Candidate Genes In Region Research Articles

Narrowing the region of candidate genes that control the development of protoscoleces of Echinococcus multilocularis in the mouse liver.

Alveolar echinococcosis is a zoonosis caused by the larval stage of Echinococcus multilocularis. In previous studies, QTL analysis using C57BL/6N (B6) and DBA/2 (D2) which differ in susceptibility suggested the presence of genes on chromosome 1 that control protoscolex development. In this study, we constructed several congenic mice with different chromosome 1 regions substituted to confirm the presence of responsible genes and to narrow down the regions where the responsible genes exist. Five lines of third-generation congenic strain were constructed and infection experiments were conducted. The results showed that the development of protoscolex was seen in the two lines, resulting to narrow-down the responsible region between 69.4cM and 70.67cM. There were 18 genes having different SNPs and 10 genes having amino acid substitutions between B6 and D2 within this region. Infection experiments with third-generation of congenic mice succeeded in narrowing down the chromosomal region determining protoscolex development, resulting to reduce the number of candidate genes. The identification of the gene responsible for protoscolex development will contribute to the control of E. multilocularis infection.

Tissue-specific transcriptome analyses unveils candidate genes for flavonoid biosynthesis, regulation and transport in the medicinal plant Ilex asprella

It is not clear that the genes involved with flavonoids synthesis, regulation and transport in Ilex asprella. Transcriptome analysis of leaf, stem and root has uncovered 28,478 differentially expressed genes (DEGs) that are involved in various biological processes. Among these, the expression of 31 candidate synthetase genes, 19 transcription factors, and 5 transporters associated with flavonoid biosynthesis varies across tissues, encompassing seven complete biosynthetic pathways (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, and anthocyanin) and one partial pathway (proanthocyanidin). Tissue-specific expression patterns suggest that the stilbenes, aurones, flavones and anthocyanin branches are more prominent in roots, as indicated by key genes such as STS(Ilex_044726), CH4ʹGT(Ilex_047989), FNS(Ilex_043640) and UFGT(Ilex_014720). In leaves, the phlobaphenes and flavonols branches are dominant, determined by CHI(Ilex_005941), FNR(Ilex_039777) and FLS(Ilex_046424). The isoflavone pathway appears to be more active in stems due to the presence of IFS(Ilex_029360), mirroring the accumulation of the intermediate metabolite chalcone, which is regulated by CHS(Ilex_047537). The absence of LAR genes implies that gallocatechin, and catechin liked proanthocyanidins cannot be synthesized in I. asprella. Meanwhile, the general phenylpropanoid pathway is more active in roots, stems than in leaves, as evidenced by the expression of PAL(Ilex_042231, Ilex_014816), C4H(Ilex_017598), and 4CL(Ilex_042033). Flavanone, dihydroflavonol and leucoanthocyanidin, key intermediates, accumulate more rapidly in stem, stem and root, respectively, regulated by CHI(Ilex_005941), F3H(Ilex_004635) and DFR(Ilex_004771). Correlation and network analyses reveal that candidate regulators and transporters are closely associated with the synthesis genes. The study provides profound snoop into flavonoids metabolism in I. asprella and offers valuable refer for medicinal plant.

