OsmiR167a-targeted auxin response factors modulate tiller angle via fine-tuning auxin distribution in rice

BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

LAZY4 acts additively with the starch-statolith-dependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in rice

Rice tiller angle is a key agronomic trait that has significant effects on the establishment of a high-yield rice population. However, the molecular mechanism underlying the control of rice tiller angle remains to be clarified. Here, we characterized the novel tiller-angle gene LAZY4 (LA4) in rice through map-based cloning. LA4 encodes a C3H2C3-type RING zinc-finger E3 ligase localized in the nucleus, and an in vitro ubiquitination assay revealed that the conserved RING finger domain is essential for its E3 ligase activity. We found that expression of LA4 can be induced by gravistimulation and that loss of LA4 function leads to defective shoot gravitropism caused by impaired asymmetric auxin redistribution upon gravistimulation. Genetic analysis demonstrated that LA4 acts in a distinct pathway from the starch biosynthesis regulators LA2 and LA3, which function in the starch-statolith-dependent pathway. Further genetic analysis showed that LA4 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport upon gravistimulation. Our studies reveal that LA4 regulates shoot gravitropism and tiller angle upstream of LA1 through a novel pathway independent of the LA2-LA3-mediated gravity-sensing mechanism, providing new insights into the rice tiller-angle regulatory network.

Enigmatic role of auxin response factors in plant growth and stress tolerance

Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.

Major quantitative trait locus qLA3.1 is related to tomato leaf angle by regulating cell length at the petiole base

KEY MESSAGE

qLA3.1, controlling leaf angle in tomato, was fine-mapped to an interval of 4.45 kb on chromosome A03, and one gene encoding auxin response factor was identified as a candidate gene. Leaf angle is a crucial trait in plant architecture that plays an important role in achieving optimal plant structure. However, there are limited reports on gene localization, cloning, and the function of plant architecture in horticultural crops, particularly regarding leaf angle. In this study, we selected 'Z3' with erect leaves and 'Heinz1706' with horizontal leaves as the phenotype and cytological observation. We combined bulked segregant analysis and fine genetic mapping to identify a candidate gene, known as, i.e., qLA3.1, which was related to tomato leaf angle. Through multiple analyses, we found that Solyc03g113410 was the most probably candidate for qLA3.1, which encoded the auxin response factor SlARF11 in tomato and was homologous to OsARF11 related to leaf angle in rice. We discovered that silencing SlARF11 resulted in upright leaves, while plants with over-expressed SlARF11 exhibited horizontal leaves. We also found that cultivars with erect leaves had a mutation from base G to base A. Moreover, quantitative analysis of plants treated with hormones indicated that SlARF11 might participate in cell elongation and the activation of genes related to auxin and brassinosteroid pathways. Transcriptome analysis further validated that SlARF11 may regulate leaf angle through hormone signaling pathways. These data support the idea that the auxin response factor SlARF11 may have an important function in tomato leaf petiole angles.

Transcription factor OsWRKY72 controls rice leaf angle by regulating LAZY1-mediated shoot gravitropism

Leaf angle is a major trait of ideal architecture, which is considered to influence rice (Oryza sativa) cultivation and grain yield. Although a few mutants with altered rice leaf inclination angles have been reported, the underlying molecular mechanism remains unclear. In this study, we showed that a WRKY transcription factor gene, OsWRKY72, was highly expressed in the leaf sheath and lamina joint. Phenotypic analyses showed that oswrky72 mutants had smaller leaf angles than the wild type, while OsWRKY72 overexpression lines exhibited an increased leaf angle. This observation suggests that OsWRKY72 functions as a positive regulator, promoting the enlargement of the leaf angle. Our bioinformatics analysis identified LAZY1 as the downstream gene of OsWRKY72. Electrophoretic mobility shift assays and dual-luciferase analysis revealed that OsWRKY72 directly inhibited LAZY1 by binding to its promoter. Moreover, knocking out OsWRKY72 enhanced shoot gravitropism, which contrasted with the phenotype of lazy1 plants. These results imply that OsWRKY72 regulates the leaf angle through gravitropism by reducing the expression of LAZY1. In addition, OsWRKY72 could directly regulate the expression of other leaf angle-related genes such as FLOWERING LOCUS T-LIKE 12 (OsFTL12) and WALL-ASSOCIATED KINASE 11 (OsWAK11). Our study indicates that OsWRKY72 contributes positively to the expansion of the leaf angle by interfering with shoot gravitropism in rice.

