OsTPP1 regulates seed germination through the crosstalk with abscisic acid in rice

OsPUKI, a PfkB protein, regulates seed germination in rice by influencing ABA synthesis

Rice seed germination is a crucial phase in rice growth and development, but its molecular mechanism has not been fully elucidated. In this study, we investigated the function of rice pfkB family gene OsPUKI in seed germination. Compared with WT (ZH11), ospuki mutants showed delayed seed germination and shorter shoot length. QRT-PCR results showed that OsPUKI was highly expressed in leaves and developing seeds of 21-day after pollination, and was highly expressed at the early stage of seed germination. GC-MS analysis demonstrated that content of abscisic acid (ABA) in ospuki-3 was higher than that in WT. QRT-PCR analysis revealed that ospuki mutants had higher transcription levels of ABA synthesis-related genes OsNCED2, OsNCED3, OsNCED4, and OsZEP1. Furthermore, it was shown that ospuki mutants were more sensitive to fluridone (Flu) during seed germination and seedling growth than WT according to exogenous Flu treatment experiments. In short, our findings suggest that OsPUKI may positively regulates rice seed germination by influencing ABA synthesis.

Loss of OsSPL8 Function Confers Improved Resistance to Glufosinate and Abiotic Stresses in Rice

Weeds are among the most significant factors contributing to decreases in crop yield and quality. Glufosinate, a nonselective, broad-spectrum herbicide, has been extensively utilized for weed control in recent decades. However, crops are usually sensitive to glufosinate. Therefore, the development of glufosinate-resistant crops is crucial for effective weed management in agriculture. In this study, we characterized a SQUAMOSA promoter-binding-like (SPL) factor, OsSPL8, which acts as a negative regulator of glufosinate resistance by inhibiting the transcription of OsGS1;1 and OsGS2 and consequently reducing GS activity. Furthermore, the loss of OsSPL8 function enhanced tolerance to drought and salt stresses. Transcriptomic comparisons between the gar18-3 mutant and wild type revealed that OsSPL8 largely downregulates stress-responsive genes and upregulates growth-related genes. We demonstrated that OsSPL8 directly regulates OsOMTN6 and OsNAC17, which influence drought tolerance. In addition, OsSPL8 directly represses the expression of salt stress tolerance-related genes such as OsHKT1.1 and OsTPP1. Collectively, our results demonstrate that OsSPL8 is a negative regulator of both glufosinate resistance and abiotic stress tolerance.

OsJMJ718, a histone demethylase gene, positively regulates seed germination in rice

Seed vigor has major impact on the rate and uniformity of seedling growth, crop yield, and quality. However, the epigenetic regulatory mechanism of crop seed vigor remains unclear. In this study, a (jumonji C) JmjC gene of the histone lysine demethylase OsJMJ718 was cloned in rice, and its roles in seed germination and its epigenetic regulation mechanism were investigated. OsJMJ718 was located in the nucleus and was engaged in H3K9 methylation. Histochemical GUS staining analysis revealed OsJMJ718 was highly expressed in seed embryos. Abiotic stress strongly induced the OsJMJ718 transcriptional accumulation level. Germination percentage and seedling vigor index of OsJMJ718 knockout lines (OsJMJ718-CR) were lower than those of the wild type (WT). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of seeds imbibed for 24 h showed an increase in H3K9me3 deposition of thousands of genes in OsJMJ718-CR. ChIP-seq results and transcriptome analysis showed that differentially expressed genes were enriched in ABA and ethylene signal transduction pathways. The content of ABA in OsJMJ718-CR was higher than that in WT seeds. OsJMJ718 overexpression enhanced sensitivity to ABA during germination and early seedling growth. In the seed imbibition stage, ABA and ethylene content diminished and augmented, separately, suggesting that OsJMJ718 may adjust rice seed germination through the ABA and ethylene signal transduction pathways. This study displayed the important function of OsJMJ718 in adjusting rice seed germination and vigor, which will provide an essential reference for practical issues, such as improving rice vigor and promoting direct rice sowing production.

