GmCCD4 controls carotenoid content in soybeans

LRM3 positively regulates stem lodging resistance by degradating MYB6 transcriptional repressor in soybean

Stem lodging resistance plays a critical role in maintaining soybean yield stability, yet the molecular mechanisms governing stem development and lodging tolerance remain poorly understood. Here, we report the characterization of lodging-related mutant 3 (lrm3), a weak-stemmed soybean line exhibiting increased lodging susceptibility. Molecular cloning revealed that LRM3 encodes a U-box E3 ubiquitin ligase that physically interacts with the transcription factor MYB6, targeting it for 26S proteasome-mediated degradation. Transcriptomic and chromatin immunoprecipitation analyses demonstrated that MYB6 binds directly to the promoter regions of PHENYLALANINE AMMONIA-LYASE (PAL) genes, repressing their transcriptional activity and consequently reducing lignin biosynthesis and secondary cell wall deposition in stems. Population genetic analysis identified three major LRM3 haplotypes, with Haplotype 1 preferentially retained in landraces and modern cultivars, suggesting artificial selection during domestication. Collectively, our findings elucidate a previously uncharacterized regulatory mechanism integrating ubiquitin-mediated proteolysis and phenylpropanoid metabolism to enhance stem mechanical strength. This study provides novel genetic insights and molecular tools for improving lodging resistance in soybean breeding programs.

Natural allelic variation of basic helix-loop-helix transcription factor 25 regulates carotenoid biosynthesis in sweet potato

Carotenoid-rich orange-fleshed sweet potato (OFSP) is an important staple diet and source of nutrition in developing countries, including Africa and Asia. However, the regulation of carotenoid biosynthesis remains to be better understood. A natural allelic variation closely linked to carotenoid biosynthesis was identified in the promoter region of the IbbHLH25 gene that encodes a basic helix-loop-helix (bHLH) transcription factor, by transcriptome and haplotype analyses of different flesh colour sweet potato accessions. An 86-bp deletion reduced the transcription of the IbbHLH25 promoter in white- and yellow-fleshed sweet potatoes; however, the deletion was absent in OFSP. IbbHLH25 was highly expressed in the storage roots of carotenoid-rich sweet potato. The overexpression of IbbHLH25 significantly increased the carotenoid contents (by 2.5-fold-6.0-fold) and proportions, especially β-carotene and β-cryptoxanthin; their contents increased by 21.2-fold-55.7-fold and 4.6-fold-9.5-fold, respectively, and their proportions increased by 48.5% and 13.0%, respectively, and the silencing of IbbHLH25 had opposite effects. IbbHLH25 formed heterodimers with IbbHLH66 to directly and synergistically activate the transcription of carotenoid biosynthesis key genes IbGGPPS, IbLCYB and IbBCH. The overexpression of IbbHLH66 significantly increased the carotenoid contents (by 2.3-fold-3.8-fold) and proportions, especially β-carotene and β-cryptoxanthin; their contents increased by 15.2-fold-25.6-fold and 3.1-fold-5.1-fold, respectively, and their proportions increased by 31.1% and 9.6%, respectively. These findings expand our understanding of bHLHs in regulating carotenoid biosynthesis and suggest additional roles in affecting carotenoid component proportions, providing candidate genes for nutritional biofortification of agricultural products.

Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Glycine max L.)