Temperature Effect on Rhizome Development in Perennial rice

Traditional agriculture is becoming increasingly not adapted to global climate change. Compared with annual rice, perennial rice has strong environmental adaptation and needs fewer natural resources and labor inputs. Rhizome, a kind of underground stem for rice to achieve perenniallity, can grow underground horizontally and then bend upward, developing into aerial stems. The temperature has a great influence on plant development. To date, the effect of temperature on rhizome development is still unknown. Fine temperature treatment of Oryza longistaminata (OL) proved that compared with higher temperatures (28-30 ℃), lower temperature (17-19 ℃) could promote the sprouting of axillary buds and enhance negative gravitropism of branches, resulting in shorter rhizomes. The upward growth of branches was earlier at low temperature than that at high temperature, leading to a high frequency of shorter rhizomes and smaller branch angles. Comparative transcriptome showed that plant hormones played an essential role in the response of OL to temperature. The expressions of ARF17, ARF25 and FucT were up-regulated at low temperature, resulting in prospectively asymmetric auxin distribution, which subsequently induced asymmetric expression of IAA20 and WOX11 between the upper and lower side of the rhizome, further leading to upward growth of the rhizome. Cytokinin and auxin are phytohormones that can promote and inhibit bud outgrowth, respectively. The auxin biosynthesis gene YUCCA1 and cytokinin oxidase/dehydrogenase gene CKX4 and CKX9 were up-regulated, while cytokinin biosynthesis gene IPT4 was down-regulated at high temperature. Moreover, the D3 and D14 in strigolactones pathways, negatively regulating bud outgrowth, were up-regulated at high temperature. These results indicated that cytokinin, auxins, and strigolactones jointly control bud outgrowth at different temperatures. Our research revealed that the outgrowth of axillary bud and the upward growth of OL rhizome were earlier at lower temperature, providing clues for understanding the rhizome growth habit under different temperatures, which would be helpful for cultivating perennial rice.

Unveiling the Regulatory Role of miRNAs in Internode Elongation: Integrated Analysis of MicroRNA and mRNA Expression Profiles across Diverse Dwarfing Treatments in Maize (Zea mays L.)

MicroRNAs are crucial regulators of gene expression in maize. However, the mechanisms through which miRNAs control internode elongation remain poorly understood. This study engineered varying levels of internode elongation inhibition, revealing that dwarfing treatments diminished gibberellin levels, curtailed cell longitudinal growth, and slowed the rate of internode elongation. Comprehensive transcriptome and miRNA profiling of the internode elongation zone showed gene expression changes that paralleled the extent of the internode length reduction. We identified 543 genes and 29 miRNAs with significant correlations to internode length, predominantly within families, including miR164 and miR396. By incorporating target gene expression levels, we pinpointed nine miRNA-mRNA pairs that are significantly associated with the regulation of the internode elongation. The inhibitory effects of these miRNAs on their target genes were confirmed through dual-luciferase reporter assays. Overexpression of miR164h in maize resulted in increased internode and cell length, suggesting a novel genetic avenue for manipulating plant stature. These miRNAs may also serve as precise spatiotemporal regulators for in vitro plant development.

Rice ILI atypical bHLH transcription factors antagonize OsbHLH157/OsbHLH158 during brassinosteroid signaling

Brassinosteroids (BRs) are a group of steroid hormones that play crucial roles in plant growth and development. Atypical bHLH transcription factors that lack the basic region for DNA binding have been implicated in BR signaling. However, the underlying mechanisms of atypical bHLHs in regulation of rice (Oryza sativa) BR signaling are still largely unknown. Here, we describe a systematic characterization of INCREASED LEAF INCLINATION (ILI) subfamily atypical bHLH transcription factors in rice. A total of 8 members, ILI1 to ILI8, with substantial sequence similarity were retrieved. Knockout and overexpression analyses demonstrated that these ILIs play unequally redundant and indispensable roles in BR-mediated growth and development in rice, with a more prominent role for ILI4 and ILI5. The ili3/4/5/8 quadruple and ili1/3/4/7/8 quintuple mutants displayed tremendous BR-related defects with severe dwarfism, erect leaves, and sterility. Biochemical analysis showed that ILIs interact with OsbHLH157 and OsbHLH158, which are also atypical bHLHs and have no obvious transcriptional activity. Overexpression of OsbHLH157 and OsbHLH158 led to drastic BR-defective growth, whereas the osbhlh157 osbhlh158 double mutant developed a typical BR-enhanced phenotype, indicating that OsbHLH157 and OsbHLH158 play a major negative role in rice BR signaling. Further transcriptome analyses revealed opposite effects of ILIs and OsbHLH157/OsbHLH158 in regulation of downstream gene expression, supporting the antagonism of ILIs and OsbHLH157/OsbHLH158 in maintaining the balance of BR signaling. Our results provide insights into the mechanism of BR signaling and plant architecture formation in rice.

