The small auxin-up RNA OsSAUR45 affects auxin synthesis and transport in rice

Comparative transcriptome and metabolome analysis reveals the differential response to salinity stress of two genotypes brewing sorghum

Salinity tolerance in brewing sorghum is a very important trait, especially in areas that are affected by soil salinity. In order to elucidate the mechanism underlying salt tolerance, we conducted a comparative analysis of the transcriptome and metabolome in two distinct sweet sorghum genotypes, namely the salt-tolerant line NY1298 and the salt-sensitive line MY1176, following exposure to salt treatment. Our initial findings indicate the presence of genotype-specific responses in brewing sorghum under salt stress conditions. Notably, there were variations in the expression of genes and metabolites among different genotypes in response to high-salt stress. Specifically, certain transcription factors belonging to the WRKY, MYB, and NAC families were identified as being involved in the response to increased external salinity. WGCNA analysis identified stage-specific gene expression for different salinity gradients in each cultivar, and explored the gene function by KEGG enrichment analysis. Combined analysis of DEGs and DEMs in hormone synthesis found AUX/IAA, SAUR, CRE1, A-ARR, PP2C, SNRK2 genes, and 3-indoleacetic acid and jasmonic acid were evidently differential expression among different salt concentrations. Taken together, our study carried out a comprehensive overview of two genotypes of brewing sorghum gene and metabolite expression differences in response to salt stress, and expanded the understanding of responsive mechanism of brewing sorghum to salt stress.

Advances in auxin synthesis, transport, and signaling in rice: implications for stress resilience and crop improvement

Auxin, a crucial plant hormone, plays a pivotal role in regulating various aspects of rice growth and development, including cell elongation, root formation, and responses to environmental stimuli. Recent breakthroughs in auxin research have revealed novel regulatory mechanisms, such as the identification of auxin-related genes like DNR1 and OsARF18, which enhance rice nitrogen use efficience and resistance to glufosinate. Additionally, advancements in understanding auxin transport and signaling pathways have highlighted their potential in optimizing tillering, root architecture, and grain yield. This review examines these molecular mechanisms and their interactions with other hormones, emphasizing their integration into breeding programs for improved rice productivity. By synthesizing these findings, we provide a comprehensive overview of how auxin research informs strategies for developing rice varieties with enhanced adaptability and optimized growth, contributing to food security and sustainable agriculture.

Genome-wide identification and expression analysis of SMALL AUXIN UP RNA (SAUR) genes in rice (Oryza sativa)

SMALL AUXIN UP RNAs (SAURs), the largest family of early auxin response genes, plays crucial roles in multiple processes, including cell expansion, leaf growth and senescence, auxin transport, tropic growth and so on. Although the rice SAUR gene family was identified in 2006, it is necessary to identify the rice SAUR gene due to the imperfection of its analysis methods. In this study, a total of 60 OsSAURs (including two pseudogenes) distributed on 10 chromosomes were identified in rice (Oryza sativa). Bioinformatics tools were used to systematically analyze the physicochemical properties, subcellular localization, motif compositions, chromosomal location, gene duplication, evolutionary relationships, auxin-responsive cis-elements of the OsSAURs. In addition, the expression profiles obtained from microarray data analysis showed that OsSAUR genes had different expression patterns in different tissues and responded to auxin treatment, indicating functional differences among members of OsSAUR gene family. In a word, this study provides basic information for SAUR gene family of rice and lays a foundation for further study on the role of SAUR in rice growth and development.

An osmesl mutant delayed rice leaf senescence through inhibiting cell death by OsBI-1

Leaf senescence following heading in rice is subject to rigorous regulation, with many of the underlying control mechanisms remaining largely unknown. In this study, we identified a novel gene, OsMESL, which exerts a positive regulatory effect on leaf senescence in rice. The T-DNA insertion mutant known as osmesl and RNA interference plants displayed a phenotype characterized by stay-green after heading. Genetic analysis indicated that the mutant phenotype could be rescued through complementation, while the overexpression of OsMESL accelerated leaf senescence after heading, underscoring OsMESL's positive regulatory role in rice leaf senescence. Subsequent investigations revealed that OsMESL modulates the process of cell death by influencing the stability of its interacting protein, the cell death suppressor OsBI-1, thereby governing leaf senescence. Furthermore, the leaves of the osmesl mutant exhibited a delayed reduction in photosynthesis, along with increased grain length and 1000-grain weight. In conclusion, we identified OsMESL as a novel positive regulator of leaf senescence in rice, which likely participates in leaf senescence through the mediation of cell death by OsBI-1, resulting in the phenotype of stay-green in the osmesl mutant after heading.

The C2H2-type zinc finger transcription factor ZmDi19-7 regulates plant height and organ size by promoting cell size in maize

The drought-induced protein 19 (Di19) gene family encodes a Cys2/His2 zinc-finger protein implicated in responses to diverse plant stressors. To date, potential roles of these proteins as transcription factors remain largely elusive in maize. Here, we show that ZmDi19-7 gene exerts pivotal functions in regulation of plant height and organ growth by modulating the cell size in maize. ZmDi19-7 physically interacts with ubiquitin receptor protein ZmDAR1b, which is indispensable in ubiquitination of ZmDi19-7 and affects its protein stability. Further genetic analysis demonstrated that ZmDAR1b act in a common pathway with ZmDi19-7 to regulate cell size in maize. ZmDi19-7, severing as a transcriptional factor, is significantly enriched in conserved DiBS element in the promoter region of ZmHSP22, ZmHSP18c, ZmSAUR25, ZmSAUR55, ZmSAUR7 and ZmXTH23 and orchestrates the expression of these genes involving in auxin-mediated cell expansion and protein processing in the endoplasmic reticulum. Thus, our findings demonstrate that ZmDi19-7 is an important newfound component of the ubiquitin-proteasome pathway in regulation of plant height and organ size in maize. These discoveries highlight potential targets for the genetic improvement of maize in the future.

IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato (Solanum tuberosum L.)

Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L-1. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato.

PpSAUR5 promotes plant growth by regulating lignin and hormone pathways

Introduction

Peach (Prunus persica) has a high nutritional and economic value. However, its overgrowth can lead to yield loss. Regulating the growth of peach trees is challenging. The small auxin-up RNA (SAUR) gene family is the largest family of auxin-responsive genes, which play important roles in plant growth and development. However, members of this gene family are rarely reported in peach.

Methods

In this study, we measured leaf area, chlorophyll and lignin content to detect the role of PpSAUR5 on growth through transgenic Arabidopsis.

Results

PpSAUR5 responds to auxin and gibberellin, promoting and inhibiting the synthesis of gibberellin and auxin, respectively. The heterologous transformation of PpSAUR5 in Arabidopsis led to enhanced growth of leaves and siliques, lightening of leaf color, decrease in chlorophyll content, increase in lignin content, abnormalities in the floral organs, and distortion of the inflorescence axis. Transcriptome data analysis of PpSAUR5 overexpression and wild-type lines revealed 854 differentially expressed genes (DEGs). GO and KEGG analyses showed that the DEGs were primarily involved in biological processes, such as cellular processes, metabolic processes, response to stimuli, and catalytic activity. These genes were mainly enriched in pathways, such as phenylalanine biosynthesis, phytohormone signaling, and MAPK signaling.

Discussion

In summary, these results suggested that PpSAUR5 might regulate tree vigor by modulating the synthesis of auxin and gibberellin. Future studies can use PpSAUR5 as a candidate gene to elucidate the potential regulatory mechanisms underlying peach tree vigor.

Screening and verification of proteins that interact with the anthocyanin-related transcription factor PbrMYB114 in 'Yuluxiang' pear

Despite extensive research highlighting the pivotal role of MYB transcription factors in regulating anthocyanin biosynthesis, the interactive regulatory network involving these MYB factors in pear fruits remains inadequately characterized. In this study, the anthocyanin-regulatory gene PbrMYB114 was successfully cloned from 'Yuluxiang' pear (Pyrus bretschneideri) fruits, and its influence on anthocyanin accumulation was confirmed through transient expression assays. Specifically, the co-transformation of PbrMYB114 with its partner PbrbHLH3 in pears served to validate the functional role of PbrMYB114. Subsequently, PbrMYB114 was employed as bait in a yeast two-hybrid screening assay, using a 'Yuluxiang' pear protein library, which led to the identification of 25 interacting proteins. Further validation of the interactions between PbrMYB114 and PbrMT2/PbrMT3 was conducted. Investigations into the role of PbrMT2 and PbrMT3 in 'Duli' seedlings (Pyrus betulaefolia) revealed their potential to enhance anthocyanin accumulation. The outcomes of these studies provide novel insights into the protein network that regulates pear anthocyanin biosynthesis, particularly the functional interactions among PbrMYB114 and associated proteins.

Genome-wide identification of the SAUR gene family and screening for SmSAURs involved in root development in Salvia miltiorrhiza

KEY MESSAGE

SmSAUR4, SmSAUR18, SmSAUR28, SmSAUR37, and SmSAUR38 were probably involved in the auxin-mediated root development in Salvia miltiorrhiza. Salvia miltiorrhiza is a widely utilized medicinal plant in China. Its roots and rhizomes are the main medicinal portions and are closely related to the quality of this herb. Previous studies have revealed that auxin plays pivotal roles in S. miltiorrhiza root development. Whether small auxin-up RNA genes (SAURs), which are crucial early auxin response genes, are involved in auxin-mediated root development in S. miltiorrhiza is worthy of investigation. In this study, 55 SmSAUR genes in S. miltiorrhiza were identified, and their physical and chemical properties, gene structure, cis-acting elements, and evolutionary relationships were analyzed. The expression levels of SmSAUR genes in different organs of S. miltiorrhiza were detected using RNA-seq combined with qRT‒PCR. The root development of S. miltiorrhiza seedlings was altered by the application of indole-3-acetic acid (IAA), and Pearson correlation coefficient analysis was conducted to screen SmSAURs that potentially participate in this physiological process. The diameter of primary lateral roots was positively correlated with SmSAUR4. The secondary lateral root number was positively correlated with SmSAUR18 and negatively correlated with SmSAUR4. The root length showed a positive correlation with SmSAUR28 and SmSAUR37 and a negative correlation with SmSAUR38. The fresh root biomass exhibited a positive correlation with SmSAUR38 and a negative correlation with SmSAUR28. The aforementioned SmSAURs were likely involved in auxin-mediated root development in S. miltiorrhiza. Our study provides a comprehensive overview of SmSAURs and provides the groundwork for elucidating the molecular mechanism underlying root morphogenesis in this species.