Transcription factor OsMYB30 increases trehalose content to inhibit α-amylase and seed germination at low temperature

Low-temperature germination (LTG) is an important agronomic trait for direct-seeding cultivation of rice (Oryza sativa). Both OsMYB30 and OsTPP1 regulate the cold stress response in rice, but the function of OsMYB30 and OsTPP1 in regulating LTG and the underlying molecular mechanism remains unknown. Employing transcriptomics and functional studies revealed a sugar signaling pathway that regulates seed germination in response to low temperature (LT). Expression of OsMYB30 and OsTPP1 was induced by LT during seed germination, and overexpressing either OsMYB30 or OsTPP1 delayed seed germination and increased sensitivity to LT during seed germination. Transcriptomics and qPCR revealed that expression of OsTPP1 was upregulated in OsMYB30-overexpressing lines but downregulated in OsMYB30-knockout lines. In vitro and in vivo experiments revealed that OsMYB30 bound to the promoter of OsTPP1 and regulated the abundance of OsTPP1 transcripts. Overaccumulation of trehalose (Tre) was found in both OsMYB30- and OsTPP1-overexpressing lines, resulting in inhibition of α-amylase 1a (OsAMY1a) gene during seed germination. Both LT and exogenous Tre treatments suppressed the expression of OsAMY1a, and the osamy1a mutant was not sensitive to exogenous Tre during seed germination. Overall, we concluded that OsMYB30 expression was induced by LT to activate the expression of OsTPP1 and increase Tre content, which thus inhibited α-amylase activity and seed germination. This study identified a phytohormone-independent pathway that integrates environmental cues with internal factors to control seed germination.

GhTPPA_2 enhancement of tobacco sugar accumulation and drought tolerance

Trehalose metabolism plays an important role in plant growth and response to abiotic stress. Trehalose-6-phosphate (Tre6P) can help regulate sugar homeostasis and act as an indication signal for intracellular sugar levels. Crop productivity can be greatly increased by altering the metabolic level of endogenous trehalose in plants, which can optimize the source-sink connection. In this study, the upland cotton GhTPP protein family was first homologously compared and 24 GhTPP genes were found. Transcriptome analysis revealed that GhTPP members had obvious tissue expression specificity. Among them, GhTPPA_2 (Gh_A12G223300.1) was predominantly expressed in leaves and bolls. The results of subcellular localization showed that GhTPPA_2 is localized in the chloroplast. Via PlantCare, we analyzed the promoters and found that the expression of GhTPPA_2 may be induced by light, abiotic stress, and hormones such as abscisic acid, ethylene, salicylic acid and jasmonic acid. In addition, GhTPPA_2 was overexpressed (TPPAoe) in tobacco, and we found that the TPPase activity of TPPAoe tobacco increased by 66 %. Soluble sugar content increased by 39 % and starch content increased by 27 %. Whereas, the transgenic tobacco had obvious growth advantages under 100 mM mannitol stress. Transcriptome sequencing results showed that the differential genes between TPPAoe and control were considerably enriched in functions related to photosynthesis, phosphate group metabolism, and carbohydrate metabolism. This study shows that GhTPPA_2 is involved in regulating sugar metabolism, improving soluble sugar accumulation and drought stress tolerance of tobacco, which provides theoretical basis for research on high yield and drought tolerance of crops.

Genome-wide identification of TPS and TPP genes in cultivated peanut (Arachis hypogaea) and functional characterization of AhTPS9 in response to cold stress

Introduction

Trehalose is vital for plant metabolism, growth, and stress resilience, relying on Trehalose-6-phosphate synthase (TPS) and Trehalose-6-phosphate phosphatase (TPP) genes. Research on these genes in cultivated peanuts (Arachis hypogaea) is limited.

Methods

This study employed bioinformatics to identify and analyze AhTPS and AhTPP genes in cultivated peanuts, with subsequent experimental validation of AhTPS9's role in cold tolerance.

