Enhancing microRNA167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa

Systematic characterization of CsbZIP transcription factors in Camelina sativa and functional analysis of CsbZIP-A12 mediating regulation of unsaturated fatty acid-enriched oil biosynthesis

The basic leucine zipper (bZIP) transcription factors (TFs) function importantly in numerous life processes in plants. However, bZIP members and their biological roles remain unknown in Camelina sativa, a worldwide promising oil crop. Here, 220 CsbZIP proteins were identified in camelina and classified into thirteen groups. Two and 347 pairs of tandem and segmental duplication genes were detected to be underwent purification selection, with segmental duplication as the main driven-force of CsbZIP gene family expansion. Most CsbZIP genes displayed a tissue-specific expression pattern. Particularly, CsbZIP-A12 significantly positively correlated with many FA/oil biosynthesis-related genes, indicating CsbZIP-A12 may regulate lipid biosynthesis. Notably, yeast one-hybrid (Y1H), β-Glucuronidase (GUS), dual-luciferase (LUC) and EMSA assays evidenced that CsbZIP-A12 located in nucleus interacted with the promoters of CsSAD2-3 and CsFAD3-3 genes responsible for unsaturated fatty acid (UFA) synthesis, thus activating their transcriptions. Overexpression of CsbZIP-A12 led to an increase of total lipid by 3.275 % compared to the control, followed with oleic and α-linolenic acid levels enhanced by 3.4 % and 5.195 %, and up-regulated the expressions of CsSAD2-3, CsFAD3-3 and CsPDAT2-3 in camelina seeds. Furthermore, heterogeneous expression of CsbZIP-A12 significantly up-regulated the expressions of NtSAD2, NtFAD3 and NtPDAT genes in tobacco plants, thereby improving the levels of total lipids and UFAs in both leaves and seeds without negative effects on other agronomic traits. Together, our findings suggest that CsbZIP-A12 upregulates FA/oil biosynthesis by activating CsSAD2-3 and CsFAD3-3 as well as possible other related genes. These data lay a foundation for further functional analyses of CsbZIPs, providing new insights into the TF-based lipid metabolic engineering to increase vegetable oil yield and health-beneficial quality in oilseeds.

MicroRNA164e suppresses NAC100 transcription factor-mediated synthesis of seed storage proteins in chickpea

Development of protein-enriched chickpea varieties necessitates an understanding of specific genes and key regulatory circuits that govern the synthesis of seed storage proteins (SSPs). Here, we demonstrated the novel involvement of Ca-miR164e-CaNAC100 in regulating SSP synthesis in chickpea. Ca-miRNA164e was significantly decreased during seed maturation, especially in high-protein accessions. The miRNA was found to directly target the transactivation conferring C-terminal region of a nuclear-localized transcription factor, CaNAC100 as revealed using RNA ligase-mediated-rapid amplification of cDNA ends and target mimic assays. The functional role of CaNAC100 was demonstrated through seed-specific overexpression (NACOE) resulting in significantly augmented seed protein content (SPC) consequential to increased SSP transcription. Further, NACOE lines displayed conspicuously enhanced seed weight but reduced numbers and yield. Conversely, a downregulation of CaNAC100 and SSP transcripts was evident in seed-specific overexpression lines of Ca-miR164e that culminated in significantly lowered SPC. CaNAC100 was additionally demonstrated to transactivate the SSP-encoding genes by directly binding to their promoters as demonstrated using electrophoretic mobility shift and dual-luciferase reporter assays. Taken together, our study for the first time established a distinct role of CaNAC100 in positively influencing SSP synthesis and its critical regulation by CamiR164e, thereby serving as an understanding that can be utilized for developing SPC-rich chickpea varieties.