Impact of cannabinoids on synapse markers in an SH-SY5Y cell culture model

Patients suffering from schizophrenic psychosis show reduced synaptic connectivity compared to healthy individuals, and often, the use of cannabis precedes the onset of schizophrenic psychosis. Therefore, we investigated if different types of cannabinoids impact methylation patterns and expression of schizophrenia candidate genes concerned with the development and preservation of synapses and synaptic function in a SH-SY5Y cell culture model. For this purpose, SH-SY5Y cells were differentiated into a neuron-like cell type as previously described. Effects of the cannabinoids delta-9-THC, HU-210, and Anandamide were investigated by analysis of cell morphology and measurement of neurite/dendrite lengths as well as determination of methylation pattern, expression (real time-qPCR, western blot) and localization (immunocytochemistry) of different target molecules concerned with the formation of synapses. Regarding the global impression of morphology, cells, and neurites appeared to be a bit more blunted/roundish and to have more structures that could be described a bit boldly as resembling transport vesicles under the application of the three cannabinoids in comparison to a sole application of retinoic acid (RA). However, there were no obvious differences between the three cannabinoids. Concerning dendrites or branch lengths, there was a significant difference with longer dendrites and branches in RA-treated cells than in undifferentiated control cells (as shown previously), but there were no differences between cannabinoid treatment and exclusive RA application. Methylation rates in the promoter regions of synapse candidate genes in cannabinoid-treated cells were in between those of differentiated cells and untreated controls, even though findings were significant only in some of the investigated genes. In other targets, the methylation rates of cannabinoid-treated cells did not only approach those of undifferentiated cells but were also valued even beyond. mRNA levels also showed the same tendency of values approaching those of undifferentiated controls under the application of the three cannabinoids for most investigated targets except for the structural molecules (NEFH, MAPT). Likewise, the quantification of expression via western blot analysis revealed a higher expression of targets in RA-treated cells compared to undifferentiated controls and, again, lower expression under the additional application of THC in trend. In line with our earlier findings, the application of RA led to higher fluorescence intensity and/or a differential signal distribution in the cell in most of the investigated targets in ICC. Under treatment with THC, fluorescence intensity decreased, or the signal distribution became similar to the dispersion in the undifferentiated control condition. Our findings point to a decline of neuronal differentiation markers in our in vitro cell-culture system under the application of cannabinoids.

Genetic mapping and molecular marker development for white flesh color in tomato.

Fruit color significantly influences the quality of horticultural crops, which affects phytochemical diversity and consumer preferences. Despite its importance, the genetic basis of the white-colored fruit in tomatoes remains poorly understood. In this study, we demonstrate that white-fleshed tomato varieties accumulate fewer carotenoids than yellow-fleshed varieties. We developed various segregating populations by hybridizing red, yellow, and white fruit tomato cultivars. Genetic analysis revealed that the white fruit color trait is controlled by a single gene that dominates both red and yellow fruits. Bulk segregant RNA sequencing provided a preliminary map of a 3.17 Mb region on chromosome 3 associated with the white color trait. Based on kompetitive allele-specific PCR (KASP) markers, we narrowed the candidate gene region to 819 kb. Within this region, we identified a 4906-bp sequence absence variation near Phytoene Synthase 1 (SlPSY1) specific to white-colored tomatoes. Genotyping of the progeny and natural populations using a single nucleotide polymorphism adjacent to this absence of variation confirmed its key role in white fruit formation. Collectively, our findings provide insights into white fruit trait formation in tomatoes, enabling tomato breeders to precisely introduce white fruit traits for commercial exploitation.

Mapping taste and flavour traits to genetic markers in lettuce Lactuca sativa

Lettuce is the most highly consumed raw leafy vegetable crop eaten worldwide, making it nutritionally important in spite of its comparatively low nutrient density in relation to other vegetables. However, the perception of bitterness caused by high levels of sesquiterpenoid lactones and comparatively low levels of sweet tasting sugars limits palatability. To assess variation in nutritional and taste-related metabolites we assessed 104 members of a Lactuca sativa cv. Salinas x L. serriola (accession UC96US23) mapping population. Plants were grown in three distinct environments, and untargeted NMR and HPLC were used as a rapid chemotyping method, from which 63 unique Quantitative Trait Loci (QTL) were identified. We were able to identify putative regulatory candidate genes underlying the QTL for fructose on linkage group 9, which accounted for up to 36 % of our population variation, and which was stable across all three growing environments; and for 15-p-hydroxyyphenylacetyllactucin-8-sulfate on linkage group 5 which has previously been identified for its low bitterness, while retaining anti-herbivory field effects. We also identified a candidate gene for flavonoid 3′,5′- hydroxylase underlying a polyphenol QTL on linkage group 5, and two further candidate genes in sugar biosynthesis on linkage groups 2 and 5. Collectively these candidate genes and their associated markers can inform a route for plant breeders to improve the palatability and nutritional value of lettuce in their breeding programmes.