Seed size is an economically important trait that directly determines the seed yield in soybean. In the current investigation, we used an integrated strategy of linkage mapping, association mapping, haplotype analysis and candidate gene analysis to determine the genetic makeup of four seed size-related traits viz., 100-seed weight (HSW), seed area (SA), seed length (SL), and seed width (SW) in soybean. Linkage mapping identified a total of 23 quantitative trait loci (QTL) associated with four seed size-related traits in the F2 population; among them, 17 were detected as novel QTLs, whereas the remaining six viz., qHSW3-1, qHSW4-1, qHSW18-1, qHSW19-1, qSL4-1 and qSW6-1 have been previously identified. Six out of 23 QTLs were major possessing phenotypic variation explained (PVE) ≥ 10%. Besides, the four QTL Clusters/QTL Hotspots harboring multiple QTLs for different seed size-related traits were identified on Chr.04, Chr.16, Chr.19 and Chr.20. Genome-wide association study (GWAS) identified a total of 62 SNPs significantly associated with the four seed size-related traits. Interestingly, the QTL viz., qHSW18-1 was identified by both linkage mapping and GWAS, and was regarded as the most stable loci regulating HSW in soybean. In-silico, sequencing and qRT-PCR analysis identified the Glyma.18G242400 as the most potential candidate gene underlying the qHSW18-1 for regulating HSW. Moreover, three haplotype blocks viz., Hap2, Hap6A and Hap6B were identified for the SW trait, and one haplotype was identified within the Glyma.18G242400 for the HSW. These four haplotypes harbor three to seven haplotype alleles across the association mapping panel of 350 soybean accessions, regulating the seed size from lowest to highest through intermediate phenotypes. Hence, the outcome of the current investigation can be utilized as a potential genetic and genomic resource for breeding the improved seed size in soybean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01525-1.

Exogenous CaCl2 reduces the oxidative cleavage of carotenoids in shredded carrots by targeting CAMTA4-mediated transcriptional repression of carotenoid degradation pathway

Carotenoid oxidative cleavage is a significant factor contributing to the color changes of shredded carrots and treatment with calcium chloride (CaCl2, 1% w/v) has been observed to alleviate the whitening symptom and color loss. However, the specific mechanism by which CaCl2 treatment suppresses carotenoid degradation remains unclear. In this study, the effect of CaCl2 and EGTA (calcium ion chelating agent) treatment on carotenoid biosynthesis and degradation in shredded carrots and the mechanism involved was investigated. CaCl2 treatment promoted the expression and activity of carotenoid biosynthetic enzyme (phytoene synthase, PSY), but inhibited the increases of the degradative enzyme activity of carotenoid cleavage dioxygenase (CCD) and down-regulated the corresponding transcripts, thus delayed the degradation of total carotenoid and maintaining higher levels of major carotenoid compounds including β-carotene, α-carotene, lycopene, and lutein in shredded carrots during storage. However, EGTA treatment promoted the gene expression and enzyme activity of CCD and increased the degradation of carotenoid compounds in shredded carrots during storage. Furthermore, the CaCl2 treatment induced DcCAMTA4, identified as a calcium decoder in shredded carrots, which, in turn, suppressed the expressions of DcCCD1 and DcCCD4 by interacting with their promoters. The transient overexpression of DcCAMTA4 in tobacco leaves led to reduced expression of NtCCD1 and NtCCD4, maintaining a higher content of carotenoids. Thus, CaCl2 alleviated the oxidative cleavage of carotenoids in shredded carrots through the DcCAMTA4-mediated carotenoid degradation pathway.

Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean

Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

Genome-wide association studies reveal novel QTLs for agronomic traits in soybean

Introduction

Soybean, as a globally significant crop, has garnered substantial attention due to its agricultural importance. The utilization of molecular approaches to enhance grain yield in soybean has gained popularity.

Methods

In this study, we conducted a genome-wide association study (GWAS) using 156 Chinese soybean accessions over a two-year period. We employed the general linear model (GLM) and the mixed linear model (MLM) to analyze three agronomic traits: pod number, grain number, and grain weight.

Results

Our findings revealed significant associations between qgPNpP-98, qgGNpP-89 and qgHGW-85 QTLs and pod number, grain number, and grain weight, respectively. These QTLs were identified on chromosome 16, a region spanning 413171bp exhibited associations with all three traits.

Discussion

These QTL markers identified in this study hold potential for improving yield and agronomic traits through marker-assisted selection and genomic selection in breeding programs.

ERF5.1 modulates carotenoid accumulation by interacting with CCD4.1 in Lycium

Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (CCD4) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in Lycium have not been discovered. Here, we annotated LbCCDs from the Lycium reference genome and found that LbCCD4.1 expression was significantly correlated with the carotenoid metabolites during Lycium five fruit developmental stages. Over-expression of LbCCD4.1 in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, LbERF5.1, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing ERF5.1 transgenic NQ's leaves. Over-expression or virus-induced gene silencing of LbERF5.1 in NQ's leaves induced a consistent up- or down-expression, respectively, of LbCCD4.1. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that ERF5.1 interacted with the promoter of CCD4.1 to increase its expression, and LbERF5.1 could bind to any one of the three predicted binding sites in the promoter of LbCCD4.1. A transcriptome analysis of LbERF5.1 and LbCCD4.1 over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between ERF5.1 and CCD4.1, which may be used to enhance carotenoid in Lycium.