PfbZIP85 Transcription Factor Mediates ω-3 Fatty Acid-Enriched Oil Biosynthesis by Down-Regulating PfLPAT1B Gene Expression in Plant Tissues

The basic leucine zipper (bZIP) transcription factor (TF) family is one of the biggest TF families identified so far in the plant kingdom, functioning in diverse biological processes including plant growth and development, signal transduction, and stress responses. For Perilla frutescens, a novel oilseed crop abundant in polyunsaturated fatty acids (PUFAs) (especially α-linolenic acid, ALA), the identification and biological functions of bZIP members remain limited. In this study, 101 PfbZIPs were identified in the perilla genome and classified into eleven distinct groups (Groups A, B, C, D, E, F, G, H, I, S, and UC) based on their phylogenetic relationships and gene structures. These PfbZIP genes were distributed unevenly across 18 chromosomes, with 83 pairs of them being segmental duplication genes. Moreover, 78 and 148 pairs of orthologous bZIP genes were detected between perilla and Arabidopsis or sesame, respectively. PfbZIP members belonging to the same subgroup exhibited highly conserved gene structures and functional domains, although significant differences were detected between groups. RNA-seq and RT-qPCR analysis revealed differential expressions of 101 PfbZIP genes during perilla seed development, with several PfbZIPs exhibiting significant correlations with the key oil-related genes. Y1H and GUS activity assays evidenced that PfbZIP85 downregulated the expression of the PfLPAT1B gene by physical interaction with the promoter. PfLPAT1B encodes a lysophosphatidate acyltransferase (LPAT), one of the key enzymes for triacylglycerol (TAG) assembly. Heterogeneous expression of PfbZIP85 significantly reduced the levels of TAG and UFAs (mainly C18:1 and C18:2) but enhanced C18:3 accumulation in both seeds and non-seed tissues in the transgenic tobacco lines. Furthermore, these transgenic tobacco plants showed no significantly adverse phenotype for other agronomic traits such as plant growth, thousand seed weight, and seed germination rate. Collectively, these findings offer valuable perspectives for understanding the functions of PfbZIPs in perilla, particularly in lipid metabolism, showing PfbZIP85 as a suitable target in plant genetic improvement for high-value vegetable oil production.

Heat stress during reproductive stages reduces camelina seed productivity and changes seed composition

Camelina (Camelina sativa L. Crantz) is a low-input oilseed crop with great potential in bioenergy and industrial oils. Improving tolerance to high temperatures is essential for camelina agronomic sustainability. Two genotypes, Suneson and Pryzeth, were exposed to a transient 14-day heat stress at 37 °C during the reproductive stages. Four cohorts of pods along the main stem, which were at different stages from fully developed pods (C1), young pods (C2), open flowers (C3) and flowering buds (C4) at the time of heat treatment, were examined for morphological and seed quality traits at maturity. The main stem length was shortened in both genotypes. Pods and seeds in all cohorts were negatively affected by heat, resulting in lower seed yield and reduced oil content. Seed size and seed weight had the greatest reduction in C1, pod size reduction was found the most in C3, and the number of fertile pods that contain at least one seed was reduced in C3 and C4. These results suggest that heat stress effects are developmental stage specific. Heat stress significantly reduced fertility during flowering and inhibited storage product biosynthesis and accumulation during seed filling which resulted in smaller and lighter seeds. Analyzing seed composition indicated that oil content decreased while protein content increased in seeds from heat treated plants. In addition, fatty acid composition was altered with the reduction of omega-3 α-linolenic acid and concomitantly increased omega-6 linoleic acid being the most significantly affected. Our results also revealed the different responses in the two genotypes examined, suggesting genetic variation in camelina germplasm which can be explored to improve heat tolerance. This study provides resources and guidance for future studies to understand genetic and physiological mechanisms of heat stress and to assist in improving the sustainability of camelina production facing climate change.

Integrated analysis of miRNA, transcriptome, and degradome sequencing provides new insights into lipid metabolism in perilla seed