Auxin homeostasis is maintained by sly-miR167-SlARF8A/B-SlGH3.4 feedback module in the development of locular and placental tissues of tomato fruits

The locular gel, produced by the placenta, is important for fruit flavor and seed development in tomato. However, the mechanism underlying locule and placenta development is not fully understood yet. Here, we show that two SlARF transcription factors, SlARF8B and SlARF8A (SlARF8A/B), promote the development of locular and placenta tissues. The expression of both SlARF8A and SlARF8B is repressed by sly-microRNA167 (sly-miR167), allowing for the activation of auxin downstream genes. In slarf8a, slarf8b, and slarf8a/b mutants, the auxin (IAA) levels are decreased, whereas the levels of inactive IAA conjugates including IAA-Ala, IAA-Asp, and IAA-Glu are increased. We further find that SlARF8B directly inhibits the expression of SlGH3.4, an acyl acid amino synthetase that conjugates the amino acids to IAA. Disruption of such auxin balance by the increased expression of SlGH3.4 or SlGH3.2 results in defective locular and placental tissues. Taken together, our findings reveal an important regulatory module constituted by sly-miR167-SlARF8A/B-SlGH3.4 during the development of locular and placenta tissues of tomato fruits.

Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon)

MAIN CONCLUSION

PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.

Auxins and grass shoot architecture: how the most important hormone makes the most important plants

Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops.

The miR167-OsARF12 module regulates rice grain filling and grain size downstream of miR159

Grain weight and quality are always determined by grain filling. Plant microRNAs have drawn attention as key targets for regulation of grain size and yield. However, the mechanisms that underlie grain size regulation remain largely unclear because of the complex networks that control this trait. Our earlier studies demonstrated that suppressed expression of miR167 (STTM/MIM167) substantially increased grain weight. In a field test, the yield increased up to 12.90%-21.94% because of a significantly enhanced grain filling rate. Here, biochemical and genetic analyses revealed the regulatory effects of miR159 on miR167 expression. Further analysis indicated that OsARF12 is the major mediator by which miR167 regulates rice grain filling. Overexpression of OsARF12 produced grain weight and grain filling phenotypes resembling those of STTM/MIM167 plants. Upon in-depth analysis, we found that OsARF12 activates OsCDKF;2 expression by directly binding to the TGTCGG motif in its promoter region. Flow cytometry analysis of young panicles from OsARF12-overexpressing plants and examination of cell number in cdkf;2 mutants verified that OsARF12 positively regulates grain filling and grain size by targeting OsCDKF;2. Moreover, RNA sequencing results suggested that the miR167-OsARF12 module is involved in the cell development process and hormone pathways. OsARF12-overexpressing plants and cdkf;2 mutants exhibited enhanced and reduced sensitivity to exogenous auxin and brassinosteroid (BR) treatment, confirming that targeting of OsCDKF;2 by OsARF12 mediates auxin and BR signaling. Our results reveal that the miR167-OsARF12 module works downstream of miR159 to regulate rice grain filling and grain size via OsCDKF;2 by controlling cell division and mediating auxin and BR signals.

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.

Restructuring plant types for developing tailor-made crops

Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.

LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice

Starch biosynthesis in gravity-sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity-sensing tissues is still unclear. We characterized a novel tiller angle gene LAZY3 (LA3) in rice through map-based cloning. Biochemical, molecular and genetic studies further demonstrated the essential roles of LA3 in gravity perception of rice shoot and tiller angle control. The shoot gravitropism and lateral auxin transport were defective in la3 mutant upon gravistimulation. We showed that LA3 encodes a chloroplast-localized tryptophan-rich protein associated with starch granules via Tryptophan-rich region (TRR) domain. Moreover, LA3 could interact with the starch biosynthesis regulator LA2, determining starch granule formation in shoot gravity-sensing tissues. LA3 and LA2 negatively regulate tiller angle in the same pathway acting upstream of LA1 to mediate asymmetric distribution of auxin. Our study defined LA3 as an indispensable factor of starch biosynthesis in rice gravity-sensing tissues that greatly broadens current understanding in the molecular mechanisms underlying the starch granule formation in gravity-sensing tissues, and provides new insights into the regulatory mechanism of shoot gravitropism and rice tiller angle.

Auxin plays a role in the adaptation of rice to anaerobic germination and seedling establishment

Auxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies revealed that excessive levels of indole-3-acetic acid(IAA) frequently cause the inhibition of plant growth and development. In this study, the high-level accumulation of endogenous IAA is observed under dark submergence, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167-ARF-GH3 pathway. The OsGH3-8 encodes an IAA-amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressing OsGH3-8 increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. Our studies reveal that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance.

Roles of auxin response factors in rice development and stress responses

Auxin signalling plays a key role in various developmental processes ranging from embryogenesis to senescence in plants. Auxin response factor (ARF), a key component of auxin signalling, functions by binding to auxin response element within promoter of auxin response genes, activating or repressing the target genes. Increasing evidences show that ARFs are crucial for plant response to stresses. This review summarises the recent advance on the functions and their regulatory pathways of rice ARFs in development and responding to stresses. The importance of OsARFs is demonstrated by their roles in triggering various physiological, biochemical and molecular reactions to resist adverse environmental conditions. We also describe the transcriptional and post-transcriptional regulation of OsARFs, and discuss the major challenges in this area.

