation and initiation of stem cells. In addition, DWT1 has a distinct function in regulating the first few embryonic cell divisions to ensure the correct orientation of the embryo in the ovary. In summary, DWT1 acts in 2 steps during rice embryo pattern formation: the initial zygotic division, and with DWL2 to establish the main body axes and stem cell fate 2 to 3 d after pollination.

Adaxial-abaxial bipolar leaf genes encode a putative cytokinin receptor and HD-Zip III, and control the formation of ectopic shoot meristems in rice

Shoot apical meristems (SAMs) continuously initiate organ formation and maintain pluripotency through dynamic genetic regulations and cell-to-cell communications. The activity of meristems directly affects the plant's structure by determining the number and arrangement of organs and tissues. We have taken a forward genetic approach to dissect the genetic pathway that controls cell differentiation around the SAM. The rice mutants, adaxial-abaxial bipolar leaf 1 and 2 (abl1 and abl2), produce an ectopic leaf that is fused back-to-back with the fourth leaf, the first leaf produced after embryogenesis. The abaxial-abaxial fusion is associated with the formation of an ectopic shoot meristem at the adaxial base of the fourth leaf primordium. We cloned the ABL1 and ABL2 genes of rice by mapping their chromosomal positions. ABL1 encodes OsHK6, a histidine kinase, and ABL2 encodes a transcription factor, OSHB3 (Class III homeodomain leucine zipper). Expression analyses of these mutant genes as well as OSH1, a rice ortholog of the Arabidopsis STM gene, unveiled a regulatory circuit that controls the formation of an ectopic meristem near the SAM at germination.

MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement

MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.

Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata

Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.

Characterization and Mapping of a Rolling Leaf Mutant Allele rlT73 on Chromosome 1BL of Wheat

Leaf rolling is regarded as an important morphological trait in wheat breeding. Moderate leaf rolling is helpful to keep leaves upright and improve the photosynthesis of plants, leading to increased yield. However, studies on the identification of genomic regions/genes associated with rolling leaf have been reported less frequently in wheat. In this study, a rolling leaf mutant, T73, which has paired spikelets, dwarfism, and delayed heading traits, was obtained from a common wheat landrace through ethyl methanesulfonate mutagenesis. The rlT73 mutation caused an increase in the number of epidermal cells on the abaxial side and the shrinkage of bulliform cells on the adaxial side, leading to an adaxially rolling leaf phenotype. Genetic analysis showed that the rolling leaf phenotype was controlled by a single recessive gene. Further Wheat55K single nucleotide polymorphism array-based bulked segregant analysis and molecular marker mapping delimited rlT73 to a physical interval of 300.29-318.33 Mb on the chromosome arm 1BL in the Chinese Spring genome. We show that a point mutation at the miRNA165/166 binding site of the HD zipper class III transcription factor on 1BL altered its transcriptional level, which may be responsible for the rolling leaf phenotype. Our results suggest the important role of rlT73 in regulating wheat leaf development and the potential of miRNA-based gene regulation for crop trait improvement.

A novel OsHB5-OsAPL-OsMADS27/OsWRKY102 regulatory module regulates grain size in rice

Grain size, a crucial trait that determines rice yield and quality, is typically regulated by multiple genes. Although numerous genes controlling grain size have been identified, the precise and dynamic regulatory network governing grain size is still not fully understood. In this study, we unveiled a novel regulatory module composed of OsHB5, OsAPL and OsMADS27/OsWRKY102, which plays a crucial role in modulating grain size in rice. As a positive regulator of grain size, OsAPL has been found to interact with OsHB5 both in vitro and in vivo. Through chromatin immunoprecipitation-sequencing, we successfully mapped two potential targets of OsAPL, namely OsMADS27, a positive regulator in grain size and OsWRKY102, a negative regulator in lignification that is also associated with grain size control. Further evidence from EMSA and chromatin immunoprecipitation-quantitative PCR experiments has shown that OsAPL acts as an upstream transcription factor that directly binds to the promoters of OsMADS27 and OsWRKY102. Moreover, EMSA and dual-luciferase reporter assays have indicated that the interaction between OsAPL and OsHB5 enhances the repressive effect of OsAPL on OsMADS27 and OsWRKY102. Collectively, our findings discovered a novel regulatory module, OsHB5-OsAPL-OsMADS27/OsWRKY102, which plays a significant role in controlling grain size in rice. These discoveries provide potential targets for breeding high-yield and high-quality rice varieties.

Advancements in Rice Leaf Development Research

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf morphology encompass transcription factors, hormones, and miRNAs. An in-depth synthesis and categorization of genes associated with leaf development, particularly those successfully cloned, hold paramount importance in unraveling the complexity of rice leaf development. Furthermore, it provides valuable insights into the potential for molecular-level manipulation of rice leaf types. This comprehensive review consolidates the stages of rice leaf development, the genes involved, molecular regulatory pathways, and the influence of plant hormones. Its objective is to establish a foundational understanding of the creation of ideal rice leaf forms and their practical application in molecular breeding.

Whole-transcriptome characterization and functional analysis of lncRNA-miRNA-mRNA regulatory networks responsive to sugarcane mosaic virus in maize resistant and susceptible inbred lines

Sugarcane mosaic virus (SCMV) is one of the most important pathogens causing maize dwarf mosaic disease, which seriously affects the yield and quality of maize. Currently, the molecular mechanism of non-coding RNAs (ncRNAs) responding to SCMV infection in maize is still uncovered. In this study, a total of 112 differentially expressed (DE)-long non-coding RNAs (lncRNAs), 24 DE-microRNAs (miRNAs), and 1822 DE-messenger RNAs (mRNAs), and 363 DE-lncRNAs, 230 DE-miRNAs, and 4376 DE-mRNAs were identified in maize resistant (Chang7-2) and susceptible (Mo17) inbred lines in response to SCMV infection through whole-transcriptome RNA sequencing, respectively. Moreover, 4874 mRNAs potentially targeted by 635 miRNAs were obtained by degradome sequencing. Subsequently, several crucial SCMV-responsive lncRNA-miRNA-mRNA networks were established, of which the expression levels of lncRNA10865-miR166j-3p-HDZ25/69 (class III homeodomain-leucine zipper 25/69) module, and lncRNA14234-miR394a-5p-SPL11 (squamosal promoter-binding protein-like 11) module were further verified. Additionally, silencing lncRNA10865 increased the accumulations of SCMV and miR166j-3p, while silencing lncRNA14234 decreased the accumulations of SCMV and SPL11 targeted by miR394a-5p. This study revealed the interactions of lncRNAs, miRNAs and mRNAs in maize resistant and susceptible materials, providing novel clues to reveal the mechanism of maize in resistance to SCMV from the perspective of competing endogenous RNA (ceRNA) regulatory networks.

Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511

Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar Nanhui 511 (NH511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation.

The miR166d/TaCPK7-D Signaling Module Is a Critical Mediator of Wheat (Triticum aestivum L.) Tolerance to K+ Deficiency

It is well established that potassium (K⁺) is an essential nutrient for wheat (Triticum aestivum L.) growth and development. Several microRNAs (miRNAs), including miR166, are reportedly vital roles related to plant growth and stress responses. In this study, a K⁺ starvation-responsive miRNA (miR166d) was identified, which showed increased expression in the roots of wheat seedlings exposed to low-K⁺ stress. The overexpression of miR166d considerably increased the tolerance of transgenic Arabidopsis plants to K⁺ deprivation treatment. Furthermore, disrupting miR166d expression via virus-induced gene silencing (VIGS) adversely affected wheat adaptation to low-K⁺ stress. Additionally, miR166d directly targeted the calcium-dependent protein kinase 7-D gene (TaCPK7-D) in wheat. The TaCPK7-D gene expression was decreased in wheat seedling roots following K⁺ starvation treatment. Silencing TaCPK7-D in wheat increased K⁺ uptake under K⁺ starvation. Moreover, we observed that the miR166d/TaCPK7-D module could affect wheat tolerance to K⁺ starvation stress by regulating TaAKT1 and TaHAK1 expression. Taken together, our results indicate that miR166d is vital for K⁺ uptake and K⁺ starvation tolerance of wheat via regulation of TaCPK7-D.

Genetic basis controlling rice plant architecture and its modification for breeding

The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.

Fine Mapping of a Pleiotropic Locus (BnUD1) Responsible for the Up-Curling Leaves and Downward-Pointing Siliques in Brassica napus

Leaves and siliques are important organs associated with dry matter biosynthesis and vegetable oil accumulation in plants. We identified and characterized a novel locus controlling leaf and silique development using the Brassica napus mutant Bnud1, which has downward-pointing siliques and up-curling leaves. The inheritance analysis showed that the up-curling leaf and downward-pointing silique traits are controlled by one dominant locus (BnUD1) in populations derived from NJAU5773 and Zhongshuang 11. The BnUD1 locus was initially mapped to a 3.99 Mb interval on the A05 chromosome with a BC₆F₂ population by a bulked segregant analysis-sequencing approach. To more precisely map BnUD1, 103 InDel primer pairs uniformly covering the mapping interval and the BC₅F₃ and BC₆F₂ populations consisting of 1042 individuals were used to narrow the mapping interval to a 54.84 kb region. The mapping interval included 11 annotated genes. The bioinformatic analysis and gene sequencing data suggested that BnaA05G0157900ZS and BnaA05G0158100ZS may be responsible for the mutant traits. Protein sequence analyses showed that the mutations in the candidate gene BnaA05G0157900ZS altered the encoded PME in the trans-membrane region (G45A), the PMEI domain (G122S), and the pectinesterase domain (G394D). In addition, a 573 bp insertion was detected in the pectinesterase domain of the BnaA05G0157900ZS gene in the Bnud1 mutant. Other primary experiments indicated that the locus responsible for the downward-pointing siliques and up-curling leaves negatively affected the plant height and 1000-seed weight, but it significantly increased the seeds per silique and positively affected photosynthetic efficiency to some extent. Furthermore, plants carrying the BnUD1 locus were compact, implying they may be useful for increasing B. napus planting density. The findings of this study provide an important foundation for future research on the genetic mechanism regulating the dicotyledonous plant growth status, and the Bnud1 plants can be used directly in breeding.

Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice

BACKGROUND

The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma.

RESULTS

In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas.

CONCLUSION

The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.

Genetic analysis of a DROOPING LEAF mutant allele dl-6 associated with a twisted and folded leaf base caused by a deficiency in midrib development in rice

The failure of midrib formation in rice leaf blades results in the drooping leaf (dl) phenotype. A normal DROOPING LEAF (DL) gene is necessary for leaf homeotic transformation, which affects midrib and pistil development. Genetic analysis was performed on a new drooping leaf (dl) mutant named dl-6 in rice. The dl-6 allelic mutant exhibited drooping leaves that were severely folded and twisted at the base but had normal flower structure. The dl-6 allele is a nuclear recessive trait that fits a 3:1 Mendelian segregation ratio. The dl-6 mutant leaves displayed an abnormal main vein (midrib-less) with undeveloped aerenchyma and vascular bundles, resulting in severe leaf drooping. The lack of a midrib in dl-6 caused weak mechanical support, which resulted in folding at the collar junction of the leaf base and downward bending. Through genetic mapping, the dl-6 allele was identified at approximately 28.2 cM on rice chromosome 3. The allele was caused by mutations within the DL (LOC_Os03g11600.1) gene, with specific amino acid substitutions and additions in the encoded protein of the YABBY transcription factor. The dl-6 mutant is a recessive allele encoding a dysfunctional YABBY transcription factor that regulates leaf midrib development and aerenchymatous clear cell structures, leading to a drooping leaf phenotype in rice.

Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize (Zea mays L.)

High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.

DRB2 Modulates Leaf Rolling by Regulating Accumulation of MicroRNAs Related to Leaf Development in Rice

As an important agronomic trait in rice (Oryza sativa), moderate leaf rolling helps to maintain the erectness of leaves and minimize shadowing between leaves, leading to improved photosynthetic efficiency and grain yield. However, the molecular mechanisms underlying rice leaf rolling still need to be elucidated. Here, we isolated a rice mutant, rl89, showing adaxially rolled leaf phenotype due to decreased number and size of bulliform cells. We confirmed that the rl89 phenotypes were caused by a single nucleotide substitution in OsDRB2 (LOC_Os10g33970) gene encoding DOUBLE-STRANDED RNA-BINDING2. This gene was constitutively expressed, and its encoded protein was localized to both nucleus and cytoplasm. Yeast two-hybrid assay showed that OsDRB2 could interact with DICER-LIKE1 (DCL1) and OsDRB1-2 respectively. qRT-PCR analysis of 29 related genes suggested that defects of the OsDRB2-miR166-OsHBs pathway could play an important role in formation of the rolled leaf phenotype of rl89, in which OsDRB2 mutation reduced miR166 accumulation, resulting in elevated expressions of the class III homeodomain-leucine zipper genes (such as OsHB1, 3 and 5) involved in leaf polarity and/or morphology development. Moreover, OsDRB2 mutation also reduced accumulation of miR160, miR319, miR390, and miR396, which could cause the abnormal leaf development in rl89 by regulating expressions of their target genes related to leaf development.