Integrative Analysis of Metabolome and Transcriptome Revealed Lutein Metabolism Contributed to Yellow Flower Formation in Prunus mume

Prunus mume is a famous ornamental woody tree with colorful flowers. P. mume with yellow flowers is one of the most precious varieties. Regretfully, metabolites and regulatory mechanisms of yellow flowers in P. mume are still unclear. This hinders innovation of flower color breeding in P. mume. To elucidate the metabolic components and molecular mechanisms of yellow flowers, we analyzed transcriptome and metabolome between 'HJH' with yellow flowers and 'ZLE' with white flowers. Comparing the metabolome of the two varieties, we determined that carotenoids made contributions to the yellow flowers rather than flavonoids. Lutein was the key differential metabolite to cause yellow coloration of 'HJH'. Transcriptome analysis revealed significant differences in the expression of carotenoid cleavage dioxygenase (CCD) between the two varieties. Specifically, the expression level of PmCCD4 was higher in 'ZLE' than that in 'HJH'. Moreover, we identified six major transcription factors that probably regulated PmCCD4 to affect lutein accumulation. We speculated that carotenoid cleavage genes might be closely related to the yellow flower phenotype in P. mume. Further, the coding sequence of PmCCD4 has been cloned from the 'HJH' petals, and bioinformatics analysis revealed that PmCCD4 possessed conserved histidine residues, ensuring its enzymatic activity. PmCCD4 was closely related to PpCCD4, with a homology of 98.16%. Instantaneous transformation analysis in petal protoplasts of P. mume revealed PmCCD4 localization in the plastid. The overexpression of PmCCD4 significantly reduced the carotenoid content in tobacco plants, especially the lutein content, indicating that lutein might be the primary substrate for PmCCD4. We speculated that PmCCD4 might be involved in the cleavage of lutein in plastids, thereby affecting the formation of yellow flowers in P. mume. This work could establish a material and molecular basis of molecular breeding in P. mume for improving the flower color.

Comparison of Bioactive Compounds and Antioxidant Activities in Differentially Pigmented Cerasus humilis Fruits

Chinese dwarf cherry (Cerasus humilis) is a wild fruit tree and medicinal plant endemic to China. Its fruits are rich in various bioactive compounds, such as flavonoids and carotenoids, which contribute greatly to their high antioxidant capacity. In this study, the contents of bioactive substances (chlorophyll, carotenoids, ascorbic acid, anthocyanin, total flavonoids, and total phenols), antioxidant capacities, 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonicacid) (ABTS+) scavenging ability, and ferric-reducing antioxidant power (FRAP)) in differentially pigmented C. humilis fruits of four varieties were determined and compared. The results revealed that anthocyanin, total flavonoids and total phenols were the three main components responsible for the antioxidant activity of C. humilis fruits. 'Jinou No.1' fruits with dark red peel and red flesh had the highest contents of anthocyanin, total flavonoids, and total phenols, as well as the highest antioxidant capacities; 'Nongda No.5' fruits with yellow-green peel and yellow flesh had the highest contents of carotenoids and chlorophyll, while 'Nongda No.6' fruit had the highest ascorbic acid content. To further reveal the molecular mechanism underlying differences in the accumulation of carotenoids and flavonoids among differentially pigmented C. humilis fruits, the expression patterns of structural genes involved in the biosynthesis of the two compounds were investigated. Correlation analysis results revealed that the content of carotenoids in C. humilis fruits was very significantly positively correlated with the expression of the ChCHYB, ChZEP, ChVDE, ChNSY, ChCCD1, ChCCD4, ChNCED1, and ChNCED5 genes (p < 0.01) and significantly negatively correlated with the expression of ChZDS (p < 0.05). The anthocyanin content was very significantly positively correlated with ChCHS, ChFLS, and ChUFGT expression (p < 0.01). The total flavonoid content was very significantly positively correlated with the expression of ChCHS, ChUFGT, and ChC4H (p < 0.01) and significantly positively correlated with ChFLS expression (p < 0.05). This study can provide a basis for understanding the differences in the accumulation of bioactive substances, and is helpful for clarifying the mechanisms underlying the accumulation of various carotenoids and flavonoids among differentially pigmented C. humilis fruits.