The identification and characterization of a plant height and grain length related gene hfr131 in rice

Plant height and grain size are important agronomic traits affecting rice yield. Various plant hormones participate in the regulation of plant height and grain size in rice. However, how these hormones cooperate to regulate plant height and grain size is poorly understood. In this study, we identified a brassinosteroid-related gene, hfr131, from an introgression line constructed using Oryza longistaminata, that caused brassinosteroid insensitivity and reduced plant height and grain length in rice. Further study showed that hfr131 is a new allele of OsBRI1 with a single-nucleotide polymorphism (G to A) in the coding region, leading to a T988I conversion at a conserved site of the kinase domain. By combining yeast one-hybrid assays, chromatin immunoprecipitation-quantitative PCR and gene expression quantification, we demonstrated that OsARF17, an auxin response factor, could bind to the promoter region of HFR131 and positively regulated HFR131 expression, thereby regulating the plant height and grain length, and influencing brassinosteroid sensitivity. Haplotype analysis showed that the consociation of OsAFR17^Hap1 /HFR131^Hap6 conferred an increase in grain length. Overall, this study identified hfr131 as a new allele of OsBRI1 that regulates plant height and grain length in rice, revealed that brassinosteroid and auxin might coordinate through OsARF17-HFR131 interaction, and provided a potential breeding target for improvement of rice yield.

Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice

Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the 'best' gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.

How rice adapts to high temperatures

High-temperature stress affects crop yields worldwide. Identifying thermotolerant crop varieties and understanding the basis for this thermotolerance would have important implications for agriculture, especially in the face of climate change. Rice (Oryza sativa) varieties have evolved protective strategies to acclimate to high temperature, with different thermotolerance levels. In this review, we examine the morphological and molecular effects of heat on rice in different growth stages and plant organs, including roots, stems, leaves and flowers. We also explore the molecular and morphological differences among thermotolerant rice lines. In addition, some strategies are proposed to screen new rice varieties for thermotolerance, which will contribute to the improvement of rice for agricultural production in the future.

Advances in structure and function of auxin response factor in plants

Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops.

Auxin regulation on crop: from mechanisms to opportunities in soybean breeding

Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) 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.

WOX11: the founder of plant organ regeneration

De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.

miR319 and its target TCP4 involved in plant architecture regulation in Brassica napus

Plant architecture is a collection of genetically controlled crop productivity and adaptation. MicroRNAs (miRNAs) have been proved to function in various biological processes, but little is known about how miRNA regulates plant architecture in rapeseed (Brassica napus L.). In this study, four small RNA libraries and two degradome libraries from shoot apex of normal and rod-like plants were sequenced. A total of 639 miRNA precursors and 16 differentially expressed miRNAs were identified in this study. In addition, 322 targets were identified through degradome sequencing. Among them, 14 targets were further validated via RNA ligase-mediated 5' rapid amplification of cDNA ends. Transgenic approach showed that increased TCP4 activity in Arabidopsis resulted in premature onset of maturation and reduced plant size along with early flowering and shortened flowering time. miR319-OE lines in Brassica napus exhibited serrated leaves and abnormal development of shoot apical meristem (SAM), which led to the deformed growth of stem and reduced plant height. In conclusion, our study lays the foundation for elucidating miRNA regulate plant architecture and provides new insight into the miR319/TCP4 module regulates plant architecture in rapeseed.

A HST1-like gene controls tiller angle through regulating endogenous auxin in common wheat

Tiller angle is one of the most important agronomic traits and one key factor for wheat ideal plant architecture, which can both increase photosynthetic efficiency and greatly enhance grain yield. Here, a deacetylase HST1-like (TaHST1L) gene controlling wheat tiller angle was identified by the combination of a genome-wide association study (GWAS) and bulked segregant analysis (BSA). Ethyl methane sulfonate (EMS)-mutagenized tetraploid wheat lines with the premature stop codon of TaHST1L exhibited significantly smaller tiller angles than the wild type. TaHST1L-overexpressing (OE) plants exhibited significantly larger tiller angles and increased tiller numbers in both winter and spring wheat, while TaHST1L-silenced RNAi plants displayed significantly smaller tiller angles and decreased tiller numbers. Moreover, TaHST1L strongly interacted with TaIAA17 and inhibited its expression at the protein level, and thus possibly improved the content of endogenous auxin in the basal tissue of tillers. The transcriptomics and metabolomics results indicated that TaHST1L might change plant architecture by mediating auxin signal transduction and regulating endogenous auxin levels. In addition, a 242-bp insertion/deletion (InDel) in the TaHST1L-A1 promoter altered transcriptional activity and TaHST1L-A1b allele with the 242-bp insertion widened the tiller angle of TaHST1L-OE transgenic rice plants. Wheat varieties with TaHST1L-A1b allele possessed the increased tiller angle and grain yield. Further analysis in wheat and its progenitors indicated that the 242-bp InDel possibly originated from wild emmer and was strongly domesticated in the current varieties. Therefore, TaHST1L involved in the auxin signalling pathway showed the big potential to improve wheat yield by controlling plant architecture.