MicroRNAs (miRNA) are small noncoding RNAs that play a crucial as molecular regulators in lipid metabolism in various oil crops. Perilla (Perilla frutescens) is a specific oil crop known for its high alpha-linolenic acid (C18:3n3, ALA) content (>65 %) in their seed oils. In view of the regulatory mechanism of miRNAs in perilla remains unclear, we conducted miRNAs and transcriptome sequencing in two cultivars with distinct lipid compositions. A total of 525 unique miRNAs, including 142 differentially expressed miRNAs was identified in perilla seeds. The 318 miRNAs targeted 7,761 genes. Furthermore, we identified 112 regulated miRNAs and their 610 target genes involved in lipid metabolism. MiR159b and miR167a as the core nodes to regulate the expression of genes in oil biosynthesis (e.g., KAS, FATB, GPAT, FAD, DGK, LPAAT) and key regulatory TFs (e.g., MYB, ARF, DOF, SPL, NAC, TCP, and bHLH). The 1,219 miRNA-mRNA regulation modules were confirmed through degradome sequencing. Notably, pf-miR159b-MYBs and pf-miR167a-ARFs regulation modules were confirmed. They exhibited significantly different expression levels in two cultivars and believed to play important roles in oil biosynthesis in perilla seeds. This provides valuable insights into the functional analysis of miRNA-regulated lipid metabolism in perilla seeds.

Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar

Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-PagGRFs, PagmiR395c-PagGA2ox1/PagLHW/PagSULTR2/PagPolyubiquitin 1, PagmiR482d-PagLAC4, PagmiR167e-PagbHLH62, and PagmiR167f/g/h-PagbHLH110 modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.

Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson

Camelina sativa (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar 'Suneson' with an N50 contig length of 12,031,512 bp and a scaffold N50 length of 32,184,682 bp. Annotation of protein-coding genes revealed 91,877 genes that encode 133,355 gene models. We identified a total of 4,467 genes that were significantly up-regulated under cold stress which were enriched in gene ontology terms associated with "response to cold" and "response to abiotic stress". Coexpression analyses revealed multiple coexpression modules that were enriched in genes differentially expressed following cold stress that had putative functions involved in stress adaptation, specifically within the plastid. With access to a highly contiguous genome assembly, comparative analyses with Arabidopsis thaliana revealed 23,625 A. thaliana genes syntenic with 45,453 Suneson genes. Of these, 24,960 Suneson genes were syntenic to 8,320 A. thaliana genes reflecting a 3 camelina homeolog to 1 Arabidopsis gene relationship and retention of all three homeologs. Some of the retained triplicated homeologs showed conserved gene expression patterns under control and cold-stressed conditions whereas other triplicated homeologs displayed diverged expression patterns revealing sub- and neo-functionalization of the homeologs at the transcription level. Access to the chromosome-scale assembly of Suneson will enable both basic and applied research efforts in the improvement of camelina as a sustainable biofuel feedstock.

Multiomics comparative analysis of the maize large grain mutant tc19 identified pathways related to kernel development

BACKGROUND

The mechanism of grain development in elite maize breeding lines has not been fully elucidated. Grain length, grain width and grain weight are key components of maize grain yield. Previously, using the Chinese elite maize breeding line Chang7-2 and its large grain mutant tc19, we characterized the grain size developmental difference between Chang7-2 and tc19 and performed transcriptomic analysis.

RESULTS

In this paper, using Chang7-2 and tc19, we performed comparative transcriptomic, proteomic and metabolomic analyses at different grain development stages. Through proteomics analyses, we found 2884, 505 and 126 differentially expressed proteins (DEPs) at 14, 21 and 28 days after pollination, respectively. Through metabolomics analysis, we identified 51, 32 and 36 differentially accumulated metabolites (DAMs) at 14, 21 and 28 days after pollination, respectively. Through multiomics comparative analysis, we showed that the phenylpropanoid pathways are influenced at transcriptomic, proteomic and metabolomic levels in all the three grain developmental stages.

CONCLUSION

We identified several genes in phenylpropanoid biosynthesis, which may be related to the large grain phenotype of tc19. In summary, our results provided new insights into maize grain development.

Engineered Cleistogamy in Camelina sativa for bioconfinement

Camelina sativa is a self-pollinating and facultative outcrossing oilseed crop. Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition, modified protein profiles, improved seed and oil yield, and enhanced drought resistance. The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into non-transgenic camelina and wild relatives. Thus, effective bioconfinement strategies need to be developed to prevent pollen-mediated gene flow (PMGF) from transgenic camelina. In the present study, we overexpressed the cleistogamy (i.e. floral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina. Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy, affected pollen germination rates after anthesis but not during anthesis, and caused a minor silicle abortion only on the main branches. We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field, and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions. Thus, the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina, and could be used for bioconfinement in other dicot species.