The elite variations in germplasms for soybean breeding

The genetic base of soybean cultivars (Glycine max (L.) Merr.) has been narrowed through selective domestication and specific breeding improvement, similar to other crops. This presents challenges in breeding new cultivars with improved yield and quality, reduced adaptability to climate change, and increased susceptibility to diseases. On the other hand, the vast collection of soybean germplasms offers a potential source of genetic variations to address those challenges, but it has yet to be fully leveraged. In recent decades, rapidly improved high-throughput genotyping technologies have accelerated the harness of elite variations in soybean germplasm and provided the important information for solving the problem of a narrowed genetic base in breeding. In this review, we will overview the situation of maintenance and utilization of soybean germplasms, various solutions provided for different needs in terms of the number of molecular markers, and the omics-based high-throughput strategies that have been used or can be used to identify elite alleles. We will also provide an overall genetic information generated from soybean germplasms in yield, quality traits, and pest resistance for molecular breeding.

Yellow Petal locus GaYP promotes flavonol biosynthesis and yellow coloration in petals of Asiatic cotton (Gossypium arboreum)

Yellow Petal locus GaYP is located on chromosome 11 and encodes a Sg6 R2R3-MYB transcription factor, which promotes flavonol biosynthesis and yellow coloration in Asiatic cotton petals. Petal color is pivotal to ornamental value and reproduction of plants. Yellow coloration in plant petals is mainly attributed to colorants including carotenoids, aurones and some flavonols. To date, the genetic regulatory mechanism of flavonol biosynthesis in petals is still to be elucidated. Here, we employed Asiatic cottons with or without deep yellow coloration in petals to address this question. Multi-omic and biochemical analysis revealed significantly up-regulated transcription of flavonol structural genes and increased levels of flavonols, especially gossypetin and 6-hydroxykaempferol, in yellow petals of Asiatic cotton. Furthermore, the Yellow Petal gene (GaYP) was mapped on chromosome 11 by using a recombinant inbred line population. It was found that GaYP encoded a transcriptional factor belonging to Sg6 R2R3-MYB proteins. GaYP could bind to the promoter of flavonol synthase gene (GaFLS) and activate the transcription of downstream genes. Knocking out of GaYP or GaFLS homologs in upland cotton largely eliminated flavonol accumulation and pale yellow coloration in petals. Our results indicated that flavonol synthesis, up-regulated by the R2R3-MYB transcription activator GaYP, was the causative factor for yellow coloration of Asiatic cotton petals. In addition, knocking out of GaYP homologs also led to decrease in anthocyanin accumulation and petal size in upland cotton, suggesting that GaYP and its homologs might modulate developmental or physiological processes beyond flavonol biosynthesis.

Flower color mutation, pink to orange, through CmGATA4 - CCD4a-5 module regulates carotenoids degradation in chrysanthemum

The carotenoids biosynthesis pathway in plants has been studied extensively, yet little is known about the regulatory mechanisms underlying this process, especially for ornamental horticulture plants. In this study, a natural variation of chrysanthemum with orange coloration was identified and compared with the wild type with pink coloration; the content and component of carotenoids were largely enriched in the mutant with orange coloration. CmCCD4a-5, the DNA sequence in both 'Pink yan' and the mutant, was identified and shown to function as a carotenoid degradation enzyme. Compared with 'Pink yan', the mutant shows lower expression level of CmCCD4a-5. Furthermore, CmGATA4 was found to have an opposite expression trend to CmCCD4a-5, and it could directly bind with the CmCCD4a-5 promoter. Taken together, this study demonstrates that CmGATA4 acts as a negative regulator of CmCCD4a-5 and, furthermore, low expression of CmCCD4a-5 resulted in carotenoid accumulation in the mutant.

Genome-wide identification and expression analysis of carotenoid cleavage oxygenase genes in Litchi (Litchi chinensis Sonn.)