Genetic dissection of branch architecture in oilseed rape (Brassica napus L.) germplasm

Branch architecture is an important factor influencing rapeseed planting density, mechanized harvest, and yield. However, its related genes and regulatory mechanisms remain largely unknown. In this study, branch angle (BA) and branch dispersion degree (BD) were used to evaluate branch architecture. Branch angle exhibited a dynamic change from an increase in the early stage to a gradual decrease until reaching a stable state. Cytological analysis showed that BA variation was mainly due to xylem size differences in the vascular bundle of the branch junction. The phenotypic analysis of 327 natural accessions revealed that BA in six environments ranged from 24.3° to 67.9°, and that BD in three environments varied from 4.20 cm to 21.4 cm, respectively. A total of 115 significant loci were detected through association mapping in three models (MLM, mrMLM, and FarmCPU), which explained 0.53%-19.4% of the phenotypic variations. Of them, 10 loci were repeatedly detected in different environments and models, one of which qBAD.A03-2 was verified as a stable QTL using a secondary segregation population. Totally, 1066 differentially expressed genes (DEGs) were identified between branch adaxial- and abaxial- sides from four extremely large or small BA/BD accessions through RNA sequencing. These DEGs were significantly enriched in the pathways related to auxin biosynthesis and transport as well as cell extension such as indole alkaloid biosynthesis, other glycan degradation, and fatty acid elongation. Four known candidate genes BnaA02g16500D (PIN1), BnaA03g10430D (PIN2), BnaC03g06250D (LAZY1), and BnaC06g20640D (ARF17) were identified by both GWAS and RNA-seq, all of which were involved in regulating the asymmetric distribution of auxins. Our identified association loci and candidate genes provide a theoretical basis for further study of gene cloning and genetic improvement of branch architecture.

Ustilaginoidea virens Nuclear Effector SCRE4 Suppresses Rice Immunity via Inhibiting Expression of a Positive Immune Regulator OsARF17

Rice false smut caused by the biotrophic fungal pathogen Ustilaginoidea virens has become one of the most important diseases in rice. The large effector repertory in U. virens plays a crucial role in virulence. However, current knowledge of molecular mechanisms how U. virens effectors target rice immune signaling to promote infection is very limited. In this study, we identified and characterized an essential virulence effector, SCRE4 (Secreted Cysteine-Rich Effector 4), in U. virens. SCRE4 was confirmed as a secreted nuclear effector through yeast secretion, translocation assays and protein subcellular localization, as well as up-regulation during infection. The SCRE4 gene deletion attenuated the virulence of U. virens to rice. Consistently, ectopic expression of SCRE4 in rice inhibited chitin-triggered immunity and enhanced susceptibility to false smut, substantiating that SCRE4 is an essential virulence factor. Furthermore, SCRE4 transcriptionally suppressed the expression of OsARF17, an auxin response factor in rice, which positively regulates rice immune responses and resistance against U. virens. Additionally, the immunosuppressive capacity of SCRE4 depended on its nuclear localization. Therefore, we uncovered a virulence strategy in U. virens that transcriptionally suppresses the expression of the immune positive modulator OsARF17 through nucleus-localized effector SCRE4 to facilitate infection.

OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice

As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.

miR167d-ARFs Module Regulates Flower Opening and Stigma Size in Rice

Flower opening and stigma exertion are two critical traits for cross-pollination during seed production of hybrid rice (Oryza sativa L.). In this study, we demonstrate that the miR167d-ARFs module regulates stigma size and flower opening that is associated with the elongation of stamen filaments and the cell arrangement of lodicules. The overexpression of miR167d (OX167d) resulted in failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule, resulting in cleistogamy. Blocking miR167d by target mimicry also led to a morphological alteration of the individual floral organs, including a reduction in stigma size and alteration of lodicule cell morphology, but did not show the cleistogamous phenotype. In addition, the four target genes of miR167d, namely ARF6, ARF12, ARF17, and ARF25, have overlapping functions in flower opening and stigma size. The loss-of-function of a single ARF gene did not influence the flower opening and stigma size, but arf12 single mutant showed a reduced plant height and aborted apical spikelets. However, mutation in ARF12 together with mutation in either ARF6, ARF17, or ARF25 led to the same defective phenotypes that were observed in OX167d, including the failed elongation of stamen filaments, increased stigma size, and morphological alteration of lodicule. These findings indicate that the appropriate expression of miR167d is crucial and the miR167d-ARFs module plays important roles in the regulation of flower opening and stigma size in rice.