Results

In the cultivated peanut genome, a total of 16 AhTPS and 17 AhTPP genes were identified. AhTPS and AhTPP genes were observed in phylogenetic analysis, closely related to wild diploid peanuts, respectively. The evolutionary patterns of AhTPS and AhTPP genes were predominantly characterized by gene segmental duplication events and robust purifying selection. A variety of hormone-responsive and stress-related cis-elements were unveiled in our analysis of cis-regulatory elements. Distinct expression patterns of AhTPS and AhTPP genes across different peanut tissues, developmental stages, and treatments were revealed, suggesting potential roles in growth, development, and stress responses. Under low-temperature stress, qPCR results showcased upregulation in AhTPS genes (AhTPS2-5, AhTPS9-12, AhTPS14, AhTPS15) and AhTPP genes (AhTPP1, AhTPP6, AhTPP11, AhTPP13). Furthermore, AhTPS9, exhibiting the most significant expression difference under cold stress, was obviously induced by cold stress in cultivated peanut, and AhTPS9-overexpression improved the cold tolerance of Arabidopsis by protect the photosynthetic system of plants, and regulates sugar-related metabolites and genes.

Discussion

This comprehensive study lays the groundwork for understanding the roles of AhTPS and AhTPP gene families in trehalose regulation within cultivated peanuts and provides valuable insights into the mechanisms related to cold stress tolerance.

Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.

Genome-Wide Identification and Expression Analysis of the Trehalose-6-phosphate Synthase and Trehalose-6-phosphate Phosphatase Gene Families in Rose (Rosa hybrida cv 'Carola') under Different Light Conditions

Trehalose, trehalose-6-phosphate synthase (TPS),and trehalose-6-phosphatase (TPP) have been reported to play important roles in plant abiotic stress and growth development. However, their functions in the flowering process of Rosa hybrida have not been characterized. In this study we found that, under a short photoperiod or weak light intensity, the content of trehalose in the shoot apical meristem of Rosa hybrida cv 'Carola' significantly decreased, leading to delayed flowering time. A total of nine RhTPSs and seven RhTPPs genes were identified in the genome. Cis-element analysis suggested that RhTPS and RhTPP genes were involved in plant hormones and environmental stress responses. Transcriptome data analysis reveals significant differences in the expression levels of RhTPSs and RhTPPs family genes in different tissues and indicates that RhTPPF and RhTPPJ are potential key genes involved in rose flower bud development under different light environments. The results of quantitative real-time reverse transcription (qRT-PCR) further indicate that under short photoperiod and weak light intensity all RhTPP members were significantly down-regulated. Additionally, RhTPS1a, RhTPS10, and RhTPS11 were up-regulated under a short photoperiod and showed a negative correlation with flowering time and trehalose content decrease. Under weak light intensity, RhTPS11 was up-regulated and negatively regulated flowering, while RhTPS5, RhTPS6, RhTPS7b, RhTPS9, and RhTPS10 were down-regulated and positively regulated flowering. This work lays the foundation for revealing the functions of RhTPS and RhTPP gene families in the regulation of rose trehalose.

The CCT transcriptional activator Ghd2 constantly delays the heading date by upregulating CO3 in rice

CONSTANS, CO-like, and TOC1 (CCT) family genes play important roles in regulating heading date, which exerts a large impact on the regional and seasonal adaptation of rice. Previous studies have shown that Grain number, plant height, and heading date2 (Ghd2) exhibits a negative response to drought stress by directly upregulating Rubisco activase and exerting a negative effect on heading date. However, the target gene of Ghd2 regulating heading date is still unknown. In this study, CO3 is identified by analyzing Ghd2 ChIP-seq data. Ghd2 activates CO3 expression by binding to the CO3 promoter through its CCT domain. EMSA experiments show that the motif CCACTA in the CO3 promoter was recognized by Ghd2. A comparison of the heading dates among plants with CO3 knocked out or overexpressed and double-mutants with Ghd2 overexpressed and CO3 knocked out shows that CO3 negatively and constantly regulates flowering by repressing the transcription of Ehd1, Hd3a, and RFT1. In addition, the target genes of CO3 are explored via a comprehensive analysis of DAP-seq and RNA-seq data. Taken together, these results suggest that Ghd2 directly binds to the downstream gene CO3, and the Ghd2-CO3 module constantly delays heading date via the Ehd1-mediated pathway.