BACKGROUND

Carotenoid cleavage oxygenases (CCOs) include the carotenoid cleavage dioxygenase (CCD) and 9-cis-epoxycarotenoid (NCED), which can catalize carotenoid to form various apocarotenoids and their derivatives, has been found that play important role in the plant world. But little information of CCO gene family has been reported in litchi (Litchi chinensis Sonn.) till date.

RESULTS

In this study, a total of 15 LcCCO genes in litchi were identified based on genome wide lever. Phylogeny analysis showed that LcCCO genes could be classified into six subfamilies (CCD1, CCD4, CCD7, CCD8, CCD-like, and NCED), which gene structure, domain and motifs exhibited similar distribution patterns in the same subfamilies. MiRNA target site prediction found that there were 32 miRNA target sites in 13 (86.7%) LcCCO genes. Cis-elements analysis showed that the largest groups of elements were light response related, following was plant hormones, stress and plant development related. Expression pattern analysis revealed that LcCCD4, LcNCED1, and LcNCED2 might be involving with peel coloration, LcCCDlike-b might be an important factor deciding fruit flavor, LcNCED2 and LcNCED3 might be related to flower control, LcNCED1 and LcNCED2 might function in fruitlet abscission, LcCCD4a1, LcCCD4a2, LcCCD1, LcCCD4, LcNCED1, and LcNCED2 might participate in postharvest storage of litchi.

CONCLUSION

Herein, Genome-wide analysis of the LcCCO genes was conducted in litchi to investigate their structure features and potential functions. These valuable and expectable information of LcCCO genes supplying in this study will offer further more possibility to promote quality improvement and breeding of litchi and further function investigation of this gene family in plant.

Identification of the carotenoid cleavage dioxygenase genes and functional analysis reveal DoCCD1 is potentially involved in beta-ionone formation in Dendrobium officinale

The carotenoids are the most widely distributed secondary metabolites in plants and can be degraded by carotenoid cleavage dioxygenase (CCD) to form apocarotenoids including an important C13 compound beta-ionone. Volatile beta-ionone can confer the violet and woody fragrance to plant essential oils, flowers, fruits, and vegetables, which therefore has been used in various industries. Dendrobium officinale is a traditional medicinal plant. However, there was limited information on the key enzymes involved in the biosynthesis of beta-ionone in D. officinale. In the present study, beta-ionone was detected in stems and leaves of D. officinale and genome-wide identification and expression profiles of CCD genes were subsequently carried out. There were nine DoCCD members in D. officinale. According to the phylogenetic relationship, DoCCD proteins were classified into six subfamilies including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS). DoCCD genes showed distinctive expression profiles and DoCCD1 gene was abundantly expressed in eight tissues. Induced expression of DoCCD1 gene resulted in discoloration of Escerichia coli strains that can accumulate carotenoids. Analysis of Gas Chromatography/Mass Spectrometer showed that DoCCD1 enzyme can cleave lycopene to produce 6-methyl-5-hepten-2-one and pseudoionone and also catalyze beta-carotene to form beta-ionone. Expression of DoCCD1 gene in Nicotiana benthamiana leaf resulted in production of abundant beta-ionone. Overall, the present study first provides valuable information on the CCD gene family in D. officinale, function of DoCCD1 gene as well as production of beta-ionone through genetic modification.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Plant carotenoids: recent advances and future perspectives

Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.

Global Transcriptome Analysis Revealed the Molecular Regulation Mechanism of Pigment and Reactive Oxygen Species Metabolism During the Stigma Development of Carya cathayensis