Biological control of potato common scab and growth promotion of potato by Bacillus velezensis Y6

Potato common scab, caused mainly by Streptomyces scabies, causes surface necrosis and reduces the economic value of potato tubers, but effective chemical control is still lacking. In this study, an attempt was made to control potato common scab by inoculating potatoes with Bacillus velezensis (B. velezensis) and to further investigate the mechanism of biological control. The results showed that B. velezensis Y6 could reduce the disease severity of potato common scab from 49.92 ± 25.74% [inoculated with Streptomyces scabies (S. scabies) only] to 5.56 ± 1.89% (inoculated with S. scabies and Y6 on the same day) and increase the potato yield by 37.32% compared with the control under pot experiment in this study. Moreover, in the field trial, it was found that Y6 could also significantly reduce disease severity from 13.20 ± 1.00% to 4.00 ± 0.70% and increase the potato yield from 2.07 ± 0.10 ton/mu to 2.87 ± 0.28 ton/mu (p < 0.01; Tukey's test). Furthermore, RNA-seq analysis indicated that 256 potato genes were upregulated and 183 potato genes were downregulated in response to B. velezensis Y6 inoculation. In addition, strain Y6 was found to induce the expression of plant growth-related genes in potato, including cell wall organization, biogenesis, brassinosteroid biosynthesis, and plant hormone transduction genes, by 1.01-4.29 times. As well as up-regulate hydroquinone metabolism-related genes and several transcription factors (bHLH, MYB, and NAC) by 1.13-4.21 times. In summary, our study will help to understand the molecular mechanism of biological control of potato common scab and improve potato yield.

The Small Auxin-Up RNA SAUR10 Is Involved in the Promotion of Seedling Growth in Rice

Small auxin-up-regulated RNAs (SAURs) are genes rapidly activated in response to auxin hormones, significantly affecting plant growth and development. However, there is limited information available about the specific functions of SAURs in rice due to the presence of extensive redundant genes. In this study, we found that OsSAUR10 contains a conserved downstream element in its 3' untranslated region that causes its transcripts to be unstable, ultimately leading to the immediate degradation of the mRNA in rice. In our investigation, we discovered that OsSAUR10 is located in the plasma membrane, and its expression is regulated in a tissue-specific, developmental, and hormone-dependent manner. Additionally, we created ossaur10 mutants using the CRISPR/Cas9 method, which resulted in various developmental defects such as dwarfism, narrow internodes, reduced tillers, and lower yield. Moreover, histological observation comparing wild-type and two ossaur10 mutants revealed that OsSAUR10 was responsible for cell elongation. However, overexpression of OsSAUR10 resulted in similar phenotypes to the wild-type. Our research also indicated that OsSAUR10 plays a role in regulating the expression of two groups of genes involved in auxin biosynthesis (OsYUCCAs) and auxin polar transport (OsPINs) in rice. Thus, our findings suggest that OsSAUR10 acts as a positive plant growth regulator by contributing to auxin biosynthesis and polar transport.

NLG1, encoding a mitochondrial membrane protein, controls leaf and grain development in rice

BACKGROUND

Mitochondrion is the key respiratory organ and participate in multiple anabolism and catabolism pathways in eukaryote. However, the underlying mechanism of how mitochondrial membrane proteins regulate leaf and grain development remains to be further elucidated.

RESULTS

Here, a mitochondria-defective mutant narrow leaf and slender grain 1 (nlg1) was identified from an EMS-treated mutant population, which exhibits narrow leaves and slender grains. Moreover, nlg1 also presents abnormal mitochondria structure and was sensitive to the inhibitors of mitochondrial electron transport chain. Map-based cloning and transgenic functional confirmation revealed that NLG1 encodes a mitochondrial import inner membrane translocase containing a subunit Tim21. GUS staining assay and RT-qPCR suggested that NLG1 was mainly expressed in leaves and panicles. The expression level of respiratory function and auxin response related genes were significantly down-regulated in nlg1, which may be responsible for the declination of ATP production and auxin content.

CONCLUSIONS

These results suggested that NLG1 plays an important role in the regulation of leaf and grain size development by maintaining mitochondrial homeostasis. Our finding provides a novel insight into the effects of mitochondria development on leaf and grain morphogenesis in rice.

GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height

Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.

Small Auxin Up RNA 56 (SAUR56) regulates heading date in rice

Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01409-w.

Overexpression of a novel small auxin-up RNA gene, OsSAUR11, enhances rice deep rootedness

BACKGROUND

Deep rooting is an important factor affecting rice drought resistance. However, few genes have been identified to control this trait in rice. Previously, we identified several candidate genes by QTL mapping of the ratio of deep rooting and gene expression analysis in rice.

RESULTS

In the present work, we cloned one of these candidate genes, OsSAUR11, which encodes a small auxin-up RNA (SAUR) protein. Overexpression of OsSAUR11 significantly enhanced the ratio of deep rooting of transgenic rice, but knockout of this gene did not significantly affect deep rooting. The expression of OsSAUR11 in rice root was induced by auxin and drought, and OsSAUR11-GFP was localized both in the plasma membrane and cell nucleus. Through an electrophoretic mobility shift assay and gene expression analysis in transgenic rice, we found that the transcription factor OsbZIP62 can bind to the promoter of OsSAUR11 and promote its expression. A luciferase complementary test showed that OsSAUR11 interacts with the protein phosphatase OsPP36. Additionally, expression of several auxin synthesis and transport genes (e.g., OsYUC5 and OsPIN2) were down-regulated in OsSAUR11-overexpressing rice plants.