Coordination of carbon assimilation, allocation, and utilization for systemic improvement of cereal yield

The growth of yield outputs is dwindling after the first green revolution, which cannot meet the demand for the projected population increase by the mid-century, especially with the constant threat from extreme climates. Cereal yield requires carbon (C) assimilation in the source for subsequent allocation and utilization in the sink. However, whether the source or sink limits yield improvement, a crucial question for strategic orientation in future breeding and cultivation, is still under debate. To narrow the knowledge gap and capture the progress, we focus on maize, rice, and wheat by briefly reviewing recent advances in yield improvement by modulation of i) leaf photosynthesis; ii) primary C allocation, phloem loading, and unloading; iii) C utilization and grain storage; and iv) systemic sugar signals (e.g., trehalose 6-phosphate). We highlight strategies for optimizing C allocation and utilization to coordinate the source-sink relationships and promote yields. Finally, based on the understanding of these physiological mechanisms, we envisage a future scenery of "smart crop" consisting of flexible coordination of plant C economy, with the goal of yield improvement and resilience in the field population of cereals crops.

Analysis of Hormone Regulation on Seed Germination of Coix Based on Muli-Omics Analysis

Seed germination is an important stage of growth and reproduction and plays an important role in the life cycle of spermatophyte. It is co-determined by both genetic and environmental factors, and plant hormone regulation may be a highly conservative mechanism. Coix lachryrma-jobi (coix) is a grain with balanced nutrition for medicine and food and has substantial production value. It is an important part of agricultural production, and the efficiency of seed germination after sowing is a key link. In this study, coix species "small white shell Xingren" was used as the experimental material, and changes in gene expression levels and metabolite enrichment in seeds were identified by transcriptome and metabonomic analysis before and after seed germination. A total of 599 metabolites, including those from amino acid metabolism, sugar metabolism, and fatty acid metabolism, were significantly increased in germinating coix. Simultaneously, 10,929 differentially expressed genes (DEGs) were identified, and functional clusters of genes were also significantly clustered in hormone-signaling and glucose and fatty acid metabolism. In addition, this study found that a considerable number of hormone-signaling genes were significantly up-regulated during seed germination, activating multiple metabolic processes. The results of our conjoint analysis of multi omics showed that glucose and fatty acid metabolism played an important role in seed germination under hormone regulation.

Abscisic Acid Enhances Trehalose Content via OsTPP3 to Improve Salt Tolerance in Rice Seedlings

Salt stress is one of the major environmental stresses that imposes constraints to plant growth and production. Abscisic acid (ABA) has been well-proven to function as a central integrator in plant under salt stress, and trehalose (Tre) has emerged as an excellent osmolyte to induce salt tolerance. However, the interacting mechanism between ABA and Tre in rice seedlings under salt stress is still obscure. Here, we found that the application of exogenous Tre significantly promoted the salt tolerance of rice seedlings by enhancing the activities of antioxidant enzymes. In addition, the expression of OsNCED3 was significantly induced by salt stress. The overexpression of the OsNCED3 gene enhanced the salt tolerance, while the knockout of OsNCED3 reduced the salt tolerance of the rice seedlings. Metabolite analysis revealed that the Tre content was increased in the OsNCED3-overexpressing seedlings and reduced in the nced3 mutant. The application of both ABA and Tre improved the salt tolerance of the nced3 mutant when compared with the WT seedling. OsTPP3 was found to be induced by both the ABA and salt treatments. Consistent with the OsNCED3 gene, the overexpression of OsTPP3 enhanced salt tolerance while the knockout of OsTPP3 reduced the salt tolerance of the rice seedlings. In addition, the Tre content was also higher in the OsTPP3-overexpressing seedling and lower in the tpp3 mutant seedling than the WT plant. The application of exogenous Tre also enhanced the salt tolerance of the tpp3 mutant plant. Overall, our results demonstrate that salt-increased ABA activated the expression of OsTPP3, which resulted in elevated Tre content and thus an improvement in the salt tolerance of rice seedlings.