Rapid function analysis of OsiWAK1 using a Dual-Luciferase assay in rice

In the past decade, the exploration of genetic resources in rice has significantly enhanced the efficacy of rice breeding. However, the exploration of genetic resources is hindered by the identification of candidate genes. To expedite the identification of candidate genes, this study examined tapetum programmed cell death-related genes OsiWAK1, OsPDT1, EAT1, TDR, and TIP2 to assess the efficacy of the Dual-Luciferase (Dual-LUC) assay in rapidly determining gene relationships. The study found that, in the Dual-LUC assay, OsiWAK1 and its various recombinant proteins exhibit comparable activation abilities on the EAT1 promoter, potentially indicating a false positive. However, the Dual-LUC assay can reveal that OsiWAK1 impacts both the function of its upstream regulatory factor OsPDT1 and the TDR/TIP2 transcription complex. By rapidly studying the relationship between diverse candidate genes and regulatory genes in a well-known trait via the Dual-LUC assay, this study provides a novel approach to expedite the determination of candidate genes such as genome-wide association study.

Association between thermogenic brown fat and genes under positive natural selection in circumpolar populations

BackgroundAdaptation to cold was essential for human migration across Eurasia. Non-shivering thermogenesis through brown adipose tissue (BAT) participates in cold adaptation because some genes involved in the differentiation and function of BAT exhibit signatures of positive natural selection in populations at high latitudes. Whether these genes are associated with the inter-individual variability in BAT thermogenesis remains unclear. In this study, we evaluated the potential associations between BAT activity and single nucleotide polymorphisms (SNPs) in candidate gene regions in East Asian populations.MethodsBAT activity induced by mild cold exposure was measured in 399 healthy Japanese men and women using fluorodeoxyglucose-positron emission tomography and computed tomography (FDG-PET/CT). The capacity for cold-induced thermogenesis and fat oxidation was measured in 56 men. Association analyses with physiological traits were performed for 11 SNPs at six loci (LEPR, ANGPTL8, PLA2G2A, PLIN1, TBX15-WARS2, and FADS1) reported to be under positive natural selection. Associations found in the FDG-PET/CT population were further validated in 84 healthy East Asian men and women, in whom BAT activity was measured using infrared thermography. Associations between the SNP genotypes and BAT activity or other related traits were tested using multiple logistic and linear regression models.ResultsOf the 11 putative adaptive alleles of the six genes, two intronic SNPs in LEPR (rs1022981 and rs12405556) tended to be associated with higher BAT activity. However, these did not survive multiple test comparisons. Associations with lower body fat percentage, plasma triglyceride, insulin, and HOMA-IR levels were observed in the FDG-PET/CT population (P < 0.05). Other loci, including TBX15-WARS2, which is speculated to mediate cold adaptation in Greenland Inuits, did not show significant differences in BAT thermogenesis.ConclusionsOur results suggest a marginal but significant association between LEPR SNPs. However, robust supporting evidence was not established for the involvement of other loci under positive natural selection in cold adaptation through BAT thermogenesis in East Asian adults. Given the pleiotropic function of these genes, factors other than cold adaptation through BAT thermogenesis, such as diet adaptation, may contribute to positive natural selection at these loci.