Melatonin Mediates Axillary Bud Outgrowth by Improving Nitrogen Assimilation and Transport in Rice

Melatonin plays an important role in plant resistance to biotic and abiotic stresses. However, whether melatonin is involved in the regulation of plant architecture, such as the formation of axillary bud outgrowth or tillering, in rice remains unknown. Here, we found that different concentrations of melatonin influenced axillary bud outgrowth in rice, and moderate melatonin concentrations also alleviated the inhibition of axillary bud outgrowth in the presence of high concentrations of basic amino acids lysine and arginine. Furthermore, transcriptome analysis demonstrated that genes involved in nitrogen metabolism and phytohormone signal transduction pathways may affect axillary bud outgrowth, which is regulated by melatonin. We determined that the differentially expressed genes glutamine synthetase OsGS2 and amino acid transporter OsAAP14, which are involved in nitrogen metabolism and are regulated by melatonin and basic amino acids, were the key regulators of axillary bud outgrowth in rice. In addition, we validated the functions of OsGS2 and OsAAP14 using rice transgenic plants with altered axillary bud outgrowth and tillers. Taken together, these results suggest that melatonin mediates axillary bud outgrowth by improving nitrogen assimilation and transport in rice.

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.

Identification of a Major QTL and Validation of Related Genes for Tiller Angle in Rice Based on QTL Analysis

An ideal plant architecture is an important condition to achieve high crop yields. The tiller angle is an important and complex polygenic trait of rice (Oryza sativa L.) plant architecture. Therefore, the discovery and identification of tiller angle-related genes can aid in the improvement of crop architecture and yield. In the present study, 222 SSR markers were used to establish a high-density genetic map of rice doubled haploid population, and a total of 8 quantitative trait loci (QTLs) were detected based on the phenotypic data of the tiller angle and tiller crown width over 2 years. Among them, four QTLs (qTA9, qCW9, qTA9-1, and qCW9-1) were overlapped at marker interval RM6235-RM24288 on chromosome 9 with a large effect value regarded as a stable major QTL. The selected promising related genes were further identified by relative gene expression analysis, which gives us a basis for the future cloning of these genes. Finally, OsSAURq9, which belongs to the SMALL AUXIN UP RNA (SAUR), an auxin-responsive protein family, was selected as a target gene. Overall, this work will help broaden our knowledge of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.

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.

The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response

Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.

Transcriptome and miRNAome analysis reveals components regulating tissue differentiation of bamboo shoots

Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. This study identified a total of 58,652 genes and 150 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild-type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis "Pachyloen") at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 14,029 (65.17%) differentially expressed genes and 68 (45.33%) differentially expressed miRNAs were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations, each between two successive stages (WTS2/TWS2_versus_WTS1/TWS1, WTS3/TWS3_versus_WTS2/TWS2, WTS4/TWS4_versus_WTS3/TWS3, and WTS5/TWS5_versus_WTS4/TWS4), and the WTTW group was composed of five combinations, each between two relative stages (TWS1-5_versus_WTS1-5). Additionally, among the phytohormones, zeatin showed more remarkable changes in concentrations than indole-3-acetic acid, gibberellic acid, and abscisic acid throughout the five stages in the WT and the TW groups. Moreover, 125 cleavage sites were identified for 387 miRNA-mRNA pairs via degradome sequencing (P < 0.05). The dual-luciferase reporter assay confirmed that 13 miRNAs bound to 12 targets. Fluorescence in situ hybridization localized miR166 and miR160 in the shoot apical meristem and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.

Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses

Background

The rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment.

Methods

In this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions.

Results

As a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs.

Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.

Functional Characterization of MdTAC1a Gene Related to Branch Angle in Apple (Malus x domestica Borkh.)

The Tiller Angle Control 1 (TAC1) gene belongs to the IGT family, which mainly controls plant branch angle, thereby affecting plant form. Two members of MdTAC1 are identified in apple; the regulation of apple branch angle by MdTAC1 is still unclear. In this study, a subcellular localization analysis detected MdTAC1a in the nucleus and cell membrane, but MdTAC1b was detected in the cell membrane. Transgenic tobacco by overexpression of MdTAC1a or MdTAC1b showed enlarged leaf angles, the upregulation of several genes, such as GA 2-oxidase (GA2ox), and a sensitive response to light and gravity. According to a qRT-PCR analysis, MdTAC1a and MdTAC1b were strongly expressed in shoot tips and vegetative buds of weeping cultivars but were weakly expressed in columnar cultivars. In the MdTAC1a promoter, there were losses of 2 bp in spur cultivars and 6 bp in weeping cultivar compared with standard and columnar cultivars. An InDel marker specific to the MdTAC1a promoter was developed to distinguish apple cultivars and F1 progeny. We identified a protein, MdSRC2, that interacts with MdTAC1a, whose encoding gene which was highly expressed in trees with large branch angles. Our results indicate that differences in the MdTAC1a promoter are major contributors to branch-angle variation in apple, and the MdTAC1a interacts with MdSRC2 to affect this trait.