ABF1 Positively Regulates Rice Chilling Tolerance via Inducing Trehalose Biosynthesis

Chilling stress seriously limits grain yield and quality worldwide. However, the genes and the underlying mechanisms that respond to chilling stress remain elusive. This study identified ABF1, a cold-induced transcription factor of the bZIP family. Disruption of ABF1 impaired chilling tolerance with increased ion leakage and reduced proline contents, while ABF1 over-expression lines exhibited the opposite tendency, suggesting that ABF1 positively regulated chilling tolerance in rice. Moreover, SnRK2 protein kinase SAPK10 could phosphorylate ABF1, and strengthen the DNA-binding ability of ABF1 to the G-box cis-element of the promoter of TPS2, a positive regulator of trehalose biosynthesis, consequently elevating the TPS2 transcription and the endogenous trehalose contents. Meanwhile, applying exogenous trehalose enhanced the chilling tolerance of abf1 mutant lines. In summary, this study provides a novel pathway 'SAPK10-ABF1-TPS2' involved in rice chilling tolerance through regulating trehalose homeostasis.

Physiological analysis reveals the mechanism of accelerated growth recovery for rice seedlings by nitrogen application after low temperature stress

Low temperature and overcast rain are harmful to directly seeding early rice, it can hinder rice growth and lower rice biomass during the seedling stage, which in turn lowers rice yield. Farmers usually use N to help rice recuperate after stress and minimize losses. However, the effect of N application on the growth recovery for rice seedlings after such low temperature stress and its associated physiological changes remain unclearly. Two temperature settings and four post-stress N application levels were used in a bucket experiment to compare B116 (strong growth recovery after stress) with B144 (weak growth recovery). The results showed that the stress (average daily temperature at 12°C for 4 days) inhibited the growth of rice seedlings. Compared to the zero N group, the N application group's seedling height, fresh weight and dry weight significantly increased after 12 days. In particular, the increases in all three growth indicators were relatively higher than that of N application at normal temperature, indicating the importance of N application to rice seedlings after low temperature stress. The antioxidant enzyme activity of rice seedlings increased significantly after N application, which reduced the damaging effect of ROS (reactive oxygen species) to rice seedlings. At the same time, the soluble protein content of seedlings showed a slow decrease, while the H₂O₂ and MDA (malondialdehyde) content decreased significantly. Nitrogen could also promote nitrogen uptake and utilization by increasing the expression of genes related to NH 4 + and NO 3 - uptake and transport, as well as improving the activity of NR (nitrate reductase) and GS (glutamine synthetase) in rice. N could affect GA₃ (gibberellin A3) and ABA (abscisic acid) levels by regulating the anabolism of GA₃ and ABA. The N application group maintained high ABA levels as well as low GA₃ levels from day 0 to day 6, and high GA₃ levels as well as low ABA levels from day 6 to day 12. The two rice varieties showed obvious characteristics of accelerated growth recovery and positive physiological changes by nitrogen application after stress, while B116 generally showed more obvious growth recovery and stronger growth-related physiological reaction than that of B144. The N application of 40 kg hm^-2 was more conducive to the rapid recovery of rice growth after stress. The above results indicated that appropriate N application promoted rice seedling growth recovery after low temperature stress mainly by increasing the activities of antioxidant enzymes and nitrogen metabolizing enzymes as well as regulating the levels of GA₃ and ABA. The results of this study will provide a reference for the regulation of N on the recovery of rice seedling growth after low temperature and weak light stress.

Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6

Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.

Rice lipid transfer protein, OsLTPL23, controls seed germination by regulating starch-sugar conversion and ABA homeostasis

Seed germination is vital for ensuring the continuity of life in spermatophyte. High-quality seed germination usually represents good seedling establishment and plant production. Here, we identified OsLTPL23, a putative rice non-specific lipid transport protein, as an important regulator responsible for seed germination. Subcellular localization analysis confirmed that OsLTPL23 is present in the plasma membrane and nucleus. The knockout mutants of OsLTPL23 were generated by CRISPR/Cas9-mediated genome editing, and osltpl23 lines significantly germinated slower and lower than the Nipponbare (NIP). Starch and soluble sugar contents measurement showed that OsLTPL23 may have alpha-amylase inhibitor activity, and high soluble sugar content may be a causal agent for the delayed seed germination of osltpl23 mutants. Transcript profiles in the germinating seeds exhibited that the abscisic acid (ABA)-responsive genes, OsABI3 and OsABI5, and biosynthesis genes, OsNCED1, OsNCED2, OsNCED3 and OsNCED4, are obviously upregulated in the osltpl23 mutants compared to NIP plants, conversely, ABA metabolism genes OsABA8ox1, OsABA8ox2 and OsABA8ox3 are stepwise decreased. Further investigations found that osltpl23 mutants displays weakened early seedling growth, with elevated gene expresssion of ABA catabolism genes and repressive transcription response of defence-related genes OsWRKY45, OsEiN3, OsPR1a, OsPR1b and OsNPR1. Integrated analysis indicated that OsLTPL23 may exert an favorable effect on rice seed germination and early seedling growth via modulating endogenous ABA homeostasis. Collectively, our study provides important insights into the roles of OsLTPL23-mediated carbohydrate conversion and endogenous ABA pathway on seed germination and early seedling growth, which contributes to high-vigor seed production in rice breeding.

The chromatin accessibility landscape of pistils and anthers in rice

Transcription activation is tightly associated with the openness of chromatin and allows direct contact between transcriptional regulators and their targeted DNA for gene expression. However, there are limited studies on the annotation of open chromatin regions (OCRs) in rice (Oryza sativa), especially those in reproductive organs. Here, we characterized OCRs in rice pistils and anthers with an assay for transposase-accessible chromatin using sequencing. Despite a large overlap, we found more OCRs in pistils than in anthers. These OCRs were enriched in gene transcription start sites (TSSs) and showed tight associations with gene expression. Transcription factor (TF) binding motifs were enriched at these OCRs as validated by TF chromatin immunoprecipitation followed by sequencing. Pistil-specific OCRs provided potential regulatory networks by binding directly to the targets, indicating that pistil-specific OCRs may be indicators of cis-regulatory elements in regulating pistil development, which are absent in anthers. We also found that open chromatin of pistils and anthers responded differently to low temperature (LT). These data offer a comprehensive overview of OCRs regulating reproductive organ development and LT responses in rice.

Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice

Due to its low cost and convenience, direct seeding is an efficient technique for the production of rice in different rice growing areas. However, anaerobic conditions are a major obstacle to the direct seeding of rice and result in poor seedling establishment, which leads to yield losses. We constructed a collection of recombinant inbred lines (RIL) comprising 275 lines derived from the H335 and CHA-1 cross by the method of single seed descent. Via a genotyping-by-sequencing (GBS) strategy, a high-density genetic map containing 2498 recombination bin markers was constructed, the average physical distance between the markers was only 149.38 Kb. After anaerobic treatment, 12 phenotypes related to both the coleoptile at germination and seedling quality at budding were evaluated. There were no significant correlations between seedling and bud traits. Genetic mapping of quantitative traits was performed for these traits across two cropping seasons. A total of 20 loci were detected, named locus 1~20. Three of them were repeatedly detected across both seasons. Six loci overlapped with those in previous reports, and nine loci were associated with multiple traits at both stages. Notably, locus 3, which is located on chromosome 2 (26,713,837 to 27,333,897 bp), was detected for both the germination and bud traits. By focusing on the locus 3 interval and by combining gene annotation and expression analyses, we identified a promising candidate gene, trehalose-6-phosphate phosphatase (OsTPP1, LOC_Os02g44230). Furthermore, RILs (G289, G379, G403, G430 and G454) that have superior phenotypes and that pyramid elite alleles were recognized. The findings of present study provide new genetic resources for direct-seeding rice (DSR) varieties for molecular breeding strategies and expand our knowledge of genetic regulation of seedling establishment under anaerobic conditions.

Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Genome-Wide Identification of Cotton (Gossypium spp.) Trehalose-6-Phosphate Phosphatase (TPP) Gene Family Members and the Role of GhTPP22 in the Response to Drought Stress

Trehalose-6-phosphate phosphatase (TPP) is a key enzyme involved in trehalose synthesis in higher plants. Previous studies have shown that TPP family genes increase yields without affecting plant growth under drought conditions, but their functions in cotton have not been reported. In this study, 17, 12, 26 and 24 TPP family genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively. The 79 TPP family genes were divided into three subgroups by phylogenetic analysis. Virus-induced gene silencing (VIGS) of GhTPP22 produced TRV::GhTPP22 plants that were more sensitive to drought stress than the control plants, and the relative expression of GhTPP22 was decreased, as shown by qRT–PCR. Moreover, we analysed the gene structure, targeted small RNAs, and gene expression patterns of TPP family members and the physicochemical properties of their encoded proteins. Overall, members of the TPP gene family in cotton were systematically identified, and the function of GhTPP22 under drought stress conditions was preliminarily verified. These findings provide new information for improving drought resistance for cotton breeding in the future.

Synergistic interaction between ABA and IAA due to moderate soil drying promotes grain filling of inferior spikelets in rice

Poor grain filling of inferior spikelets is becoming a severe problem in some super rice varieties with large panicles. Moderate soil drying (MD) after pollination has been proven to be a practical strategy to promote grain filling. However, the molecular mechanisms underlying this phenomenon remain largely unexplored. Here, transcriptomic analysis of the most active grain filling stage revealed that both starch metabolism and phytohormone signaling were significantly promoted by MD treatment, accompanied by increased enzyme activities of starch synthesis and elevated abscisic acid (ABA) and indole-3-acetic acid (IAA) content in the inferior spikelet. Moreover, the IAA biosynthesis genes OsYUC11 and OsTAR2 were upregulated, while OsIAA29 and OsIAA24, which encode two repressors of auxin signaling, were downregulated by MD, implying a regulation of both IAA biosynthesis and auxin signal transduction in the inferior spikelet by MD. A notable improvement in grain filling of the inferior spikelet was found in the aba8ox2 mutant, which is mutated in an ABA catabolism gene. In contrast, overexpression of OsABA8ox2 significantly reduced grain filling. Interestingly, not only the IAA content, but also the expression of IAA biosynthesis and auxin-responsive genes displayed a similar trend to that in the inferior spikelet under MD. In addition, several OsTPP genes were downregulated in the inferior spikelets of both MD/ABA-treated wild-type plants and the aba8ox2 mutant, resulting in lower trehalose content and higher levels of -6-phosphate (T6P), thereby increasing the expression of OsTAR2, a target of T6P. Taken together, our results suggest that the synergistic interaction of ABA-mediated accumulation of IAA promotes grain filling of inferior spikelets under MD.