CONCLUSIONS

This study revealed a novel gene OsSAUR11 positively regulates deep rooting in rice, which provides an empirical basis for future improvement of rice root architecture and drought resistance.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1^NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

Genome-Wide Identification and Functional Analysis of the Roles of SAUR Gene Family Members in the Promotion of Cucumber Root Expansion

Auxin serves as an essential regulator of the expression of many different genes in plants, thereby regulating growth and development. The specific functional roles of members of the SAUR (small auxin-up RNA) auxin early response gene family in the development of cucumber plants, however, remain to be fully clarified. Here, 62 SAUR family genes were identified, followed by their classification into 7 groups that included several functionally associated cis-regulatory elements. Phylogenetic tree and chromosomal location-based analyses revealed a high degree of homology between two cucumber gene clusters and other plants in the Cucurbitaceae family. These findings, together with the results of an RNA-seq analysis, revealed high levels of CsSAUR31 expression within the root and male flower tissues. Plants overexpressing CsSAUR31 exhibited longer roots and hypocotyls. Together, these results provide a basis for further efforts to explore the roles that SAUR genes play in cucumber plants, while also expanding the pool of available genetic resources to guide research focused on plant growth and development.

Overexpression of maize GOLDEN2 in rice and maize calli improves regeneration by activating chloroplast development

Golden2 (G2), a member of the GARP transcription factor superfamily, regulates several biological processes and phytohormone signaling pathways in plants. In this study, we used a rice codon-optimized maize G2 gene (rZmG2) to improve the regeneration efficiency of rice and maize calli for genetic transformation. We isolated a promoter driving strong and callus-specific expression from rice to drive rZmG2 transcription from a transgene after transformation of two indica and two japonica rice cultivars. The resulting rZmG2 transgenic calli turned green in advance at the differentiation stage, thus significantly raising the regeneration rates of the transgenic indica and japonica rice plants relative to control transformations. Similar effect of this gene on improving maize transformation was also observed. Transcriptome sequencing and RT-qPCR analyses showed that many rice genes related to chloroplast development and phytohormones are upregulated in rZmG2-transgenic calli. These results demonstrate that rZmG2 can promote embryogenic callus differentiation and improve regeneration efficiency by activating chloroplast development and phytohormone pathways. We also established a heat-inducible Cre/loxP-based gene-excision system to remove rZmG2 and the antibiotic selectable gene after obtaining the transgenic plants. This study provides a useful tool for functional genomics work and biotechnology in plants.

Genome-wide identification and expression analysis of the SAUR gene family in foxtail millet (Setaria italica L.)

BACKGROUND

Auxin performs important functions in plant growth and development processes, as well as abiotic stress. Small auxin-up RNA (SAUR) is the largest gene family of auxin-responsive factors. However, the knowledge of the SAUR gene family in foxtail millet is largely obscure.

RESULTS

In the current study, 72 SiSAUR genes were identified and renamed according to their chromosomal distribution in the foxtail millet genome. These SiSAUR genes were unevenly distributed on nine chromosomes and were classified into three groups through phylogenetic tree analysis. Most of the SiSAUR members from the same group showed similar gene structure and motif composition characteristics. Analysis of cis-acting elements showed that many hormone and stress response elements were identified in the promoter region of SiSAURs. Gene replication analysis revealed that many SiSAUR genes were derived from gene duplication events. We also found that the expression of 10 SiSAURs was induced by abiotic stress and exogenous hormones, which indicated that SiSAUR genes may participated in complex physiological processes.

CONCLUSIONS

Overall, these results will be valuable for further studies on the biological role of SAUR genes in foxtail development and response to stress conditions and may shed light on the improvement of the genetic breeding of foxtail millet.

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.

The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet

Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice-foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as Si3g11200 (OsDER1), Si1g27910 (OsMADS6), Si7g27560 (GS5), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as Si3g11200 affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.

Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat

Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.

Map-based cloning and transcriptome analysis of the more-tiller and small-grain mutant in rice

A G to T nucleotide substitution of OsTSG2 led to more tillers and smaller grains in rice by participating in phytohormone signal transduction and starch and sucrose metabolism. Rice is one of the most important food crops worldwide. Grain size and tiller number are the most important factors determining rice yield. The more-tiller and small-grain 2 (tsg2) mutant in rice, developed by ethyl methanesulfonate (EMS) mutagenesis, has smaller grains, more tillers, and a higher yield per plant relative to the wild-type (WT). Based on the genetic analysis, the tsg2 traits were conferred by a single recessive nuclear gene located on the long arm of chromosome 2. After fine-mapping the OsTSG2 locus, a G to T nucleotide substitution was identified, which resulted in an A to S mutation in a highly conserved domain of the growth-regulation factor protein. The single-strand conformation polymorphism (SSCP) marker was developed based on the SNP associated with the phenotypic segregation of traits. The functional complementation of OsTSG2 from the tsg2 mutant to the WT led to an increase in grain size and weight. The differentially expressed genes (DEGs) identified by RNA sequencing were involved in phytohormone signal transduction and starch and sucrose metabolism. Enzyme-linked immunosorbent assay (ELISA) analysis detected variation in the indole acetic acid (IAA) and jasmonic acid (JA) content in the tsg2 inflorescence, while the cellular organization, degree of chalkiness, gel consistency, amylose content, and alkaline spreading value were affected in the tsg2 grains. The findings elucidated the regulatory mechanisms of the tsg2 traits. This mutant could be used in marker-assisted breeding for high-yield and good-quality rice.

Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat

Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.