Heat Stress Decreases Rice Grain Weight: Evidence and Physiological Mechanisms of Heat Effects Prior to Flowering

Heat stress during the preflowering panicle initiation stage seriously decreases rice grain weight in an invisible way and has not been given enough attention. The current review aims to (i) specify the heat effects on rice grain weight during the panicle initiation stage compared with the most important grain-filling stage; and (ii) discuss the physiological mechanisms of the decreased rice grain weight induced by heat during panicle initiation in terms of assimilate supply and phytohormone regulation, which are key physiological processes directly regulating rice grain weight. We emphasize that the effect of heat during the panicle initiation stage on rice grain weight is more serious than that during the grain-filling stage. Heat stress during the panicle initiation stage induces alterations in endogenous phytohormones, leading to the inhibition of the photosynthesis of functional leaves (source) and the formation of vascular bundles (flow), thus reducing the accumulation and transport of nonstructural carbohydrates and the growth of lemmata and paleae. The disruptions in the "flow" and restrictions in the preanthesis "source" tissue reduce grain size directly and decrease grain plumpness indirectly, resulting in a reduction in the final grain weight, which could be the direct physiological causes of the lower rice grain weight induced by heat during the panicle initiation stage. We highlight the seriousness of preflowering heat stress on rice grain weight, which can be regarded as an invisible disaster. The physiological mechanisms underlying the lower grain weight induced by heat during panicle initiation show a certain novelty because they distinguish this stage from the grain-filling stage. Additionally, a number of genes that control grain size through phytohormones have been summarized, but their functions have not yet been fully tested under heat conditions, except for the Grain Size and Abiotic stress tolerance 1 (GSA1) and BRASSINOSTEROID INSENSITIVE1 (OsBRI1) genes, which are reported to respond rapidly to heat stress. The mechanisms of reduced rice grain weight induced by heat during the panicle initiation stage should be studied in more depth in terms of molecular pathways.

CkREV regulates xylem vessel development in Caragana korshinskii in response to drought

Drought stress poses severe threat to the development and even the survival status of plants. Plants utilize various methods responding to drought, among which the forming of more well-developed xylem in leaf vein in woody plants deserves our attention. Herein, we report a transcription factor CkREV from HD-ZIP III family in Caragana korshinskii, which possesses significant functions in drought response by regulating xylem vessel development in leaf vein. Research reveal that in C. korshinskii the expression level of CkREV located in xylem vessel and adjacent cells will increase as the level of drought intensifies, and can directly induce the expression of CkLAX3, CkVND6, CkVND7, and CkPAL4 by binding to their promoter regions. In Arabidopsis thaliana, CkREV senses changes in drought stress signals and bidirectionally regulates the expression of related genes to control auxin polar transport, vessel differentiation, and synthesis of cell wall deposits, thereby significantly enhancing plant drought tolerance. In conclusion, our findings offer a novel understanding of the regulation of CkREV, a determinant of leaf adaxial side, on the secondary development of xylem vessels in leaf vein to enhance stress tolerance in woody plants.

The HD-Zip transcription factor SlHB15A regulates abscission by modulating jasmonoyl-isoleucine biosynthesis

Plant organ abscission, a process that is important for development and reproductive success, is inhibited by the phytohormone auxin and promoted by another phytohormone, jasmonic acid (JA). However, the molecular mechanisms underlying the antagonistic effects of auxin and JA in organ abscission are unknown. We identified a tomato (Solanum lycopersicum) class III homeodomain-leucine zipper transcription factor, HOMEOBOX15A (SlHB15A), which was highly expressed in the flower pedicel abscission zone and induced by auxin. Knocking out SlHB15A using clustered regularly interspaced short palindromic repeats-associated protein 9 technology significantly accelerated abscission. In contrast, overexpression of microRNA166-resistant SlHB15A (mSlHB15A) delayed abscission. RNA sequencing and reverse transcription-quantitative PCR analyses showed that knocking out SlHB15A altered the expression of genes related to JA biosynthesis and signaling. Furthermore, functional analysis indicated that SlHB15A regulates abscission by depressing JA-isoleucine (JA-Ile) levels through inhabiting the expression of JASMONATE-RESISTANT1 (SlJAR1), a gene involved in JA-Ile biosynthesis, which could induce abscission-dependent and abscission-independent ethylene signaling. SlHB15A bound directly to the SlJAR1 promoter to silence SlJAR1, thus delaying abscission. We also found that flower removal enhanced JA-Ile content and that application of JA-Ile severely impaired the inhibitory effects of auxin on abscission. These results indicated that SlHB15A mediates the antagonistic effect of auxin and JA-Ile during tomato pedicel abscission, while auxin inhibits abscission through the SlHB15A-SlJAR1 module.

Genetic and transcriptomic dissection of an artificially induced paired spikelets mutant of wheat (Triticum aestivum L.)