Molecular basis underlying rice tiller angle: Current progress and future perspectives

Crop plant architecture is an important agronomic trait that contributes greatly to crop yield. Tiller angle is one of the most critical components that determine crop plant architecture, which in turn substantially affects grain yield mainly owing to its large influence on plant density. Gravity is a fundamental physical force that acts on all organisms on earth. Plant organs sense gravity to control their growth orientation, including tiller angle in rice (Oryza sativa). This review summarizes recent research advances made using rice tiller angle as a research model, providing insights into domestication of rice tiller angle, genetic regulation of rice tiller angle, and shoot gravitropism. Finally, we propose that current discoveries in rice can shed light on shoot gravitropism and improvement of plant tiller/branch angle in other species, thereby contributing to agricultural production in the future.

MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling

Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.

Transcription factor OsbZIP49 controls tiller angle and plant architecture through the induction of indole-3-acetic acid-amido synthetases in rice

Tiller angle is an important determinant of plant architecture in rice (Oryza sativa L.). Auxins play a critical role in determining plant architecture; however, the underlying metabolic and signaling mechanisms are still largely unknown. In this study, we have identified a member of the bZIP family of TGA class transcription factors, OsbZIP49, that participates in the regulation of plant architecture and is specifically expressed in gravity-sensing tissues, including the shoot base, nodes and lamina joints. Transgenic rice plants overexpressing OsbZIP49 displayed a tiller-spreading phenotype with reduced plant height and internode lengths. In contrast, CRISPR/Cas9-mediated knockout of OsbZIP49 resulted in a compact architecture. Follow-up studies indicated that the effects of OsbZIP49 on tiller angles are mediated through changes in shoot gravitropic responses. Additionally, we provide evidence that OsbZIP49 activates the expression of indole-3-acetic acid-amido synthetases OsGH3-2 and OsGH3-13 by directly binding to TGACG motifs located within the promoters of both genes. Increased GH3-catalyzed conjugation of indole-3-acetic acid (IAA) in rice transformants overexpressing OsbZIP49 resulted in the increased accumulation of IAA-Asp and IAA-Glu, and a reduction in local free auxin, tryptamine and IAA-Glc levels. Exogenous IAA or naphthylacetic acid (NAA) partially restored shoot gravitropic responses in OsbZIP49-overexpressing plants. Knockout of OsbZIP49 led to reduced expression of both OsGH3-2 and OsGH3-13 within the shoot base, and increased accumulation of IAA and increased OsIAA20 expression levels were observed in transformants following gravistimulation. Taken together, the present results reveal the role transcription factor OsbZIP49 plays in determining plant architecture, primarily due to its influence on local auxin homeostasis.

N. S, Pachamuthu K, Chenna S, Nair A, Shivaprasad PV. Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions

RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α-clade and β-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and noncoding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities and their contribution to the regulation of gene expression.

Population Structure of Nation-Wide Rice in Thailand

BACKGROUND

Thailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.

RESULTS

The result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure.

CONCLUSION

The population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.

Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc

Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.

AUXIN RESPONSE FACTORS 6 and 17 control the flag leaf angle in rice by regulating secondary cell wall biosynthesis of lamina joints

Flag leaf angle impacts the photosynthetic capacity of densely grown plants and is thus an important agronomic breeding trait for crop architecture and yield. The hormone auxin plays a key role in regulating this trait, yet the underlying molecular and cellular mechanisms remain unclear. Here, we report that two rice (Oryza sativa) auxin response factors (ARFs), OsARF6 and OsARF17, which are highly expressed in lamina joint tissues, control flag leaf angle in response to auxin. Loss-of-function double osarf6 osarf17 mutants displayed reduced secondary cell wall levels of lamina joint sclerenchymatous cells (Scs), resulting in an exaggerated flag leaf angle and decreased grain yield under dense planting conditions. Mechanical measurements indicated that the mutant lamina joint tissues were too weak to support the weight of the flag leaf blade, resembling the phenotype of the rice increased leaf angle1 (ila1) mutant. We demonstrate that OsARF6 and OsARF17 directly bind to the ILA1 promoter independently and synergistically to activate its expression. In addition, auxin-induced ILA1 expression was dependent on OsARF6 and OsARF17. Collectively, our study reveals a mechanism that integrates auxin signaling with the secondary cell wall composition to determine flag leaf angle, providing breeding targets in rice, and potentially other cereals, for this key trait.