Mapping the molecular landscape of Lotus japonicus nodule organogenesis through spatiotemporal transcriptomics

Legumes acquire nitrogen-fixing ability by forming root nodules. Transferring this capability to more crops could reduce our reliance on nitrogen fertilizers, thereby decreasing environmental pollution and agricultural production costs. Nodule organogenesis is complex, and a comprehensive transcriptomic atlas is crucial for understanding the underlying molecular events. Here, we utilized spatial transcriptomics to investigate the development of nodules in the model legume, Lotus japonicus. Our investigation has identified the developmental trajectories of two critical regions within the nodule: the infection zone and peripheral tissues. We reveal the underlying biological processes and provide gene sets to achieve symbiosis and material exchange, two essential aspects of nodulation. Among the candidate regulatory genes, we illustrate that LjNLP3, a transcription factor belonging to the NIN-LIKE PROTEIN family, orchestrates the transition of nodules from the differentiation to maturation. In summary, our research advances our understanding of nodule organogenesis and provides valuable data for developing symbiotic nitrogen-fixing crops.

Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development

BackgroundCassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated.ResultsIn this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars.ConclusionsOur findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

Mapping and Candidate Gene Analysis of the Low-Temperature-Sensitive Albino Gene OsLTSA8 in Rice Seedlings.

Chloroplasts are organelles responsible for photosynthesis in plants, providing energy for growth and development. However, the genetic regulatory mechanisms underlying early chloroplast development in rice remain incompletely understood. In this study, we identified a rice seedling thermosensitive chlorophyll-deficient mutant, osltsa8, and the genetic analysis of two F2 populations suggested that this trait may be controlled by more than one pair of alleles. Through reciprocal F2 populations and QTL-seq technology, OsLTSA8 was mapped to the interval of 24,280,402-25,920,942 bp on rice chromosome 8, representing a novel albino gene in rice. Within the candidate gene region of OsLTSA8, there were 258 predicted genes, among which LOC_Os08g39050, LOC_Os08g39130, and LOC_Os08g40870 encode pentatricopeptide repeat (PPR) proteins. RNA-seq identified 18 DEGs (differentially expressed genes) within the candidate interval, with LOC_Os08g39420 showing homology to the pigment biosynthesis-related genes Zm00001d017656 and Sb01g000470; LOC_Os08g39430 and LOC_Os08g39850 were implicated in chlorophyll precursor synthesis. RT-qPCR was employed to assess the expression levels of LOC_Os08g39050, LOC_Os08g39130, LOC_Os08g40870, LOC_Os08g39420, LOC_Os08g39430, and LOC_Os08g39850 in the wild-type and mutant plants. Among them, the differences in the expression levels of LOC_Os08g39050 and LOC_Os08g39430 were the most significant. This study will contribute to further elucidating the molecular mechanisms of rice chloroplast development.

A nested reciprocal experimental design to map the genetic architecture of transgenerational phenotypic plasticity.

Extensive studies have revealed the ecological and evolutionary significance of phenotypic plasticity, but little is known about how it is inherited between generations and the genetic architecture of its transgenerational inheritance. To address these issues, we design a mapping study by growing Arabidopsis thaliana RILs in high- and low-light environments and further growing their offspring RILs from each maternal light environment in the same contrasting environments. This tree-like design of the controlled ecological experiment provides a framework for analysing the genetic regulation of phenotypic plasticity and its non-genetic inheritance. We implement the computational approach of functional mapping to identify specific QTLs for transgenerational phenotypic plasticity. By estimating and comparing the plastic response of leaf-number growth trajectories to light environment between generations, we find that the maternal environment affects phenotypic plasticity, whereas transgenerational plasticity is shaped by the offspring environment. The genetic architecture underlying the light-induced change of leaf number not only changes from parental to offspring generations, but also depends on the maternal environment the parental generation experienced and the offspring environment the offspring generation is experiencing. Most plasticity QTLs are annotated to the genomic regions of candidate genes for specific biological functions. Our computational-experimental design provides a unique insight into dissecting the non-genetic and genetic mechanisms of phenotypic plasticity shaping plant adaptation and evolution in various forms.

A Novel 10-Base Pair Deletion in the First Exon of GmHY2a Promotes Hypocotyl Elongation, Induces Early Maturation, and Impairs Photosynthetic Performance in Soybean.