Morphological, genetic and transcriptomic characterizations of an EMS-induced wheat paired spikelets (PS) mutant were performed. A novel qualitative locus WPS1 on chromosome 1D was identified. Grain yield of wheat is significantly associated with inflorescence or spike architecture. However, few genes related to wheat spike development have been identified and their underlying mechanisms are largely unknown. In this study, we characterized an ethyl methanesulfonate (EMS)-induced wheat mutant, wheat paired spikelets 1 (wps1). Unlike a single spikelet that usually develops at each node of rachis, a secondary spikelet appeared below the primary spikelet at most of the rachis nodes of wps1. The microscope observation showed that the secondary spikelet initiated later than the primary spikelet. Genetic analysis suggested that the PS of wps1 is controlled by a single dominant nuclear gene, designated WHEAT PAIRED SPIKELETS 1 (WPS1). Further RNA-seq based bulked segregant analysis and molecular marker mapping localized WPS1 in an interval of 208.18-220.92 Mb on the chromosome arm 1DL, which is different to known genes related to spike development in wheat. By using wheat omics data, TraesCS1D02G155200 encoding a HD-ZIP III transcription factor was considered as a strong candidate gene for WPS1. Transcriptomic analysis indicated that PS formation in wps1 is associated with auxin-related pathways and may be regulated by networks involving TB1, Ppd1, FT1, VRN1, etc. This study laid the solid foundation for further validation of the causal gene of WPS1 and explored its regulatory mechanism in PS formation and inflorescence development, which may benefit to kernel yield improvement of wheat based on optimization or design of spike architecture in the future.

HD-Zip III Gene Family: Identification and Expression Profiles during Leaf Vein Development in Soybean

Leaf veins constitute the transport network for water and photosynthetic assimilates in vascular plants. The class III homeodomain-leucine zipper (HD-Zip III) gene family is central to the regulation of vascular development. In this research, we performed an overall analysis of the HD-Zip III genes in soybean (Glycine max L. Merr.). Our analysis included the phylogeny, conservation domains and cis-elements in the promoters of these genes. We used the quantitative reverse transcription-polymerase chain reaction to characterize the expression patterns of HD-Zip III genes in leaf vein development and analyze the effects of exogenous hormone treatments. In this study, twelve HD-Zip III genes were identified from the soybean genome and named. All soybean HD-Zip III proteins contained four highly conserved domains. GmHB15-L-1 transcripts showed steadily increasing accumulation during all stages of leaf vein development and were highly expressed in cambium cells. GmREV-L-1 and GmHB14-L-2 had nearly identical expression patterns in soybean leaf vein tissues. GmREV-L-1 and GmHB14-L-2 transcripts remained at stable high levels at all xylem developmental stages. GmREV-L-1 and GmHB14-L-2 were expressed at high levels in the vascular cambium and xylem cells. Overall, GmHB15-L-1 may be an essential regulator that is responsible for the formation or maintenance of soybean vein cambial cells. GmREV-L-1 and GmHB14-L-2 were correlated with xylem differentiation in soybean leaf veins. This study will pave the way for identifying the molecular mechanism of leaf vein development.

In-frame editing of transcription factor gene RDD1 to suppress miR166 recognition influences nutrient uptake, photosynthesis, and grain quality in rice

The transcription factor-encoding gene RDD1 increases the uptake of nutrient ions, photosynthetic activity under ambient and high CO₂ conditions, and grain productivity, and microRNA166 (miR166) regulates its transcript levels. This study found that CRISPR/Cas9 genome editing of rice plants to inhibit miR166-RDD1 transcript pairing (R1-Cas plants) increased RDD1 transcript levels, NH₄⁺ and PO₄^3- uptake, and photosynthetic activity under high CO₂ conditions in rice. However, the panicle weight of the R1-Cas plants decreased compared with the wild-type (WT) plants. Adversely, changes in environmental conditions, such as high CO₂ or high temperatures, showed insignificant differences in the panicle weight between the WT and R1-Cas plants despite a largely increased panicle weight observed in the transgenic RDD1-overexpressing plants. Moreover, both the R1-Cas and transgenic RDD1-overexpressing plants that were matured in a growth chamber demonstrated an improved grain appearance quality or a decrease in the number of chalky grains compared with the WT plants. These results suggest that the in-frame mutagenesis of RDD1 to suppress miR166-RDD1 transcript pairing contributes to the improved grain appearance of rice.

RLM1, Encoding an R2R3 MYB Transcription Factor, Regulates the Development of Secondary Cell Wall in Rice

Leaf morphology is an important component of rice ideal plant type. To date, many regulatory genes influencing leaf morphology in rice have been cloned, and their underlying molecular regulatory mechanism has been preliminarily clarified. However, the fine regulation relationship of leaf morphogenesis and plant type remains largely elusive. In this study, a rolling-leaf mutant, named rlm1-D, was obtained and controlled by a pair of dominant nuclear genes. Cytological observations revealed that the rlm1 was mainly caused by abnormal deposition of secondary cell walls. Molecular evidence showed ectopic expression of a MYB-type transcription factor LOC_Os05g46610 was responsible for the phenotype of rlm1-D. A series of experiments, including the transcription factor-centered technology, DNA-binding assay, and electrophoretic mobility shift assay, verified that RLM1 can bind to the promoter of OsCAD2, a key gene responsible for lignin biosynthesis in rice. An interacting partner of RLM1, OsMAPK10, was identified. Multiple biochemical assays confirmed that OsMAPK10 interacted with RLM1. OsMAPK10 positively regulated the lignin content in the leaves and stems of rice. Moreover, OsMAPK10 contributes to RLM1 activation of downstream target genes. In particular, RLM1 is exclusively expressed in the stems at the mature plant stage. The yield of RLM1 knockdown lines increased by over 11% without other adverse agricultural trait penalties, indicating great practical application value. A MAPK-MYB-OsCAD2 genetic regulatory network controlling SCW was proposed, providing a theoretical significance and practical value for shaping the ideal plant type and improving rice yield.

MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat

Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.

Identification and Fine Mapping of a Locus Related to Leaf Up-Curling Trait (Bnuc3) in Brassica napus

Leaf trait is an important target trait in crop breeding programs. Moderate leaf curling may be a help for improving crop yield by minimizing the shadowing by leaves. Mining locus for leaf curling trait is of significance for plant genetics and breeding researches. The present study identified a novel rapeseed accession with up-curling leaf, analyzed the up-curling leaf trait inheritance, and fine mapped the locus for up-curling leaf property (Bnuc3) in Brassica napus. Genetic analysis revealed that the up-curling leaf trait is controlled by a single dominant locus, named BnUC3. We performed an association study of BnUC3 with single nucleotide polymorphism (SNP) markers using a backcross population derived from the homozygous up-curling leaf line NJAU-M1295 and the canola variety ‘zhongshuang11’ with typical flat leaves, and mapped the BnUC3 locus in a 1.92 Mb interval of chromosome A02 of B. napus. To further map BnUC3, 232 simple sequence repeat (SSR) primers and four pairs of Insertion/Deletion (InDel) primers were developed for the mapping interval. Among them, five SSR markers and two InDel markers were polymorphic. By these markers, the mapping interval was narrowed to 92.0 kb using another F₂ population. This fine mapping interval has 11 annotated genes among which BnaA02T0157000ZS were inferred to be candidate casual genes for up-curling leaf based on the cloned sequence analysis, gene functionality, and gene expression analysis. The current study laid a foundational basis for further elucidating the mechanism of BnUC3 and breeding of variety with up-curling leaf.