LAZY2 controls rice tiller angle through regulating starch biosynthesis in gravity-sensing cells

Rice (Oryza sativa) tiller angle is a key component for achieving ideal plant architecture and higher grain yield. However, the molecular mechanism underlying rice tiller angle remains elusive. We characterized a novel rice tiller angle mutant lazy2 (la2) and isolated the causative gene LA2 through map-based cloning. Biochemical, molecular and genetic studies were conducted to elucidate the LA2-involved tiller angle regulatory mechanism. The la2 mutant shows large tiller angle with impaired shoot gravitropism and defective asymmetric distribution of auxin. We found that starch granules in amyloplasts are completely lost in the gravity-sensing leaf sheath base cells of la2, whereas the seed development is not affected. LA2 encodes a novel chloroplastic protein that can interact with the starch biosynthetic enzyme Oryza sativa plastidic phosphoglucomutase (OspPGM) to regulate starch biosynthesis in rice shoot gravity-sensing cells. Genetic analysis showed that LA2 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport. Our studies revealed that LA2 acts as a novel regulator of rice tiller angle by specifically regulating starch biosynthesis in gravity-sensing cells, and established the framework of the starch-statolith-dependent rice tiller angle regulatory pathway, providing new insights into the rice tiller angle regulatory network.

Key wheat GRF genes constraining wheat tillering of mutant dmc

Tillering is a key agronomy trait for wheat (Triticum aestivum L.) production. Previously, we have reported a dwarf-monoculm wheat mutant (dmc) obtained from cultivar Guomai 301 (wild type, WT), and found growth regulating factors (GRFs) playing important roles in regulating wheat tillering. This study is to systematically investigate the roles of all the wheat GRFs (T. aestivum GRFs, TaGRFs) in regulating tillering, and screen out the key regulators. A total of 30 TaGRFs were identified and their physicochemical properties, gene structures, conserved domains, phylogenetic relationships and tissue expression profiles were analyzed. The expression levels of all the TaGRFs were significantly lower in dmc than those in WT at early tillering stage, and the abnormal expressions of TaGRF2-7(A, B, D), TaGRF5-7D, TaGRF10-6(A, B, D) and TaGRF11-2A were major causes constraining the tillering of dmc. The transcriptions of TaGRFs were significantly affected by exogenous indole acetic acid (IAA) and gibberellin acid (GA3) applications, which suggested that TaGRFs as well as IAA, GA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of GRF genes in wheat.

OsARF11 Promotes Growth, Meristem, Seed, and Vein Formation during Rice Plant Development

The plant hormone auxin acts as a mediator providing positional instructions in a range of developmental processes. Studies in Arabidopsis thaliana L. show that auxin acts in large part via activation of Auxin Response Factors (ARFs) that in turn regulate the expression of downstream genes. The rice (Oryza sativa L.) gene OsARF11 is of interest because of its expression in developing rice organs and its high sequence similarity with MONOPTEROS/ARF5, a gene with prominent roles in A. thaliana development. We have assessed the phenotype of homozygous insertion mutants in the OsARF11 gene and found that in relation to wildtype, osarf11 seedlings produced fewer and shorter roots as well as shorter and less wide leaves. Leaves developed fewer veins and larger areoles. Mature osarf11 plants had a reduced root system, fewer branches per panicle, fewer grains per panicle and fewer filled seeds. Mutants had a reduced sensitivity to auxin-mediated callus formation and inhibition of root elongation, and phenylboronic acid (PBA)-mediated inhibition of vein formation. Taken together, our results implicate OsARF11 in auxin-mediated growth of multiple organs and leaf veins. OsARF11 also appears to play a central role in the formation of lateral root, panicle branch, and grain meristems.

Rice GROWTH-REGULATING FACTOR7 Modulates Plant Architecture through Regulating GA and Indole-3-Acetic Acid Metabolism

Plant-specific GROWTH-REGULATING FACTORs (GRFs) participate in central developmental processes, including leaf and root development; inflorescence, flower, and seed formation; senescence; and tolerance to stresses. In rice (Oryza sativa), there are 12 GRFs, but the role of the miR396-OsGRF7 regulatory module remains unknown. Here, we report that OsGRF7 shapes plant architecture via the regulation of auxin and GA metabolism in rice. OsGRF7 is mainly expressed in lamina joints, nodes, internodes, axillary buds, and young inflorescences. Overexpression of OsGRF7 causes a semidwarf and compact plant architecture with an increased culm wall thickness and narrowed leaf angles mediated by shortened cell length, altered cell arrangement, and increased parenchymal cell layers in the culm and adaxial side of the lamina joints. Knockout and knockdown lines of OsGRF7 exhibit contrasting phenotypes with severe degradation of parenchymal cells in the culm and lamina joints at maturity. Further analysis indicated that OsGRF7 binds the ACRGDA motif in the promoters of a cytochrome P450 gene and AUXIN RESPONSE FACTOR12, which are involved in the GA synthesis and auxin signaling pathways, respectively. Correspondingly, OsGRF7 alters the contents of endogenous GAs and auxins and sensitivity to exogenous phytohormones. These findings establish OsGRF7 as a crucial component in the OsmiR396-OsGRF-plant hormone regulatory network that controls rice plant architecture.