Plants photoreceptors perceive changes in light quality and intensity and thereby regulate plant vegetative growth and reproductive development. By screening a γ irradiation-induced mutant library of the soybean (Glycine max) cultivar "Dongsheng 7", we identified Gmeny, a mutant with elongated nodes, yellowed leaves, decreased chlorophyll contents, altered photosynthetic performance, and early maturation. An analysis of bulked DNA and RNA data sampled from a population segregating for Gmeny, using the BVF-IGV pipeline established in our laboratory, identified a 10 bp deletion in the first exon of the candidate gene Glyma.02G304700. The causative mutation was verified by a variation analysis of over 500 genes in the candidate gene region and an association analysis, performed using two populations segregating for Gmeny. Glyma.02G304700 (GmHY2a) is a homolog of AtHY2a in Arabidopsis thaliana, which encodes a PΦB synthase involved in the biosynthesis of phytochrome. A transcriptome analysis of Gmeny using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed changes in multiple functional pathways, including photosynthesis, gibberellic acid (GA) signaling, and flowering time, which may explain the observed mutant phenotypes. Further studies on the function of GmHY2a and its homologs will help us to understand its profound regulatory effects on photosynthesis, photomorphogenesis, and flowering time.

An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells.

Long interspersed element 1 (LINE-1; L1) are a family of transposons that occupy ~17% of the human genome. Though a small number of L1 copies remain capable of autonomous transposition, the overwhelming majority of copies are degenerate and immobile. Nevertheless, both mobile and immobile L1s can exert pleiotropic effects (promoting genome instability, inflammation, or cellular senescence) on their hosts, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSD17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for regulators of transposon RNA levels.

Revealing ANXA6 as a Novel Autophagy-related Target for Pre-eclampsia Based on the Machine Learning

Background: Preeclampsia (PE) is a severe pregnancy complication associated with autophagy. Objective: This research sought to uncover autophagy-related genes in pre-eclampsia through bioinformatics and machine learning. Methods: GSE75010 from the GEO series was subjected to WGCNA to identify key modular genes in PE. Autophagy genes retrieved from the THANATOS overlapped with the modular genes to yield PErelated autophagy genes. Furthermore, the crucial step involved the utilization of two machine learning algorithms (LASSO and SVM-RFE) for dimensionality reduction. The candidate gene was further verified by quantitative reverse transcription polymerase chain reaction, western blot, and immunohistochemistry. Preliminary experiments were conducted on HTR-8/SVneo cell lines to explore the role of candidate genes in autophagy regulation. Results: WGCNA identified 291 genes from 5 hubs, and after overlapping with 1087 autophagy-related genes obtained from THANATOS, 42 PE-related ARGs were identified. ANXA6 was recognized as a potential target through SVM-RFE and LASSO analyses. The mRNA and protein expression of ANXA6 were verified in placenta samples. In HTR8/SVneo cells, modulating ANXA6 expression altered autophagy levels. Knocking down ANXA6 resulted in an anti-autophagy effect, which was reversed by treatment with CAL101, an inhibitor of PI3K, Akt, and mTOR. Conclusion: We observed that ANXA6 may serve as a possible PE action target and that autophagy may be crucial to the pathogenesis of PE.

Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data

The discovery of upstream regulatory genes of a gene of interest still remains challenging. Here we applied a scalable computational method to unbiasedly predict candidate regulatory genes of critical transcription factors by searching the whole genome. We illustrated our approach with a case study on the master regulator FOXP3 of human primary regulatory T cells (Tregs). While target genes of FOXP3 have been identified, its upstream regulatory machinery still remains elusive. Our methodology selected five top-ranked candidates that were tested via proof-of-concept experiments. Following knockdown, three out of five candidates showed significant effects on the mRNA expression of FOXP3 across multiple donors. This provides insights into the regulatory mechanisms modulating FOXP3 transcriptional expression in Tregs. Overall, at the genome level this represents a high level of accuracy in predicting upstream regulatory genes of key genes of interest.