LF1 regulates the lateral organs polarity development in rice

The patterning of adaxial-abaxial tissues plays a vital role in the morphology of lateral organs, which is maintained by antagonism between the genes that specify adaxial and abaxial tissue identity. The homeo-domain leucine zipper class III (HD-ZIP III) family genes regulate adaxial identity; however, little information is known about the physical interactions or transcriptionally regulated downstream genes of HD-ZIP III. In this study, we identified a dominant rice mutant, lateral floret 1 (lf1), which has defects in lateral organ polarity. LF1 encodes the HD-ZIP III transcription factor, which expressed in the adaxial area of lateral organs. LF1 can activate directly the expression of LITTLE ZIPPER family gene OsZPR4 and HD-ZIP II family gene OsHOX1, and OsZPR4 and OsHOX1 respectively interact with LF1 to form a heterodimer to repress the transcriptional activity of LF1. LF1 influences indole-3-acetic acid (IAA) content by directly regulating the expression of OsYUCCA6. Therefore, LF1 forms negative feedback loops between OsZPR4 and OsHOX1 to affect IAA content, leading to the regulation of lateral organs polarity development. These results reveal the cross-talk among HD-ZIP III, LITTLE ZIPPER, and HD-ZIP II proteins and provide new insights into the molecular mechanisms underlying the polarity development of lateral organs.

YABBY Genes in the Development and Evolution of Land Plants

Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.

Curled Flag Leaf 2, Encoding a Cytochrome P450 Protein, Regulated by the Transcription Factor Roc5, Influences Flag Leaf Development in Rice

Moderate curling generally causes upright leaf blades, which favors the establishment of ideal plant architecture and increases the photosynthetic efficiency of the population, both of which are desirable traits for super hybrid rice (Oryza sativa L.). In this study, we identified a novel curled-leaf mutant, curled flag leaf 2 (cfl2), which shows specific curling at the base of the flag leaf owing to abnormal epidermal development, caused by enlarged bulliform cells and increased number of papillae with the disordered distribution. Map-based cloning reveals that CFL2 encodes a cytochrome P450 protein and corresponds to the previously reported OsCYP96B4. CFL2 was expressed in all analyzed tissues with differential abundance and was downregulated in the clf1 mutant [a mutant harbors a mutation in the homeodomain leucine zipper IV (HD-ZIP IV) transcription factor Roc5]. Yeast one-hybrid and transient expression assays confirm that Roc5 could directly bind to the cis-element L1 box in the promoter of CFL2 before activating CFL2 expression. RNA sequencing reveals that genes associated with cellulose biosynthesis and cell wall-related processes were significantly upregulated in the cfl2 mutant. The components of cell wall, such as lignin, cellulose, and some kinds of monosaccharide, were altered dramatically in the cfl2 mutant when compared with wild-type "Jinhui10" (WT). Taken together, CFL2, as a target gene of Roc5, plays an important role in the regulation of flag leaf shape by influencing epidermis and cell wall development.

Maize microRNA166 Inactivation Confers Plant Development and Abiotic Stress Resistance

MicroRNAs are important regulators in plant developmental processes and stress responses. In this study, we generated a series of maize STTM166 transgenic plants. Knock-down of miR166 resulted in various morphological changes, including rolled leaves, enhanced abiotic stress resistance, inferior yield-related traits, vascular pattern and epidermis structures, tassel architecture, as well as abscisic acid (ABA) level elevation and indole acetic acid (IAA) level reduction in maize. To profile miR166 regulated genes, we performed RNA-seq and qRT-PCR analysis. A total of 178 differentially expressed genes (DEGs) were identified, including 118 up-regulated and 60 down-regulated genes. These DEGs were strongly enriched in cell and intercellular components, cell membrane system components, oxidoreductase activity, single organism metabolic process, carbohydrate metabolic process, and oxidation reduction process. These results indicated that miR166 plays important roles in auxin and ABA interaction in monocots, yet the specific mechanism may differ from dicots. The enhanced abiotic stress resistance is partly caused via rolling leaves, high ABA content, modulated vascular structure, and the potential changes of cell membrane structure. The inferior yield-related traits and late flowering are partly controlled by the decreased IAA content, the interplay of miR166 with other miRNAs and AGOs. Taken together, the present study uncovered novel functions of miR166 in maize, and provide insights on applying short tandem target mimics (STTM) technology in plant breeding.

A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.

Patterning a Leaf by Establishing Polarities

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial-abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established and maintained by YABBY family and KANADI family proteins. The activities of adaxial and abaxial regulators are coordinated by ASYMMETRIC LEAVES2 and auxin. Establishment of the proximodistal axis involves the BTB/POZ domain proteins BLADE-ON-PETIOLE1 and 2, whereas homeobox genes PRESSED FLOWER and WUSCHEL-RELATED HOMEOBOX1 mediate leaf development along the mediolateral axis. This review summarizes recent advances in leaf polarity establishment with a focus on the regulatory networks involved.

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.

HvHOX9, a novel homeobox leucine zipper transcription factor, positively regulates aluminum tolerance in Tibetan wild barley

Aluminum (Al) toxicity is the primary limiting factor of crop production on acid soils. Tibetan wild barley germplasm is a valuable source of potential genes for breeding barley with acid and Al tolerance. We performed microRNA and RNA sequencing using wild (XZ16, Al-tolerant; XZ61, Al-sensitive) and cultivated (Dayton, Al-tolerant) barley. A novel homeobox-leucine zipper transcription factor, HvHOX9, was identified as a target gene of miR166b and functionally characterized. HvHOX9 was up-regulated by Al stress in XZ16 (but unchanged in XZ61 and Dayton) and was significantly induced only in root tip. Phylogenetic analysis showed that HvHOX9 is most closely related to wheat TaHOX9 and orthologues of HvHOX9 are present in the closest algal relatives of Zygnematophyceae. Barley stripe mosaic virus-induced gene silencing of HvHOX9 in XZ16 led to significantly increased Al sensitivity but did not affect its sensitivity to other metals and low pH. Disruption of HvHOX9 did not change Al concentration in the root cell sap, but led to more Al accumulation in root cell wall after Al exposure. Silencing of HvHOX9 decreased H+ influx after Al exposure. Our findings suggest that miR166b/HvHOX9 play a critical role in Al tolerance by decreasing root cell wall Al binding and increasing apoplastic pH for Al detoxification in the root.