Identification and Investigation of the Genetic Variations and Candidate Genes Responsible for Seed Weight via GWAS in Paper Mulberry

Seeds directly determine the survival and population size of woody plants, but the genetic basis of seed weight in woody plants remain poorly explored. To identify genetic variations and candidate genes responsible for seed weight in natural woody populations, we investigated the hundred-seed weight of 198 paper mulberry individuals from different areas. Our results showed that the hundred-seed weight of paper mulberry was significantly associated with the bioclimatic variables of sampling sites, which increased from south to north along the latitudinal-temperature gradient. Using 2,414,978 high-quality SNPs from re-sequencing data, the genome-wide association analysis of the hundred-seed weight was performed under three models, which identified 148, 19 and 12 associated genes, respectively. Among them, 25 candidate genes were directly hit by the significant SNPs, including the WRKY transcription factor, fatty acid desaturase, F-box protein, etc. Most importantly, we identified three crucial genetic variations in the coding regions of candidate genes (Bp02g2123, Bp01g3291 and Bp10g1642), and significant differences in the hundred-seed weight were detected among the individuals carrying different genotypes. Further analysis revealed that Bp02g2123 encoding a fatty acid desaturase (FAD) might be a key factor affecting the seed weight and local climate adaptation of woody plants. Furthermore, the genome-wide investigation and expression analysis of FAD genes were performed, and the results suggested that BpFADs widely expressed in various tissues and responded to multiple phytohormone and stress treatments. Overall, our study identifies valuable genetic variations and candidate genes, and provides a better understanding of the genetic basis of seed weight in woody plants.

4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs

Background

The yield and quality of soybean oil are determined by seed oil-related traits, and metabolites/lipids act as bridges between genes and traits. Although there are many studies on the mode of inheritance of metabolites or traits, studies on multi-dimensional genetic network (MDGN) are limited.

Results

In this study, six seed oil-related traits, 59 metabolites, and 107 lipids in 398 recombinant inbred lines, along with their candidate genes and miRNAs, were used to construct an MDGN in soybean. Around 175 quantitative trait loci (QTLs), 36 QTL-by-environment interactions, and 302 metabolic QTL clusters, 70 and 181 candidate genes, including 46 and 70 known homologs, were previously reported to be associated with the traits and metabolites, respectively. Gene regulatory networks were constructed using co-expression, protein–protein interaction, and transcription factor binding site and miRNA target predictions between candidate genes and 26 key miRNAs. Using modern statistical methods, 463 metabolite–lipid, 62 trait–metabolite, and 89 trait–lipid associations were found to be significant. Integrating these associations into the above networks, an MDGN was constructed, and 128 sub-networks were extracted. Among these sub-networks, the gene–trait or gene–metabolite relationships in 38 sub-networks were in agreement with previous studies, e.g., oleic acid (trait)–GmSEI–GmDGAT1a–triacylglycerol (16:0/18:2/18:3), gene and metabolite in each of 64 sub-networks were predicted to be in the same pathway, e.g., oleic acid (trait)–GmPHS–d-glucose, and others were new, e.g., triacylglycerol (16:0/18:1/18:2)–GmbZIP123–GmHD-ZIPIII-10–miR166s–oil content.

Conclusions

This study showed the advantages of MGDN in dissecting the genetic relationships between complex traits and metabolites. Using sub-networks in MGDN, 3D genetic sub-networks including pyruvate/threonine/citric acid revealed genetic relationships between carbohydrates, oil, and protein content, and 4D genetic sub-networks including PLDs revealed the relationships between oil-related traits and phospholipid metabolism likely influenced by the environment. This study will be helpful in soybean quality improvement and molecular biological research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02191-1.

An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism

The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.

MYB1R1 and MYC2 Regulate ω-3 Fatty Acid Desaturase Involved in ABA-Mediated Suberization in the Russet Skin of a Mutant of 'Dangshansuli' (Pyrus bretschneideri Rehd.)