The impact of drought on phellem development: Identification of novel gene regulators and evidence of photosynthetic activity in cork oak stems

Quercus suber (cork oak) is a sustainably exploited forest resource, producing a unique renewable raw material known as cork. With drought events imposing a negative impact on tree vitality, further research is needed to enhance our understanding of the genetic and environmental factors regulating cork development, to foster the resilience of cork oak ecosystems. We focused on characterizing long-term drought-induced molecular adaptations occurring in stems, and identifying key genetic pathways regulating phellem development. One-year-old cork oak plants were grown for 6 months under well-watered, or water-deficit (WD) conditions and main stems were targeted for histological characterization and transcriptomic analysis. WD treatment reduced meristem activity at both vascular cambium and phellogen, impairing secondary growth. Transcriptional analysis revealed a global downregulation of genes related to cell division, differentiation, and cell wall biogenesis in phellem, inner bark, and xylem under WD conditions. Phellem and inner bark showed upregulation of photosynthesis-related genes, highlighting a determinant role of stem photosynthesis in the adaptation to long-term drought. We show that developing phellem cells contain chloroplasts and their abundance increases under WD. Lastly, we propose new candidate regulatory genes involved in regulating phellogen activity and demonstrate the role of phellem in drought-induced bark photosynthesis in young plants.

Genome-wide association study dissecting drought resistance-associated loci based on physiological traits in common bean

Genetic improvement of drought resistance is one of the main breeding goals for common bean, so molecular markers must be identified to facilitate drought resistance breeding. In this study, we evaluated the proline, trehalose, raffinose, and stachyose contents of 210 common bean accessions under two watering conditions and found large variations in all four. The coefficients of variation ranged from 21.21% for proline content to 78.69% for stachyose content under well-watered conditions, and from 20.11% for proline content to 50.08% for trehalose content under drought stress. According to our genome-wide association analysis, 32 quantitative trait loci were associated with drought resistance, seven of which overlapped with known loci. Four hotspot regions were identified at Pv01, Pv07 and Pv11. A set of candidate genes was identified, including genes encoding MYB, bZIP, bHLH, ERF, and protein kinases. Among these genes, Phvul.001G189400, Phvul.007G273000 and Phvul.008G270500 were annotated as bZIP, ERF and WRKY, respectively. These genes are reportedly involved in drought stress responses in Arabidopsis thaliana and were induced by drought stress in common bean. Significant SNPs in six candidate gene regions formed different haplotypes, and phenotypic analysis revealed significant differences among the haplotypes. These results provide new insight into the genetic basis of drought resistance in common bean and reveal candidate genes and superior natural variations that will be useful for improving common bean.

Integrative Metabolome and Transcriptome Analyses Reveal the Pericarp Coloration Mechanisms in Bitter Melon (Momordica charantia L.)

Pericarp colors are critical agronomic traits that affect the quality and economic values of fruits. Although a diversity of bitter melon pericarp (BMP) colors is available, the fruit pigmentation mechanisms remain elusive. Hence, this study aimed to unveil the key metabolites and molecular mechanisms underlying variation in BMP coloration through integrative metabolomics and transcriptomics analyses of four differently colored genotypes, including K1102 (grayish orange), 262 (grayish yellow), 1392 (very soft green), and K115 (dark grayish cyan). The four BMPs exhibited significant metabolite profile and transcriptional differences, as over 112 and 1865 DAMs (differentially accumulated metabolites) and DEGs (differentially expressed genes), respectively, were identified. The variation in the content of six anthocyanins, including malvidin 3-O-glucoside, petunidin 3-O-glucoside, rosinidin O-hexoside, cyanidin, cyanidin 3-p-hydroxybenzoylsophoroside-5-glucoside, and pelargonidin 3-O-beta-D-glucoside, might be the major driving factor of BMP color changes. Notably, malvidin 3-O-glucoside, rosinidin O-hexoside, and petunidin 3-O-glucoside are the dominant pigments in K115, while carotenoids and other flavonoids may contribute to other colors. Candidate flavonoid structural and regulatory (MYBs, NACs, MADSs, bHLHs, and bZIPs) genes were identified. Of them, gene13201 (anthocyanin reductase), gene8173 (polyphenol oxidase), gene2136 (NAC43), gene19593 (NAC104), and gene15171 (tetrapyrrole-binding protein) might play essential roles in K115 pericarp color development. Our findings deepen our understanding of BMP pigmentation and provide fundamental resources for higher-valued bitter melon breeding perspectives.