Euryale Small Auxin Up RNA62 promotes cell elongation and seed size by altering the distribution of indole-3-acetic acid under the light

Euryale (Euryale ferox Salisb.) is an aquatic crop used as both food and drug in Asia, but its utilization is seriously limited due to low yield. Previously, we hypothesized that Euryale small auxin up RNAs (EuSAURs) regulate seed size, but the underlying biological functions and molecular mechanisms remain unclear. Here, we observed that the hybrid Euryale lines (HL) generate larger seeds with higher indole-3-acetic acid (IAA) concentrations than those in the North Gordon Euryale (WT). Histological analysis suggested that a larger ovary in HL is attributed to longer cells around. Overexpression of EuSAUR62 in rice (Oryza sativa L.) resulted in larger glumes and grains and increased the length of glume cells. Immunofluorescence and protein interaction assays revealed that EuSAUR62 modulates IAA accumulation around the rice ovary by interacting with the rice PIN-FORMED 9, an auxin efflux carrier protein. Euryale basic region/leucine zipper 55 (EubZIP55), which was highly expressed in HL, directly binds to the EuSAUR62 promoter and activated the expression of EuSAUR62. Constant light increased the expression of both EubZIP55 and EuSAUR62 with auxin-mediated hook curvature in HL seedlings. Overall, we proposed that EuSAUR62 is a molecular bridge between light and IAA and plays a crucial role in regulating the size of the Euryale seed.

A Long Noncoding RNA Derived from lncRNA-mRNA Networks Modulates Seed Vigor

The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under cold stress have been elusive. In this study, we performed strand-specific whole transcriptome sequencing in germinated rice seeds under cold stress and normal temperature. A total of 6258 putative lncRNAs were identified and expressed in a stage-specific manner compared to mRNA. By investigating the targets of differentially expressed (DE) lncRNAs of LT-I (phase I of low temperature)/NT-I (phase I of normal temperature), it was shown that the auxin-activated signaling pathway was significantly enriched, and twenty-three protein-coding genes with most of the members of the SAUR family located in chromosome 9 were identified as the candidate target genes that may interact with five lncRNAs. A seed vigor-related lncRNA, SVR, which interplays with the members of the SAUR gene family in cis was eventually identified. The CRISPR/Cas 9 engineered mutations in SVR cause delay of germination. The findings provided new insights into the connection between lncRNAs and the auxin-activated signaling pathway in the regulation of rice seed vigor.

Genome-Wide Identification of TaSAUR Gene Family Members in Hexaploid Wheat and Functional Characterization of TaSAUR66-5B in Improving Nitrogen Use Efficiency

Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. Although Small Auxin Up-regulated RNAs (SAURs) participate in diverse biological processes, the function of SAURs in the nitrogen starvation response has not been well-studied. Here, we identified 308 TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of most TaSAURs contain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of the TaSAUR family members, a nitrogen starvation responsive gene, TaSAUR66-5B, can promote the growth of Arabidopsis and wheat roots. In addition, overexpression of TaSAUR66-5B in Arabidopsis up-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpression TaSAUR66-5B may promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression of TaSAUR66-5B in wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of the TaSAUR gene family and lays a foundation for elucidating the functions of TaSAURs in improving nitrogen utilization efficiency in wheat.

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.

Leaf Mutant 7 Encoding Heat Shock Protein OsHSP40 Regulates Leaf Size in Rice

Leaf size is an important agronomic trait directly affecting yield in rice, and thus understanding the genes determining leaf size is important in breeding. In this study, one Leaf Mutant 7 (lm7) with small leaf size was isolated using ethyl methane sulphonate (EMS) mutagenesis from the japonica Zhenggeng 1925. MutMap by whole genome resequencing of phenotypic bulks revealed that LM7 is likely located in the 133 kb region on chromosome 7 using F₂ population from a cross between lm7 and wild-type (WT) Zhenggeng 1925. The candidate gene encoding heat shock protein OsHSP40 for LM7 was functionally validated. Disruption of this gene in Oshsp40 mutants significantly reduced the leaf size compared with that of WT in rice. Microscopic examination showed that OsHSP40 modulated leaf size via regulating the veins formation and cell size/cell number. Nucleotide diversity analysis indicated that a single nucleotide polymorphism (SNP) variation of C to T in the coding region of OsHSP40 may cause small leaves among rice accessions. Therefore, the natural variation of OsHSP40 contributing to leaf size might be useful for rice breeding.

Genetic variations in ZmSAUR15 contribute to the formation of immature embryo-derived embryonic calluses in maize

The ability of immature maize (Zea mays) embryos to form embryonic calluses (ECs) is highly genotype dependent, which limits transgenic breeding development in maize. Here, we report the association map-based cloning of ZmSAUR15 using an association panel (AP) consisting of 309 inbred lines with diverse formation abilities for ECs. We demonstrated that ZmSAUR15, which encodes a small auxin-upregulated RNA, acts as a negative effector in maize EC induction. Polymorphisms in the ZmSAUR15 promoter that influence the expression of ZmSAUR15 transcripts modulate the EC induction capacity in maize. ZmSAUR15 is involved in indole-3-acetic acid biosynthesis and cell division in immature embryo-derived callus. The ability of immature embryos to induce EC formation can be improved by the knockout of ZmSAUR15, which consequently increases the callus regeneration efficiency. Our study provides new insights into overcoming the genotypic limitations associated with EC formation and improving genetic transformation in maize.