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize

Bulliform cells comprise specialized cell types that develop on the adaxial (upper) surface of grass leaves, and are patterned to form linear rows along the proximodistal axis of the adult leaf blade. Bulliform cell patterning affects leaf angle and is presumed to function during leaf rolling, thereby reducing water loss during temperature extremes and drought. In this study, epidermal leaf impressions were collected from a genetically and anatomically diverse population of maize inbred lines. Subsequently, convolutional neural networks were employed to measure microscopic, bulliform cell-patterning phenotypes in high-throughput. A genome-wide association study, combined with RNAseq analyses of the bulliform cell ontogenic zone, identified candidate regulatory genes affecting bulliform cell column number and cell width. This study is the first to combine machine learning approaches, transcriptomics, and genomics to study bulliform cell patterning, and the first to utilize natural variation to investigate the genetic architecture of this microscopic trait. In addition, this study provides insight toward the improvement of macroscopic traits such as drought resistance and plant architecture in an agronomically important crop plant.

Fine mapping and candidate gene analysis of a QTL associated with leaf rolling index on chromosome 4 of maize (Zea mays L.)

One QTL qLRI4 controlling leaf rolling index on chromosome 4 was finely mapped, and ZmOCL5, a member of the HD-Zip class IV genes, is likely a candidate. Leaf rolling is an important agronomic trait related to plant architecture that can change the light condition and photosynthetic efficiency of the population. Here, we isolated one EMS-induced mutant in Chang7-2 background with extreme abaxial rolling leaf, named abrl1. Histological analysis showed that the increased number and area of bulliform cells may contribute to abaxial rolling leaf in abrl1. The F₂ and F_2:3 populations derived from Wu9086 with flat leaves and abrl1 were developed to map abrl1. Non-Mendelian segregation of phenotypic variation was observed in these populations and five genomic regions controlling the leaf rolling index (LRI) were identified, which could be due to the phenotypic difference between Chang7-2 and Wu9086. Moreover, one major QTL qLRI4 on chromosome 4 was further validated and finely mapped to a genetic interval between InDel13 and InDel10, with a physical distance of approximately 277 kb using NIL populations, among which one 602-bp insertion was identified in the promoter region of HD-Zip class IV gene Zm00001d049443 (named as ZmOCL5) of abrl1 compared with wild-type Chang7-2. Remarkably, the 602-bp InDel was associated with LRI in an F₂ population developed by crossing abrl1 mutant and its wild-type. In addition, the 602-bp insertion increased ZmOCL5 promoter activity and expression. Haplotype analysis demonstrated that the 602-bp insertion was a rare mutation event. Taken together, we propose that the rolled leaf in the abrl1 mutant may be partially attributed to the 602-bp insertion, which may be an attractive target for the genetic improvement of LRI in maize.

Overexpression of OsAGO1b Induces Adaxially Rolled Leaves by Affecting Leaf Abaxial Sclerenchymatous Cell Development in Rice

BACKGROUND

ARGONAUTE 1 (AGO1) proteins can recruit small RNAs to regulate gene expression, involving several growth and development processes in Arabidopsis. Rice genome contains four AGO1 genes, OsAGO1a to OsAGO1d. However, the regulatory functions to rice growth and development of each AGO1 gene are still unknown.

RESULTS

We obtained overexpression and RNAi transgenic lines of each OsAGO1 gene. However, only up- and down-regulation of OsAGO1b caused multiple abnormal phenotypic changes in rice, indicating that OsAGO1b is the key player in rice growth and organ development compared with other three OsAGO1s. qRT-PCR assays showed that OsAGO1b was almost unanimously expressed in leaves at different developmental stages, and strongly expressed in spikelets at S1 to S3 stages. OsAGO1b is a typical AGO protein, and co-localized in both the nucleus and cytoplasm simultaneously. Overexpression of OsAGO1b caused adaxially rolled leaves and a series of abnormal phenotypes, such as the reduced tiller number and plant height. Knockdown lines of OsAGO1b showed almost normal leaves, but the seed setting percentage was significantly reduced accompanied by the disturbed anther patterning and reduced pollen fertility. Further anatomical observation revealed that OsAGO1b overexpression plants showed the partially defective development of sclerenchymatous cells on the abaxial side of leaves. In situ hybridization showed OsAGO1b mRNA was uniformly accumulated in P1 to P3 primordia without polarity property, suggesting OsAGO1b did not regulate the adaxial-abaxial polarity development directly. The expression levels of several genes related to leaf polarity development and vascular bundle differentiation were observably changed. Notably, the accumulation of miR166 and TAS3-siRNA was decreased, and their targeted OSHBs and OsARFs were significantly up-regulated. The mRNA distribution patterns of OSHB3 and OsARF4 in leaves remained almost unchanged between ZH11 and OsAGO1b overexpression lines, but their expression levels were enhanced at the regions of vascular bundles and sclerenchymatous cell differentiation.

CONCLUSIONS

In summary, we demonstrated OsAGO1b is the leading player among four OsAGO1s in rice growth and development. We propose that OsAGO1b may regulate the abaxial sclerenchymatous cell differentiation by affecting the expression of OSHBs in rice.