Russeting, a disorder of pear fruit skin, is mainly caused by suberin accumulation on the inner part of the outer epidermal cell layers. ABA was identified as a crucial phytohormone in suberification. Here, we demonstrated that the ABA content in russet pear skin was higher than in green skin. Then, ABA was applied to explore the changes in phenotype and suberin composition coupled with RNA-Seq and metabolomics to investigate the probably regulatory pathway of ABA-mediated suberification. The results showed that ABA treatment increased the expression of ω-3 fatty acid desaturase (FAD) and the content of α-linolenic acid. We identified 17 PbFADs in white pear, and the expression of PbFAD3a was induced by ABA. In addition, the role of PbFAD3a in promoting suberification has been demonstrated by overexpression in Arabidopsis and VIGS assays in the fruitlets. GUS staining indicated that the promoter of PbFAD3a was activated by ABA. Furthermore, MYC2 and MYB1R1 have been shown to bind to the PbFAD3a promoter directly and this was induced by ABA via yeast one-hybrid (Y1H) screening and qRT-PCR. In summary, our study found that ABA induces the expression of MYC2 and MYB1R1 and activates the PbFAD3a promoter, contributing to the formation of russet pear skin. Functional identification of key transcription factors will be the goal of future research. These findings reveal the molecular mechanism of ABA-mediated suberization in the russet skin and provide a good foundation for future studies on the formation of russet skin.

Maize miR167-ARF3/30-polyamine oxidase 1 module-regulated H2O2 production confers resistance to maize chlorotic mottle virus

Maize chlorotic mottle virus (MCMV) is the key pathogen causing maize lethal necrosis (MLN). Due to the sharply increased incidence of MLN in many countries, there is an urgent need to identify resistant lines and uncover the underlying resistance mechanism. Here, we showed that the abundance of maize (Zea mays) microR167 (Zma-miR167) positively modulates the degree of resistance to MCMV. Zma-miR167 directly targets Auxin Response Factor3 (ZmARF3) and ZmARF30, both of which negatively regulate resistance to MCMV. RNA-sequencing coupled with gene expression assays revealed that both ZmARF3 and ZmARF30 directly bind the promoter of Polyamine Oxidase 1 (ZmPAO1) and activate its expression. Knockdown or inhibition of enzymatic activity of ZmPAO1 suppressed MCMV infection. Nevertheless, MCMV-encoded p31 protein directly targets ZmPAO1 and enhances the enzyme activity to counteract Zma-miR167-mediated defense to some degree. We uncovered a role of the Zma-miR167-ZmARF3/30 module for restricting MCMV infection by regulating ZmPAO1 expression, while MCMV employs p31 to counteract this defense.

Identification of miRNA-mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree (Camellia oleifera)

Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal value that is widely planted in southern China. However, there is no report on the identification of the miRNAs involved in lipid metabolism and seed development in the high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the key periods of oil formation and accumulation in the seeds of tea oil camellia and identified miRNA–mRNA regulatory modules involved in lipid metabolism and seed development. Sixteen small RNA libraries for four development stages of seed oil biosynthesis in high- and low-oil cultivars were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families, and 40 novel miRNAs were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 upregulated miRNAs, and 21 downregulated miRNAs. An integrated analysis of the miRNA and mRNA transcriptome sequence data revealed that 10 miRNA–mRNA regulatory modules were related to lipid metabolism; for example, the regulatory modules of ath-miR858b–MYB82/MYB3/MYB44 repressed seed oil biosynthesis, and a regulation module of csi-miR166e-5p–S-ACP-DES6 was involved in the formation and accumulation of oleic acid. A total of 23 miRNA–mRNA regulatory modules were involved in the regulation of the seed size, such as the regulatory module of hpe-miR162a_L-2–ARF19, involved in early seed development. A total of 12 miRNA–mRNA regulatory modules regulating growth and development were identified, such as the regulatory modules of han-miR156a_L+1–SPL4/SBP2, promoting early seed development. The expression changes of six miRNAs and their target genes were validated using quantitative real-time PCR, and the targeting relationship of the cpa-miR393_R-1–AFB2 regulatory module was verified by luciferase assays. These data provide important theoretical values and a scientific basis for the genetic improvement of new cultivars of tea oil camellia in the future.