Hickory (Carya cathayensis Sarg.) is a monoecious plant of the genus Carya of the Juglandaceae family. Its nuts contain a number of nutritional compounds and are deeply loved by consumers. Interestingly, it was observed that the color of hickory stigma changed obviously from blooming to mature. However, the molecular mechanism underlying color formation during stigma development and the biological significance of this phenomenon was mostly unknown. In this work, pigment content, reactive oxygen species (ROS) removal capacity, and transcriptome analysis of developing stigma of hickory at 4 differential sampling time points (S1, S2, S3, and S4) were performed to reveal the dynamic changes of related pigment, antioxidant capacity, and its internal molecular regulatory mechanism. It was found that total chlorophyll content was decreased slightly from S1 to S4, while total carotenoids content was increased from S1 to S3 but decreased gradually from S3 to S4. Total anthocyanin content continued to increase during the four periods of stigma development, reaching the highest level at the S4. Similarly, the antioxidant capacity of stigma was also gradually improved from S1 to S4. Furthermore, transcriptome analysis of developing hickory stigma identified 31,027 genes. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters. Cluster 5 was enriched with some genes responsible for porphyrin and chlorophyll metabolism, carotenoid metabolism, and photosynthesis. Meanwhile, cluster 10 was enriched with genes related to flavonoid metabolism, including anthocyanin involved in ROS scavenging, and its related genes were mainly distributed in cluster 12. Based on the selected threshold values, a total of 10432 differentially expressed genes were screened out and enriched in the chlorophyll, carotenoid, anthocyanin, and ROS metabolism. The expression trends of these genes provided plausible explanations for the dynamic change of color and ROS level of hickory stigma with development. qRT-PCR analyses were basically consistent with the results of RNA-seq. The gene co-regulatory networks of pigment and ROS metabolism were further constructed and MYB113 (CCA0887S0030) and WRKY75 (CCA0573S0068) were predicted to be two core transcriptional regulators. These results provided in-depth evidence for revealing the molecular mechanism of color formation in hickory stigma and its biological significance.

DcCCD4 catalyzes the degradation of α-carotene and β-carotene to affect carotenoid accumulation and taproot color in carrot

Carotenoids are important natural pigments that give bright colors to plants. The difference in the accumulation of carotenoids is one of the key factors in the formation of various colors in carrot taproots. Carotenoid cleavage dioxygenases (CCDs), including CCD and 9-cis epoxycarotenoid dioxygenase, are the main enzymes involved in the cleavage of carotenoids in plants. Seven CCD genes have been annotated from the carrot genome. In this study, through expression analysis, we found that the expression level of DcCCD4 was significantly higher in the taproot of white carrot (low carotenoid content) than orange carrot (high carotenoid content). The overexpression of DcCCD4 in orange carrots caused the taproot color to be pale yellow, and the contents of α- and β-carotene decreased sharply. Mutant carrot with loss of DcCCD4 function exhibited yellow color (the taproot of the control carrot was white). The accumulation of β-carotene was also detected in taproot. Functional analysis of the DcCCD4 enzyme in vitro showed that it was able to cleave α- and β-carotene at the 9, 10 (9', 10') double bonds. In addition, the number of colored chromoplasts in the taproot cells of transgenic carrots overexpressing DcCCD4 was significantly reduced compared with that in normal orange carrots. Results showed that DcCCD4 affects the accumulation of carotenoids through cleavage of α- and β-carotene in carrot taproot.

Overexpression of a carrot BCH gene, DcBCH1, improves tolerance to drought in Arabidopsis thaliana

BACKGROUND

Carrot (Daucus carota L.), an important root vegetable, is very popular among consumers as its taproot is rich in various nutrients. Abiotic stresses, such as drought, salt, and low temperature, are the main factors that restrict the growth and development of carrots. Non-heme carotene hydroxylase (BCH) is a key regulatory enzyme in the β-branch of the carotenoid biosynthesis pathway, upstream of the abscisic acid (ABA) synthesis pathway.

RESULTS

In this study, we characterized a carrot BCH encoding gene, DcBCH1. The expression of DcBCH1 was induced by drought treatment. The overexpression of DcBCH1 in Arabidopsis thaliana resulted in enhanced tolerance to drought, as demonstrated by higher antioxidant capacity and lower malondialdehyde content after drought treatment. Under drought stress, the endogenous ABA level in transgenic A. thaliana was higher than that in wild-type (WT) plants. Additionally, the contents of lutein and β-carotene in transgenic A. thaliana were lower than those in WT, whereas the expression levels of most endogenous carotenogenic genes were significantly increased after drought treatment.

CONCLUSIONS

DcBCH1 can increase the antioxidant capacity and promote endogenous ABA levels of plants by regulating the synthesis rate of carotenoids, thereby regulating the drought resistance of plants. These results will help to provide potential candidate genes for plant drought tolerance breeding.