Effect of Thermospermine on the Growth and Expression of Polyamine-Related Genes in Rice Seedlings

A mutant defective in the biosynthesis of thermospermine, acaulis5 (acl5), shows a dwarf phenotype with excess xylem vessels in Arabidopsis thaliana. Exogenous supply of thermospermine remarkably represses xylem differentiation in the root of seedlings, indicating the role of thermospermine in proper repression of xylem differentiation. However, the effect of thermospermine has rarely been investigated in other plant species. In this paper, we examined its effect on the growth and gene expression in rice seedlings. When grown with thermospermine, rice seedlings had no clearly enlarged metaxylem vessels in the root. Expression of OsACL5 was reduced in response to thermospermine, suggesting a negative feedback control of thermospermine biosynthesis like in Arabidopsis. Unlike Arabidopsis, however, rice showed up-regulation of phloem-expressed genes, OsHB5 and OsYSL16, by one-day treatment with thermospermine. Furthermore, expression of OsPAO2 and OsPAO6, encoding extracellular polyamine oxidase whose orthologs are not present in Arabidopsis, was induced by both thermospermine and spermine. These results suggest that thermospermine affects the expression of a subset of genes in rice different from those affected in Arabidopsis.

Fine mapping of an up-curling leaf locus (BnUC1) in Brassica napus

BACKGROUND

Leaf shape development research is important because leaf shapes such as moderate curling can help to improve light energy utilization efficiency. Leaf growth and development includes initiation of the leaf primordia and polar differentiation of the proximal-distal, adaxial-abaxial, and centrolateral axes. Changes in leaf adaxial-abaxial polarity formation, auxin synthesis and signaling pathways, and development of sclerenchyma and cuticle can cause abnormal leaf shapes such as up-curling leaf. Although many genes related to leaf shape development have been reported, the detailed mechanism of leaf development is still unclear. Here, we report an up-curling leaf mutant plant from our Brassica napus germplasm. We studied its inheritance, mapped the up-curling leaf locus BnUC1, built near-isogenic lines for the Bnuc1 mutant, and evaluated the effect of the dominant leaf curl locus on leaf photosynthetic efficiency and agronomic traits.

RESULTS

The up-curling trait was controlled by one dominant locus in a progeny population derived from NJAU5734 and Zhongshuang 11 (ZS11). This BnUC1 locus was mapped in an interval of 2732.549 kb on the A05 chromosome of B. napus using Illumina Brassica 60 K Bead Chip Array. To fine map BnUC1, we designed 201 simple sequence repeat (SSR) primers covering the mapping interval. Among them, 16 polymorphic primers that narrowed the mapping interval to 54.8 kb were detected using a BC₆F₂ family population with 654 individuals. We found six annotated genes in the mapping interval using the B. napus reference genome, including BnaA05g18250D and BnaA05g18290D, which bioinformatics and gene expression analyses predicted may be responsible for leaf up-curling. The up-curling leaf trait had negative effects on the agronomic traits of 30 randomly selected individuals from the BC₆F₂ population. The near-isogenic line of the up-curling leaf (ZS11-UC1) was constructed to evaluate the effect of BnUC1 on photosynthetic efficiency. The results indicated that the up-curling leaf trait locus was beneficial to improve the photosynthetic efficiency.

CONCLUSIONS

An up-curling leaf mutant Bnuc1 was controlled by one dominant locus BnUC1. This locus had positive effects on photosynthetic efficiency, negative effects on some agronomic traits, and may help to increase planting density in B. napus.

Morphogenesis of flattened unifacial leaves in Juncus prismatocarpus (Juncaceae)

To reveal the mode of morphogenesis of flattened unifacial leaves, we analysed the cell division direction and distribution on the leaf blade of Juncus prismatocarpus. Using the pulse-chase 5-ethynyl-2'-deoxyuridine method, we quantified and mapped the cell division direction on the leaf blade of J. prismatocarpus and compared the distribution of thickening cell divisions with the expression pattern of DROOPING LEAF (DL), a key gene involved in leaf blade thickening. Thickening cell divisions were the most abundant (> 45%) among all cell division directions on the leaf blade of J. prismatocarpus from the early plastochron 2 stage through the plastochron 3 stage. Mapping of cell divisions indicated that cell divisions in a particular direction were not restricted to a particular domain but were distributed diffusely throughout the entire cross-sectional area of the leaf blade. Gradient analysis indicated that the distribution of thickening cell divisions of the adaxial domain was denser than that of the abaxial domain. Contrary to the prolonged and diffuse distribution of thickening cell divisions, DL expression was transient and restricted in a narrow band. Our results suggest that a diffuse 'thickening meristem' plays the key role in the development of flattened unifacial leaves.

Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs

MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.

Genome-wide identification and characterization of HD-ZIP genes in potato

HD-ZIP (Homeodomain leucine zipper) transcription factors play an important regulatory role in stress resistance in plants. The purpose of this study was to analyze the characteristics of the HD-ZIP genes/proteins and to study their expression profiles under high and low temperature conditions in potato (Solanum tuberosum L.). A strict homology search was used to find 43 HD-ZIP genes located on potato chromosomes 1-12. Exons/introns, protein features and conserved motifs were analyzed, and six segment duplications were identified from 43 HD-ZIP genes. Then, we analyzed the data from the PGSC (Potato Genome Sequencing Consortium) database regarding the expression of 43 HD-ZIP genes that were induced by biotic and abiotic stresses and phytohormone treatments and conducted an expression analysis for these genes across all potato life stages. Additionally, the expression levels of 13 HD-ZIP genes were analyzed under high temperature (37 °C) and low temperature (4 °C) conditions. The results showed that the transcript levels of all 13 genes changed, which indicated that these genes respond to heat and cold in plants. Especially for StHOX20, the expression significantly upregulated in roots at 37 °C and 4 °C. Our findings laid the foundation and provided clues for understanding the biological functions of HD-ZIP family genes.

A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cul) in cucumber (Cucumis sativus L.)

We identified two curly-leaf (cul) mutants in cucumber. Map-based cloning revealed that both mutants are due to allelic mutations in the CsPHB gene, a homolog of the Arabidopsis PHABULOSA which encodes a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor. Leaf rolling is an important agronomic trait in crop breeding. Moderate leaf rolling minimizes shadowing between leaves, leading to improved photosynthetic efficiency. Although a number of genes controlling rolled leaf have been identified from rice and other plant species, none have been mapped or cloned in cucurbit crops. In this study, we identified and characterized two curly leaf (cul) mutants, cul-1 and cul-2 in cucumber. With map-based cloning, we show that cul-1 and cul-2 are allelic mutations and CsPHB (Csa6G525430) was the candidate gene for both mutants. The CsPHB gene encoded a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor. A single non-synonymous mutation in the fourth and fifth exons of the CsPHB was responsible for the cul-1 and cul-2 mutant phenotypes, respectively. The single-nucleotide substitutions in cul-1 and cul-2 were both located in cs-miRNA165/166 complementary sites of CsPHB. The expression level of CsPHB gene in multiple organs of cul-1 and cul-2 mutants was higher than that in the wild type, while the expression of cs-miRNA165/166 in the two genotypes showed the opposite trend. We speculate that disruption of the binding between the mutant allele of CsPHB and cs-miRNA165/166 leads to the curly-leaf phenotype. This is the first report to clone and characterize the CsPHB gene in the family Cucurbitaceae. Taken together, these results support CsPHB as an important player in the modulation of leaf shape development in cucumber.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.