Zinc application after low temperature stress promoted rice tillers recovery: Aspects of nutrient absorption and plant hormone regulation

Low temperature during the vegetative stage depresses rice tillering. Zinc (Zn) can promote rice tiller growth and improve plant resistance to abiotic stress. Consequently, Zn application after low temperature might be an effective approach to promote rice tiller recovery. A water culture experiment with treatments of two temperatures (12 °C and 20 °C) and three Zn concentrations (0.08 μM, 0.15 μM and 0.31 μM ZnSO₄·7H₂O) was conducted to determine by analyzing rice tiller growth, nutrient absorption and hormones metabolism. The results showed that low temperature reduced rice tiller numbers and leaf age, decreased as well. Increasing Zn application after low temperature could enhance not only rice tiller growth rate but also N metabolism and tillering recovery, and correlation analysis showed a significantly positive correlation between tiller increment and Zn and N accumulation after low temperature. In addition, higher cytokinin (CTK)/auxin (IAA) ratio was maintained by promoted synthesis of CTK and IAA as well as enhanced IAA transportation from tiller buds to other parts with increased Zn application after cold stress, which resulted in accelerated germination and growth of tiller buds. These results highlighted that Zn application after low temperature promoted rice tiller recovery by increasing N and Zn accumulation and maintaining hormones balance.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

Comparative transcriptome analysis of root types in salt tolerant and sensitive rice varieties in response to salinity stress

Salinity tolerance in rice is a very important trait, especially in areas that are affected by soil salinity, such as tsunami-devastated areas and coastal regions in rice-producing countries. The roots are the key organs that first detect and respond to salinity stress; thus, it is important to have an understanding of how roots contribute to salinity tolerance in agricultural crops. After salinity treatment of the salt tolerant (Mulai) and sensitive (IR29) rice varieties, it appeared that among the three types of roots, the L-type lateral roots (LLR) were the most sensitive to salinity stress in Mulai and the most tolerant in IR29. The nodal roots (NR) and the S-type lateral roots (SLR) were all negatively affected by salinity treatment in both rice varieties. In order to elucidate the molecular mechanism of the difference in stress response among rice root types, the RNA-seq transcriptome profiles of NR, LLR, and SLR were analyzed in Mulai and IR29. Between the two rice varieties, more transporters were found to participate in the regulation of salt tolerance in Mulai roots, such as those involved in ion and sugar transport. In IR29, many of the genes detected were associated with transcription regulation, including stress-inducible genes such as NAC, WRKY and MYB. Among the different root types, gene expression in LLR and SLR were significantly regulated in both rice varieties. Taken together, the genes identified in this study may be utilized in the varietal improvement of rice with very specific root traits that can enhance tolerance to salinity stress.

Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

Meta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

RNA-Sequencing Reveals Differentially Expressed Rice Genes Functionally Associated with Defense against BPH and WBPH in RILs Derived from a Cross between RP2068 and TN1

BACKGROUND

Rice is staple food for over two billion people. Planthoppers like BPH and WBPH occur together in most of rice growing regions across Asia and cause extensive yield loss by feeding and transmission of disease-causing viruses. Chemical control of the pest is expensive and ecologically disastrous; breeding resistant varieties is an acceptable option. But most of such efforts are focused on BPH with an assumption that these varieties will also be effective against WBPH. No critical studies are available to understand rice resistance, common or otherwise, against these two planthoppers.

RESULTS

Our studies aimed to understand the defense mechanisms in rice line RP2068 against BPH and WBPH through RNA sequencing analysis of a RIL line TR3RR derived from the cross TN1 (susceptible) and RP2068 (resistant) after infestation with BPH or WBPH. Results revealed higher number of differentially expressed genes (DEGs) in BPH infested plants than in WBPH infested plants when compared with the uninfested plants. These DEGs could be grouped into UPUP, DNDN, UPDN and DNUP groups based on whether the DEGs were up (UP) or down (DN) regulated against BPH and WBPH, respectively. Gene ontology analysis, specially of members of the last two groups, revealed differences in plant response to the two planthoppers. Abundance of miRNAs and detection of their target genes also indicated that separate sets of genes were suppressed or induced against BPH and WBPH. These results were validated through the analysis of expression of 27 genes through semi-quantitative and quantitative real-time RT-PCR using a set of five RILs that were genetically identical but with different reaction against the two planthoppers. Coupled with data obtained through pathway analysis involving these 27 genes, expression studies revealed common and differential response of rice RP2068 against BPH and WBPH. Trehalose biosynthesis, proline transport, methylation were key pathways commonly upregulated; glucosinolate biosynthesis, response to oxidative stress, proteolysis, cytokinesis pathways were commonly down regulated; photosynthesis, regulation of transcription, expression and transport of peptides and defense related pathways were exclusively upregulated against WBPH; MYB transcription factor mediated defense induction was exclusive to BPH.

CONCLUSION

Rice defense against the two sympatric planthoppers: BPH and WBPH has distinct features in RP2068. Hence, a conscious combination of resistance to these two pests is essential for effective field management.

The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.

Leaf width gene LW5/D1 affects plant architecture and yield in rice by regulating nitrogen utilization efficiency

Leaves are the primary structures responsible for photosynthesis, making leaf morphology one of the most important traits of rice plant architecture. Both plant architecture and nutrient utilization jointly affect rice yield, however, their molecular association is still poorly understood. We identified a rice mutant, leaf width 5 (lw5), that displayed small grains and wide leaves and possesses characteristics typical of a small "sink" and a large "source". Map-based cloning and CRISPR-Cas9 gene editing indicated that LW5 affects both the plant architecture and yield. It is an allele of D1, encoding the rice G protein α subunit. The loss of LW5 functioning leads to an increase in the rate of photosynthesis, vascular bundles, and chlorophyll content. However, the grain-straw ratio and the rate of grain filling decreased significantly. The detection results of ¹⁵N-ammonium nitrate and an expression analysis of genes associated with nitrogen demonstrated that LW5 serves an important role in nitrate uptake and transport. LW5 affects plant architecture and grain size by regulating nitrogen transfer. These results provide a theoretical foundation for further research surrounding the molecular mechanism of "source-sink" balance in rice and suggest novel methods of molecular design for the cultivation of breeding super rice in ideal plant types.

Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

The SAUR41 subfamily of SMALL AUXIN UP RNA genes is abscisic acid inducible to modulate cell expansion and salt tolerance in Arabidopsis thaliana seedlings

BACKGROUND AND AIMS

Most primary auxin response genes are classified into three families: AUX/IAA, GH3 and SAUR genes. Few studies have been conducted on Arabidopsis thaliana SAUR genes, possibly due to genetic redundancy among different subfamily members. Data mining on arabidopsis transcriptional profiles indicates that the SAUR41 subfamily members of SMALL AUXIN UP RNA genes are, strikingly, induced by an inhibitory phytohormone, abscisic acid (ABA). We aimed to reveal the physiological roles of arabidopsis SAUR41 subfamily genes containing SAUR40, SAUR41, SAUR71 and SAUR72.

METHODS

Transcriptional responses of arabidopsis SAUR41 genes to phytohormones were determined by quantitative real-time PCR. Knock out of SAUR41 genes was carried out with the CRISPR/Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9) genome editing technique. The saur41/40/71/72 quadruple mutants, SAUR41 overexpression lines and the wild type were subjected to ultrastructural observation, transcriptome analysis and physiological characterization.

KEY RESULTS

Transcription of arabidopsis SAUR41 subfamily genes is activated by ABA but not by gibberellic acids and brassinosteroids. Quadruple mutations in saur41/40/71/72 led to reduced cell expansion/elongation in cotyledons and hypocotyls, opposite to the overexpression of SAUR41; however, an irregular arrangement of cell size and shape was observed in both cases. The quadruple mutants had increased transcription of calcium homeostasis/signalling genes in seedling shoots, and the SAUR41 overexpression lines had decreased transcription of iron homeostasis genes in roots and increased ABA biosynthesis in shoots. Notably, both the quadruple mutants and the SAUR41 overexpression lines were hypersensitive to salt stress during seedling establishment, whereas specific expression of SAUR41 under the ABA-responsive RD29A (Responsive to Desiccation 29A) promoter in the quadruple mutants rescued the inhibitory effect of salt stress.

CONCLUSIONS

The SAUR41 subfamily genes of arabidopsis are ABA inducible to modulate cell expansion, ion homeostasis and salt tolerance. Our work may provide new candidate genes for improvement of plant abiotic stress tolerance.

SAUR49 Can Positively Regulate Leaf Senescence by Suppressing SSPP in Arabidopsis

The involvement of SMALL AUXIN-UP RNA (SAUR) proteins in leaf senescence has been more and more acknowledged, but the detailed mechanisms remain unclear. In the present study, we performed yeast two-hybrid assays and identified SAUR49 as an interactor of SENESCENCE SUPPRESSED PROTEIN PHOSPHATASE (SSPP), which is a PP2C protein phosphatase that negatively regulates Arabidopsis leaf senescence by suppressing the leucine-rich repeat receptor-like protein kinase SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (SARK), as reported previously by our group. The interaction between SAUR49 and SSPP was further confirmed in planta. Functional characterization revealed that SAUR49 is a positive regulator of leaf senescence. The accumulation level of SAUR49 protein increased during natural leaf senescence in Arabidopsis. The transcript level of SAUR49 was upregulated during SARK-induced premature leaf senescence but downregulated during SSPP-mediated delayed leaf senescence. Overexpression of SAUR49 significantly accelerated both natural and dark-induced leaf senescence in Arabidopsis. More importantly, SAUR49 overexpression completely reversed SSPP-induced delayed leaf senescence. In addition, overexpression of SAUR49 reversed the decreased plasma membrane H+-ATPase activity mediated by SSPP. Taken together, the results showed that SAUR49 functions in accelerating the leaf senescence process via the activation of SARK-mediated leaf senescence signaling by suppressing SSPP. We further identified four other SSPP-interacting SAURs, SAUR30, SAUR39, SAUR41 and SAUR72, that may act redundantly with SAUR49 in regulating leaf senescence. All these observations indicated that certain members of the SAUR family may serve as an important hub that integrates various hormonal and environmental signals with senescence signals in Arabidopsis.

Wheat straw increases the defense response and resistance of watermelon monoculture to Fusarium wilt

BACKGROUND

Wheat straw is a rich resource worldwide. Straw return is an effective strategy to alleviate soil-borne diseases on monoculture watermelon. Previous studies focus on soil structure, physical and chemical properties; however, little is known about the molecular responses on host plant.

RESULTS

No significant difference on the population of Fusarium oxysporum f.sp. niveum race 1(Fon1) in rhizosphere soil was found between control (no addition of wheat straw) and the treated groups (addition of 1% (T1) or 2% (T2) wheat straw). RNA-Seq analysis showed that 3419 differentially expressed genes were clustered into 8 profiles. KEGG analysis revealed that phenylpropanoid biosynthesis and plant hormone signal transduction were involved in wheat straw induced response in monoculture watermelon. Genes in lignin biosynthesis were found to be upregulated, and the lignin and auxin contents were higher in T1 and T2 compared to the control. Lignin was also enriched and the Fon1 population decreased in watermelon roots treated with wheat straw. The enzyme activities of phenylalanine ammonia-lyase and peroxidase were increased.

CONCLUSIONS

Our data suggest that the addition of wheat straw enhances the defense response to Fon1 infection in watermelon through increasing lignin and auxin biosynthesis.

Identification and Expression of SAUR Genes in the CAM Plant Agave

Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave's leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.

Narrow leaf 1 (NAL1) regulates leaf shape by affecting cell expansion in rice (Oryza sativa L.)