GmPGL2, Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean

Chloroplast biogenesis and development are highly complex processes requiring interactions between plastids and nuclear genomic products. Pentatricopeptide repeat (PPR) proteins play an essential role in the development of chloroplasts; however, it remains unclear how RNA editing factors influence soybean development. In this study, a Glycine max pale green leaf 2 mutant (Gmpgl2) was identified with decreased chlorophyll contents. Genetic mapping revealed that a single-nucleotide deletion at position 1949 bp in the Glyma.05g132700 gene in the Gmpgl2 mutant, resulting in a truncated GmPGL2 protein. The nuclear-encoded GmPGL2 is a PLS-type PPR protein that localizes to the chloroplasts. The C-to-U editing efficiencies of rps16, rps18, ndhB, ndhD, ndhE, and ndhF were reduced in the Gmpgl2 mutant. RNA electrophoresis mobility shift assay (REMSA) analysis further revealed that GmPGL2 binds to the immediate upstream sequences at RNA editing sites of rps16 and ndhB in vitro, respectively. In addition, GmPGL2 was found to interact with GmMORF8, GmMORF9, and GmORRM6. These results suggest that GmPGL2 participates in C-to-U RNA editing via the formation of a complex RNA editosome in soybean chloroplasts.

Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds

Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during seed maturation and storage, consistent with previous studies of provitamin A biofortified grains. In contrast, stacking with Orange (OR ^His ), a gene that initiates chromoplast biogenesis, dramatically enhances provitamin A and total carotenoid content and stability. Up to 65- and 10-fold increases of β-carotene and total carotenoids, respectively, with provitamin A carotenoids composing over 63% were observed in the seeds containing OR ^His and PSY. Co-expression of Homogentisate geranylgeranyl transferase (HGGT) with OR ^His and PSY further increases carotenoid accumulation and stability during seed maturation and storage. Moreover, knocking-out of β-carotene hydroxylase 2 (BCH2) by CRISPR/Cas9 not only potentially facilitates β-carotene accumulation but also minimizes the negative effect of carotenoid over production on seed germination. Our findings provide new insights into various processes on carotenoid accumulation and stability in seeds and establish a multiplexed strategy to simultaneously target carotenoid biosynthesis, turnover, and stable storage for carotenoid biofortification in crop seeds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00046-1.

Integrated Transcriptomics and Metabolomics Analyses Provide Insights Into the Response of Chongyi Wild Mandarin to Candidatus Liberibacter Asiaticus Infection

Candidatus Liberibacter asiaticus (CLas) is the causative agent of Huanglongbing (HLB), which has caused great economic losses to the citrus industry. The molecular mechanism of the host response to CLas in wild citrus germplasm has been reported less. Eighteen weeks after inoculation via grafting, all the CLas-inoculated Chongyi wild mandarin (Citrus reticulata) were positive and showed severe anatomical aberrations, suggesting its susceptibility to HLB. Transcriptomics and metabolomics analyses of leaves, barks, and roots from mock-inoculated (control) and CLas-inoculated seedlings were performed. Comparative transcriptomics identified 3,628, 3,770, and 1,716 differentially expressed genes (DEGs) between CLas-infected and healthy tissues in the leaves, barks, and roots, respectively. The CLas-infected tissues had higher transcripts per kilobase per million values and more genes that reached their maximal expression, suggesting that HLB might cause an overall increase in transcript accumulation. However, HLB-triggered transcriptional alteration showed tissue specificity. In the CLas-infected leaves, many DEGs encoding immune receptors were downregulated. In the CLas-infected barks, nearly all the DEGs involved in signaling and plant-pathogen interaction were upregulated. In the CLas-infected roots, DEGs encoding enzymes or transporters involved in carotenoid biosynthesis and nitrogen metabolism were downregulated. Metabolomics identified 71, 62, and 50 differentially accumulated metabolites (DAMs) in the CLas-infected leaves, barks and roots, respectively. By associating DEGs with DAMs, nitrogen metabolism was the only pathway shared by the three infected tissues and was depressed in the CLas-infected roots. In addition, 26 genes were determined as putative markers of CLas infection, and a hypothesized model for the HLB susceptibility mechanism in Chongyi was proposed. Our study may shed light on investigating the molecular mechanism of the host response to CLas infection in wild citrus germplasm.