Differentially Expressed MicroRNAs Link Cellular Physiology to Phenotypic Changes in Rice Under Stress Conditions

Plant microRNAs (miRNAs) and their target genes have important functional roles in nutrition deficiency and stress response. However, the underlying mechanisms relating relative expression of miRNAs and target mRNAs to morphological adjustments are not well defined. By combining miRNA expression profiles, corresponding target genes and transcription factors that bind to computationally identified over-represented cis-regulatory elements (CREs) common in miRNAs and target gene promoters, we implement a strategy that identifies a set of differentially expressed regulatory interactions which, in turn, relate underlying cellular mechanisms to some of the phenotypic changes observed. Integration of experimentally reported individual interactions with identified regulatory interactions explains how (i) during mineral deficiency osa-miR167 inhibits shoot growth but activates adventitious root growth by influencing free auxin content; (ii) during sulfur deficiency osa-miR394 is involved in adventitious root growth inhibition, sulfur and iron homeostasis, and auxin-mediated regulation of sulfur homeostasis; (iii) osa-miR399 contributes to cross-talk between cytokinin and phosphorus deficiency signaling; and (iv) a feed-forward loop involving the osa-miR166, trihelix and HD-ZIP III transcription factors may regulate leaf senescence during drought. This strategy not only identifies various regulatory interactions connecting phenotypic changes with cellular or molecular events triggered by stress, but also provides a framework to deepen our understanding of stress cellular physiology.

MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice

MicroRNAs (miRNAs) are 20- to 24-nucleotide small noncoding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (Oryza sativa). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice. The expression of miR166 in the roots of rice seedlings was reduced after Cd treatment. Overexpression of miR166 in rice improved Cd tolerance, a result associated with the reduction of Cd-induced oxidative stress in transgenic rice plants. Furthermore, overexpression of miR166 reduced both Cd translocation from roots to shoots and Cd accumulation in the grains. miR166 targets genes encoding the class-III homeodomain-Leu zipper (HD-Zip) family proteins in plants. In rice, HOMEODOMAIN CONTAINING PROTEIN4 (OsHB4) gene (Os03g43930), which encodes an HD-Zip protein, was up-regulated by Cd treatment but down-regulated by overexpression of miR166 in transgenic rice plants. Overexpression of OsHB4 increased Cd sensitivity and Cd accumulation in the leaves and grains of transgenic rice plants. By contrast, silencing OsHB4 by RNA interference enhanced Cd tolerance in transgenic rice plants. These results indicate a critical role for miR166 in Cd accumulation and tolerance through regulation of its target gene, OsHB4, in rice.

The Polycistronic miR166k-166h Positively Regulates Rice Immunity via Post-transcriptional Control of EIN2

MicroRNAs (miRNAs) are small RNAs acting as regulators of gene expression at the post-transcriptional level. In plants, most miRNAs are generated from independent transcriptional units, and only a few polycistronic miRNAs have been described. miR166 is a conserved miRNA in plants targeting the HD-ZIP III transcription factor genes. Here, we show that a polycistronic miRNA comprising two miR166 family members, miR166k and miR166h, functions as a positive regulator of rice immunity. Rice plants with activated MIR166k-166h expression showed enhanced resistance to infection by the fungal pathogens Magnaporthe oryzae and Fusarium fujikuroi, the causal agents of the rice blast and bakanae disease, respectively. Disease resistance in rice plants with activated MIR166k-166h expression was associated with a stronger expression of defense responses during pathogen infection. Stronger induction of MIR166k-166h expression occurred in resistant but not susceptible rice cultivars. Notably, the ethylene-insensitive 2 (EIN2) gene was identified as a novel target gene for miR166k. The regulatory role of the miR166h-166k polycistron on the newly identified target gene results from the activity of the miR166k-5p specie generated from the miR166k-166h precursor. Collectively, our findings support a role for miR166k-5p in rice immunity by controlling EIN2 expression. Because rice blast is one of the most destructive diseases of cultivated rice worldwide, unraveling miR166k-166h-mediated mechanisms underlying blast resistance could ultimately help in designing appropriate strategies for rice protection.

Knockdown of Rice MicroRNA166 Confers Drought Resistance by Causing Leaf Rolling and Altering Stem Xylem Development

MicroRNAs are 19- to 22-nucleotide small noncoding RNAs that have been implicated in abiotic stress responses. In this study, we found that knockdown of microRNA166, using the Short Tandem Target Mimic (STTM) system, resulted in morphological changes that confer drought resistance in rice (Oryza sativa). From a large-scale screen for miRNA knockdown lines in rice, we identified miR166 knockdown lines (STTM166); these plants exhibit a rolled-leaf phenotype, which is normally displayed by rice plants under drought stress. The leaves of STTM166 rice plants had smaller bulliform cells and abnormal sclerenchymatous cells, likely causing the rolled-leaf phenotype. The STTM166 plants had reduced stomatal conductance and showed decreased transpiration rates. The STTM166 lines also exhibited altered stem xylem and decreased hydraulic conductivity, likely due to the reduced diameter of the xylem vessels. Molecular analyses identified rice HOMEODOMAIN CONTAINING PROTEIN4 (OsHB4), a member of HD-Zip III gene family, as a major target of miR166; moreover, rice plants overexpressing a miR166-resistant form of OsHB4 resembled the STTM166 plants, including leaf rolling and higher drought resistance. The genes downstream of miR166-OsHB4 consisted of polysaccharide synthesis-related genes that may contribute to cell wall formation and vascular development. Our results suggest that drought resistance in rice can be increased by manipulating miRNAs, which leads to developmental changes, such as leaf rolling and reduced diameter of the xylem, that mimic plants' natural responses to water-deficit stress.