The narrow leaf1 (nal1) mutant of rice (Oryza sativa L.) exhibits a narrow leaf phenotype. Previous studies have shown that NAL1 modulates leaf size by affecting vein patterning and cell division; however, the underlying mechanism remains unclear. Here, we report that the nal1 mutant shows reduced size of the leaf abaxial epidermal cells and culm parenchyma cells compared with the wild type (WT), indicating that NAL1 also regulates cell expansion. To understand the molecular mechanism of the reduced cell size phenotype, leaves of 40-day-old nal1 mutant and WT seedlings were subjected to RNA-Seq analysis, which has identified 4277 differentially expressed genes (DEGs) between WT and the nal1 mutant. Gene ontology (GO) enrichment analysis revealed a large number of genes down-regulated in the nal1 mutant were involved in cell wall formation. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that NAL1-regulated DEGs, such as ARFs and SAURs, were mapped in auxin signal transduction and auxin-regulated cell expansion pathways. A combination of RNA-Seq analysis and gene expression validation using RT-qPCR suggested that NAL1 is involved in the regulation of auxin-mediated acid growth in rice. These results indicate that, in addition to controlling cell division, NAL1 controls leaf width, at least partially, through its effect on cell expansion, probably via the acid growth mechanism.

Selenium downregulates auxin and ethylene biosynthesis in rice seedlings to modify primary metabolism and root architecture

Selenium modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings. Selenium (Se) at low concentrations can control root growth through interaction with hormone biosynthesis. Auxin and ethylene have been shown to control the root architecture, with most of the information obtained from the eudicots such Arabidopsis and Nicotiana tabacum. Here, we presented the effects of Se on auxin and ethylene pathways and examined their impact on primary metabolism and root system architecture in rice (Oryza sativa L.) seedlings. Se treatment increased elongation of primary root, but decreased the number and length of lateral roots. Se led to decreased expression of genes associated with the biosynthesis of auxin and ethylene, concomitantly with reduced production of these hormones by the roots. Moreover, Se decreased the abundance of transcripts encoding auxin transport proteins. Indole-3-acetic acid (IAA) treatment overrode the repressive effect of Se on lateral root growth. The ethylene synthesis inhibitor L-α-(2-aminoethoxyvinyl)-glycine (AVG) increased elongation of primary root, whereas the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) resulted in the opposite effect. Soluble sugars accumulate in roots of rice seedlings under Se treatment. Thus, Se modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings.

The RIN-regulated Small Auxin-Up RNA SAUR69 is involved in the unripe-to-ripe phase transition of tomato fruit via enhancement of the sensitivity to ethylene

Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to the initiation of the ripening process remain elusive, although the presumed role of active hormone interplay has often been postulated. To unravel the putative role of auxin in the unripe-to-ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl-SAUR69, previously identified as a RIN target gene, using reverse genetics approaches. Auxin signalling undergoes dramatic decline at the onset of ripening in wild-type fruit, but not in the nonripening rin mutant. Sl-SAUR69 exhibits reduced expression in rin and its up-regulation results in premature initiation of ripening, whereas its down-regulation extends the time to ripening. Overexpression of Sl-SAUR69 reduces proton pump activity and polar auxin transport, and ectopic expression in Arabidopsis alters auxin transporter abundance, further arguing for its active role in the regulation of auxin transport. The data support a model in which Sl-SAUR69 represses auxin transport, thus generating auxin minima, which results in enhanced ethylene sensitivity. This defines a regulation loop, fed by ethylene and auxin as the main hormonal signals and by RIN and Sl-SAUR69 as modulators of the balance between the two hormones.

The SAUR gene family: the plant's toolbox for adaptation of growth and development

The family of small auxin up-regulated RNA (SAUR) genes is a family of auxin-responsive genes with ~60-140 members in most higher plant species. Despite the early discovery of their auxin responsiveness, their function and mode of action remained unknown for a long time. In recent years, the importance of SAUR genes in the regulation of dynamic and adaptive growth, and the molecular mechanisms by which SAUR proteins act are increasingly well understood. SAURs play a central role in auxin-induced acid growth, but can also act independently of auxin, tissue specifically regulated by various other hormone pathways and transcription factors. In this review, we summarize recent advances in the characterization of the SAUR genes in Arabidopsis and other plant species. We particularly elaborate on their capacity to fine-tune growth in response to internal and external signals, and discuss the breakthroughs in understanding the mode of action of SAURs in relation to their complex regulation.

Ectopic expression of a Brassica rapa AINTEGUMENTA gene (BrANT-1) increases organ size and stomatal density in Arabidopsis

The AINTEGUMENTA-like (AIL) family plays a central role in regulating the growth and development of organs in many plants. However, little is known about the characteristics and functions of the AIL family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a genome-wide analysis was performed to identify the members of the AIL family in Chinese cabbage. We identified three ANT genes and six ANT-like genes of Chinese cabbage, most of which were differentially expressed in different organs or tissues. Furthermore, compared with the wild-type line, the size of different organs in the 35S-BrANT-1 line was significantly increased by promoting cell proliferation. Meanwhile, over-expression of BrANT-1 also increases the stomatal number and delays the leaf senescence. Transcriptome analyses revealed that a set of cell proliferation and stoma development genes were up-regulated, while the senescence-associated genes were down-regulated, suggesting these genes may be involved in BrANT-1 regulated processes for controlling organ size, stomatal density and leaf senescence. In summary, this study offers important insights into the characteristics and functions of the ANT genes in Chinese cabbage, and provides a promising strategy to improve yield or head size in Chinese cabbage breeding programs.