Genome-Wide Analysis of the Fatty Acid Desaturase Gene Family Reveals the Key Role of PfFAD3 in α-Linolenic Acid Biosynthesis in Perilla Seeds

Perilla (Perilla frutescens), a traditional medicinal and oilseed crop in Asia, contains extremely high levels of polyunsaturated α-linolenic acid (ALA) (up to 60.9%) in its seeds. ALA biosynthesis is a multistep process catalyzed by fatty acid desaturases (FADs), but the FAD gene family in perilla has not been systematically characterized. Here, we identified 42 PfFADs in the perilla genome and classified them into five subfamilies. Subfamily members of PfFADs had similar exon/intron structures, conserved domain sequences, subcellular localizations, and cis-regulatory elements in their promoter regions. PfFADs also possessed various expression patterns. PfFAD3.1 was highly expressed in the middle stage of seed development, whereas PfFAD7/8.3 and PfFAD7/8.5 were highly expressed in leaf and later stages of seed development, respectively. Phylogenetic analysis revealed that the evolutionary features coincided with the functionalization of different subfamilies of PUFA desaturase. Heterologous overexpression of PfFAD3.1 in Arabidopsis thaliana seeds increased ALA content by 17.68%–37.03%. These findings provided insights into the characteristics and functions of PfFAD genes in perilla.

Small RNA profiling for identification of microRNAs involved in regulation of seed development and lipid biosynthesis in yellowhorn

BACKGROUND

Yellowhorn (Xanthoceras sorbifolium), an endemic woody oil-bearing tree, has become economically important and is widely cultivated in northern China for bioactive oil production. However, the regulatory mechanisms of seed development and lipid biosynthesis affecting oil production in yellowhorn are still elusive. MicroRNAs (miRNAs) play crucial roles in diverse aspects of biological and metabolic processes in seeds, especially in seed development and lipid metabolism. It is still unknown how the miRNAs regulate the seed development and lipid biosynthesis in yellowhorn.

RESULTS

Here, based on investigations of differences in the seed growth tendency and embryo oil content between high-oil-content and low-oil-content lines, we constructed small RNA libraries from yellowhorn embryos at four seed development stages of the two lines and then profiled small RNA expression using high-throughput sequencing. A total of 249 known miRNAs from 46 families and 88 novel miRNAs were identified. Furthermore, by pairwise comparisons among the four seed development stages in each line, we found that 64 miRNAs (53 known and 11 novel miRNAs) were differentially expressed in the two lines. Across the two lines, 15, 11, 10, and 7 differentially expressed miRNAs were detected at 40, 54, 68, and 81 days after anthesis, respectively. Bioinformatic analysis was used to predict a total of 2654 target genes for 141 differentially expressed miRNAs (120 known and 21 novel miRNAs). Most of these genes were involved in the fatty acid biosynthetic process, regulation of transcription, nucleus, and response to auxin. Using quantitative real-time PCR and an integrated analysis of miRNA and mRNA expression, miRNA-target regulatory modules that may be involved in yellowhorn seed size, weight, and lipid biosynthesis were identified, such as miR172b-ARF2 (auxin response factor 2), miR7760-p3_1-AGL61 (AGAMOUS-LIKE 61), miR319p_1-FAD2-2 (omega-6 fatty acid desaturase 2-2), miR5647-p3_1-DGAT1 (diacylglycerol acyltransferase 1), and miR7760-p5_1-MED15A (Mediator subunit 15a).

CONCLUSIONS

This study provides new insights into the important regulatory roles of miRNAs in the seed development and lipid biosynthesis in yellowhorn. Our results will be valuable for dissecting the post-transcriptional and transcriptional regulation of seed development and lipid biosynthesis, as well as improving yellowhorn in northern China.