Sugars and the speed of life-Metabolic signals that determine plant growth, development and death

Plant growth and development depend on the availability of carbohydrates synthesised in photosynthesis (source activity) and utilisation of these carbohydrates for growth (sink activity). External conditions, such as temperature, nutrient availability and stress, can affect source as well as sink activity. Optimal utilisation of resources is under circadian clock control. This molecular timekeeper ensures that growth responses are adjusted to different photoperiod and temperature settings by modulating starch accumulation and degradation accordingly. For example, during the night, starch degradation is required to provide sugars for growth. Under favourable growth conditions, high sugar availability stimulates growth and development, resulting in an overall accelerated life cycle of annual plants. Key signalling components include trehalose-6-phosphate (Tre6P), which reflects sucrose availability and stimulates growth and branching when the conditions are favourable. Under sink limitation, Tre6P does, however, inhibit night-time starch degradation. Tre6P interacts with Sucrose-non-fermenting1-Related Kinase1 (SnRK1), a protein kinase that inhibits growth under starvation and stress conditions and delays development (including flowering and senescence). Tre6P inhibits SnRK1 activity, but SnRK1 increases the Tre6P to sucrose ratio under favourable conditions. Alongside Tre6P, Target of Rapamycin (TOR) stimulates processes such as protein synthesis and growth when sugar availability is high. In annual plants, an accelerated life cycle results in early leaf and plant senescence, thus shortening the lifespan. While the availability of carbohydrates in the form of sucrose and other sugars also plays an important role in seasonal life cycle events (phenology) of perennial plants, the sugar signalling pathways in perennials are less well understood.

Analysis of gene expression in early seed germination of rice: landscape and genetic regulation

BACKGROUND

Seed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. However, a specific genome-wide analysis of early seed germination in rice is still obscure.

RESULTS

In this study, the physiological characteristics of rice seed during seed germination are determined to define key points of early seed germination. Transcriptome analyses of early phase of seed germination provided deeper insight into the genetic regulation landscape. Many genes involved in starch-to-sucrose transition were differentially expressed, especially alpha-amylase 1b and beta-amylase 2, which were predominantly expressed. Differential exon usage (DEU) genes were identified, which were significantly enriched in the pathway of starch and sucrose metabolism, indicating that DEU events were critical for starch-to-sucrose transition at early seed germination. Transcription factors (TFs) were also dramatic expressed, including the abscisic acid (ABA) responsive gene, OsABI5, and gibberellic acid (GA) responsive genes, GAI. Moreover, GAI transactivated GA responsive gene, GAMYB in vivo, indicating a potential pathway involved in early seed germination process. In addition, CBL-interacting protein kinase (CIPK) genes, such as CIPK13, CIPK14 and CIPK17 were potentially interacted with other proteins, indicating its pivotal role at early seed germination.

CONCLUSION

Taken together, gene regulation of early seed germination in rice was complex and protein-to-gene or protein-to-protein interactions were indispensable.

In Silico and Transcription Analysis of Trehalose-6-phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence

Trehalose-6-phosphate phosphatase (TPP) genes take part in trehalose metabolism and also in stress tolerance, which has been well documented in many species but poorly understood in wheat. The present research has identified a family of 31 TPP genes in Triticum aestivum L. through homology searches and classified them into five clades by phylogenetic tree analysis, providing evidence of an evolutionary status with Hordeum vulgare, Brachypodium distachyon and Oryza sativa. The exon-intron distribution revealed a discrete evolutionary history and projected possible gene duplication occurrences. Furthermore, different computational approaches were used to analyze the physical and chemical properties, conserved domains and motifs, subcellular and chromosomal localization, and three-dimensional (3-D) protein structures. Cis-regulatory elements (CREs) analysis predicted that TaTPP promoters consist of CREs related to plant growth and development, hormones, and stress. Transcriptional analysis revealed that the transcription levels of TaTPPs were variable in different developmental stages and organs. In addition, qRT-PCR analysis showed that different TaTPPs were induced under salt and drought stresses and during leaf senescence. Therefore, the findings of the present study give fundamental genomic information and possible biological functions of the TaTPP gene family in wheat and will provide the path for a better understanding of TaTPPs involvement in wheat developmental processes, stress tolerance, and leaf senescence.