Multi-omics analysis reveals novel loci and a candidate regulatory gene of unsaturated fatty acids in soybean (Glycine max (L.) Merr)

BackgroundSoybean is a major oil crop; the nutritional components of soybean oil are mainly controlled by unsaturated fatty acids (FA). Unsaturated FAs mainly include oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). The genetic architecture of unsaturated FAs in soybean seeds has not been fully elucidated, although many independent studies have been conducted. A 3 V multi-locus random single nucleotide polymorphism (SNP)-effect mixed linear model (3VmrMLM) was established to identify quantitative trait loci (QTLs) and QTL-by-environment interactions (QEIs) for complex traits.ResultsIn this study, 194 soybean accessions with 36,981 SNPs were calculated using the 3VmrMLM model. As a result, 94 quantitative trait nucleotides (QTNs) and 19 QEIs were detected using single-environment (QTN) and multi-environment (QEI) methods. Three significant QEIs, namely rs4633292, rs39216169, and rs14264702, overlapped with a significant single-environment QTN.ConclusionsFor QTNs and QEIs, further haplotype analysis of candidate genes revealed that the Glyma.03G040400 and Glyma.17G236700 genes were beneficial haplotypes that may be associated with unsaturated FAs. This result provides ideas for the identification of soybean lipid-related genes and provides insights for breeding high oil soybean varieties in the future.

JrATHB-12 mediates JrMYB113 and JrMYB27 to control the anthocyanin levels in different types of red walnut

Red walnut has broad market prospects because it is richer in anthocyanins than ordinary walnut. However, the mechanism driving anthocyanin biosynthesis in red walnut is still unknown. We studied two types of red walnut, called red walnut 1 (R1), with a red pericarp and seed coat, and red walnut 2 (R2), with a red seed coat only. R1 mostly contained cyanidin-3-O-galactoside, while R2 contained a various amounts of cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside. The LDOX-2 (LOC109007163) and LDOX-3 (LOC109010746) genes, which encode leucoanthocyanidin dioxygenase/anthocyanidin synthase (LDOX/ANS), were preliminarily indicated as the crucial genes for anthocyanin biosynthesis in R1 and R2, respectively. The MYB differential genes analysis showed that MYB27 and MYB113 are specifically expressed in the red parts of R1 and R2, respectively, and they are regarded as candidate regulatory genes. Ectopic expression in Arabidopsis and transient injection in walnut showed that both MYB27 and MYB113 were located in the nucleus and promoted anthocyanin accumulation, while MYB27 promoted the expression of LDOX-2, and MYB113 promoted the expression of LDOX-3 and UAGT-3. Yeast one-hybrid and electrophoretic mobility shift assays showed that MYB27 could only bind to the LDOX-2 promoter, while MYB113 could bind to the promoters of both LDOX-3 and UAGT-3. In addition, we also identified an HD-Zip transcription factor, ATHB-12, which is specifically expressed in the pericarp. After silencing the expression of ATHB-12, the R2 pericarp turned red, and MYB113 expression increased. Further experiments showed that ATHB-12 could specifically interact with MYB113 and bind to its promoter. This suggests that MYB27 controls R1 coloration by regulating LDOX-2, while MYB113 controls R2 coloration by regulating LDOX-3 and UAGT-3, but ATHB-12 can specifically bind to and inhibit the MYB113 of the R2 pericarp so that it becomes unpigmented. This study reveals the anthocyanin biosynthetic mechanisms in two different types of red walnut and provides a scientific basis for the selection and breeding of red walnut varieties.