Bm-miR172c-5p Regulates Lignin Biosynthesis and Secondary Xylem Thickness by Altering the Ferulate 5 Hydroxylase Gene in Bacopa monnieri

MicroRNAs (miRNAs) are small non-coding, endogenous RNAs containing 20-24 nucleotides that regulate the expression of target genes involved in various plant processes. A total of 1,429 conserved miRNAs belonging to 95 conserved miRNA families and 12 novel miRNAs were identified from Bacopa monnieri using small RNA sequencing. The Bm-miRNA target transcripts related to the secondary metabolism were further selected for validation. The Bm-miRNA expression in shoot and root tissues was negatively correlated with their target transcripts. The Bm-miRNA cleavage sites were mapped within the coding or untranslated region as depicted by the modified RLM-RACE. In the present study, we validate three miRNA targets, including asparagine synthetase, cycloartenol synthase and ferulate 5 hydroxylase (F5H) and elucidate the regulatory role of Bm-miR172c-5p, which cleaves the F5H gene involved in the lignin biosynthesis. Overexpression (OE) of Bm-miR172c-5p precursor in B. monnieri suppresses F5H gene, leading to reduced lignification and secondary xylem thickness under control and drought stress. By contrast, OE of endogenous target mimics (eTMs) showed enhanced lignification and secondary xylem thickness leading to better physiological response under drought stress. Taken together, we suggest that Bm-miRNA172c-5p might be a key player in maintaining the native phenotype of B. monnieri under control and different environmental conditions.

Genome-wide association study for candidate genes controlling seed yield and its components in rapeseed (Brassica napus subsp. napus)

Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01060-9.

Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis

Sphingolipids are essential membrane components and signal molecules, but their regulatory role in cotton embryo growth is largely unclear. In this study, we evaluated the effects of treatment with the sphingolipid synthesis inhibitor fumonisin B1 (FB1), the serine palmityl transferase (SPT) inhibitor myriocin, the SPT sphingolipid product DHS (d18:0 dihydrosphingosine), and the post-hydroxylation DHS product PHS (t18:0 phytosphingosine) on embryo growth in culture, and performed comparative transcriptomic analysis on control and PHS-treated samples. We found that FB1 could inhibit cotton embryo development. At the five-day ovule/embryo developmental stage, PHS was the most abundant sphingolipid. An SPT enzyme inhibitor reduced the fresh weight of embryos, while PHS had the opposite effect. The transcriptomic analysis identified 2769 differentially expressed genes (1983 upregulated and 786 downregulated) in the PHS samples. A large number of transcription factors were highly upregulated, such as zinc finger, MYB, NAC, bHLH, WRKY, MADS, and GRF in PHS-treated samples compared to controls. The lipid metabolism and plant hormone (auxin, brassinosteroid, and zeatin) related genes were also altered. Our findings provide target metabolites and genes for cotton seed improvement.

Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

BACKGROUND

Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored.

RESULTS

In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5' cDNA ends (5'-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development.

CONCLUSIONS

Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey!

Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.

Increased expression of fatty acid and ABC transporters enhances seed oil production in camelina

BACKGROUND

Lipid transporters play an essential role in lipid delivery and distribution, but their influence on seed oil production in oilseed crops is not well studied.

RESULTS

Here, we examined the effect of two lipid transporters, FAX1 (fatty acid export1) and ABCA9 (ATP-binding cassette transporter subfamily A9) on oil production and lipid metabolism in the oilseed plant Camelina sativa. Overexpression (OE) of FAX1 and ABCA9 increased seed weight and size, with FAX1-OEs and ABCA9-OEs increasing seed length and width, respectively, whereas FAX1/ABCA9-OEs increasing both. FAX1-OE and ABCA9-OE displayed additive effects on seed oil content and seed yield. Also, OE of FAX1 and ABCA9 affected membrane lipid composition in developing pods, especially on phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The expression of some genes involved in seed oil synthesis, such as DGAT2, PDAT1, and LEC1, was increased in developing seeds of FAX1- and/or ABCA9-OEs.

CONCLUSION

These results indicate that increased expression of FAX1 and ABCA9 can potentially be applied to improving camelina oil production.

Differential expression of SlKLUH controlling fruit and seed weight is associated with changes in lipid metabolism and photosynthesis-related genes

The sizes of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the locus fw3.2, an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affect organ size is poorly understood. We found that higher expression of SlKLUH increased cell proliferation in the pericarp within 5 d post-anthesis in tomato near-isogenic lines. Differential gene expression analyses showed that lower expression of SlKLUH was associated with increased expression of genes involved in lipid metabolism. Lipidomic analysis revealed that repression of SlKLUH mainly increased the contents of certain non-phosphorus glycerolipids and phospholipids and decreased the contents of four unknown lipids. Co-expression network analyses revealed that lipid metabolism was possibly associated with but not directly controlled by SlKLUH, and that this gene instead controls photosynthesis-related processes. In addition, many transcription factors putatively involved in the KLUH pathway were identified. Collectively, we show that SlKLUH regulates fruit and seed weight which is associated with altered lipid metabolism. The results expand our understanding of fruit and seed weight regulation and offer a valuable resource for functional studies of candidate genes putatively involved in regulation of organ size in tomato and other crops.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

Background

WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.

Results

A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.

Conclusions

The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07189-3.

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

Rice tiller angle determines plant growth density and further contributes grain production. Although a few genes have been characterized to regulate tiller angle in rice, the molecular mechanism underlying the control of tiller angle via microRNA is poorly understood. Here, we report that rice tiller angle is controlled by OsmiR167a-targeted auxin response factors OsARF12, OsARF17 and OsARF25. In the overexpression of OsMIR167a plants, the expression of OsARF12, OsARF17 and OsARF25 was severely repressed and displayed larger tiller angle as well as the osarf12/osarf17 and osarf12/ osarf25 plants. In addition, those plants showed compromised abnormal auxin distribution and less sensitive to gravity. We also demonstrate that OsARF12, OsARF17 and OsARF25 function redundantly and might be involved in HSFA2D and LAZY1-dependent asymmetric auxin distribution pathway to control rice tiller angle. Our results reveal that OsmiR167a represses its targets, OsARF12, OsARF17 and OsARF25, to control rice tiller angle by fine-tuning auxin asymmetric distribution in shoots.

Into the Seed: Auxin Controls Seed Development and Grain Yield

Seed development, which involves mainly the embryo, endosperm and integuments, is regulated by different signaling pathways, leading to various changes in seed size or seed weight. Therefore, uncovering the genetic and molecular mechanisms of seed development has great potential for improving crop yields. The phytohormone auxin is a key regulator required for modulating different cellular processes involved in seed development. Here, we provide a comprehensive review of the role of auxin biosynthesis, transport, signaling, conjugation, and catabolism during seed development. More importantly, we not only summarize the research progress on the genetic and molecular regulation of seed development mediated by auxin but also discuss the potential of manipulating auxin metabolism and its signaling pathway for improving crop seed weight.

Mapping quantitative trait loci for seed traits in Camelina sativa

Genetic dissection of oil content and seed size in Camelina sativa was conducted by QTL mapping using a SNP-based linkage map and a recombinant inbred population. Camelina (Camelina sativa L. Crantz) is an oilseed crop that has great potential to provide sustainable feedstock for biofuel production and to improve dryland agriculture. A major breeding objective for camelina is to increase seed size and oil content. Understanding the genetics behind variations of seed size and associated traits such as oil content would help breeders develop varieties of increased oil yield that are more robust, easier to plant and harvest, and better for oil processing. In this study, we developed a recombinant inbred population derived from the two camelina accessions, Suneson and Pryzeth, with contrasting traits, especially seed size and oil content. Using 189 lines, a genetic map was constructed containing 2376 single nucleotide polymorphism markers spanning 2034.6 cM of 20 linkage groups with an average density of 1.5 cM per locus. Field trials were conducted for 2 years (2017 and 2018) in two environments (dryland and irrigated) in Bozeman, Montana. The results revealed important correlations of seed size with other associated traits such as oil content, pod size and seed number per pod. Significant QTLs were also discovered for these traits. The results of this study are the first step to isolate genes controlling seed development and oil accumulation and to develop advanced varieties of camelina better adapted to modern agriculture by marker-assisted breeding.