The functions of laccase gene GhLAC15 in fiber colouration and development in brown-colored cotton.

The monotonicity of color type in naturally colored cottons (NCCs) has become the main limiting factor to their widespread use, simultaneously coexisting with poor fiber quality. The synchronous improvement of fiber quality and color become more urgent and crucial as the demand for sustainable development increases. The homologous gene of wild cotton Gossypium stocksii LAC15 in G. hirsutum, GhLAC15, was also dominantly expressed in the developing fibers of brown cotton XC20 from 5 DPA (day post anthesis) to 25 DPA, especially at the secondary cell wall thickening stage (20 DPA and 25 DPA). In XC20 plants with downregulated GhLAC15 (GhLAC15i), a remarkable reduction in proanthocyanidins (PAs) and lignin contents was observed. Some of the key genes in the phenylpropane and flavonoid biosynthesis pathway were down-regulated in GhLAC15i plants. Notably, the fiber length of GhLAC15i plants showed an obvious increase and the fiber color was lightened. Moreover, we found that the thickness of cotton fiber cell wall was decreased in GhLAC15i plants and the fiber surface became smoother compared to that of WT. Taken together, this study revealed that GhLAC15 played an important role in PAs and lignin biosynthesis in naturally colored cotton fibers. It might mediate fiber color and fiber quality by catalyzing PAs oxidation and lignin polymerization, ultimately regulating fiber colouration and development.

Genetic factors explaining anthocyanin pigmentation differences.

BACKGROUND: Anthocyanins are important contributors to coloration across a wide phylogenetic range of plants. Biological functions of anthocyanins span from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins. RESULTS: A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties was performed within numerous plant species covering the taxonomic diversity of flowering plants. The literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from four previous studies were reanalyzed to determine the genes possibly responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the intraspecific pigmentation differences was quantified. Differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are significantly more prone to account for pigmentation differences compared to bHLH or WD40 genes. Among the structural genes, DFR genes are most often associated with anthocyanin loss. CONCLUSIONS: These findings support previous assumptions about the susceptibility of transcriptional regulation to evolutionary changes and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent prevalent role in the specificity of the MBW complex.

Avian Predators Avoid Attacking Fly-Mimicking Beetles: A Field Experiment on Evasive Mimicry Using Artificial Prey.

AbstractMany Neotropical beetles present coloration patterns mimicking red-eyed flies, which are presumably evasive mimicry models. However, the role of predators in selecting for evasive mimics in nature remains untested. In a field experiment, we used nontoxic plasticine replicas of a specialized fly-mimicking beetle species, which we placed on the host plants of the beetles. We show that replicas painted with reddish patches simulating the eyes of flesh flies experienced a much lower predation rate than control replicas. We found that beak marks were the most frequent signs of attack on plasticine replicas, underlining the potential selective pressure exerted by birds. Replicas that matched the size of the beetles suffered higher predation than smaller or larger replicas. The predation rate was also higher for beetle replicas exposed during the warm and wet season, when adult beetles occur. Our results support predator-mediated selection of mimic beetles, highlighting that reddish spots resembling flies' eyes comprise an important trait in reducing attack by avian predators.

SUnSeT: spectral unmixing of hyperspectral images for phenotyping soybean seed traits.

KEY MESSAGE: Hyperspectral features enable accurate classification of soybean seeds using linear discriminant analysis and GWAS for novel seed trait genes. Evaluating crop seed traits such as size, shape, and color is crucial for assessing seed quality and improving agricultural productivity. The introduction of the SUnSet toolbox, which employs hyperspectral sensor-derived image analysis, addresses this necessity. In a validation test involving 420 seed accessions from the Korean Soybean Core Collections, the pixel purity index algorithm identified seed- specific hyperspectral endmembers to facilitate segmentation. Various metrics extracted from ventral and lateral side images facilitated the categorization of seeds into three size groups and four shape groups. Additionally, quantitative RGB triplets representing seven seed coat colors, averaged reflectance spectra, and pigment indices were acquired. Machine learning models, trained on a dataset comprising 420 accession seeds and 199 predictors encompassing seed size, shape, and reflectance spectra, achieved accuracy rates of 95.8% for linear discriminant analysis model. Furthermore, a genome-wide association study utilizing hyperspectral features uncovered associations between seed traits and genes governing seed pigmentation and shapes. This comprehensive approach underscores the effectiveness of SUnSet in advancing precision agriculture through meticulous seed trait analysis.

Transcriptomics and metabolomics reveal the mechanism of metabolites changes in Cymbidium tortisepalum var. longibracteatum colour mutation cultivars.

BACKGROUND: Foliage color is considered an important ornamental character of Cymbidium tortisepalum (C. tortisepalum), which significantly improves its horticultural and economic value. However, little is understood on the formation mechanism underlying foliage-color variations. METHODS: In this study, we applied a multi-omics approach based on transcriptomics and metabolomics, to investigate the biomolecule mechanisms of metabolites changes in C. tortisepalum colour mutation cultivars. RESULTS: A total of 508 genes were identified as differentially expressed genes (DEGs) between wild and foliage colour mutation C. tortisepalum cultivars based on transcriptomic data. KEGG enrichment of DEGs showed that genes involved in phenylalanine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis and brassinosteroid biosynthesis were most significantly enriched. A total of 420 metabolites were identified in C. tortisepalum using UPLC-MS/MS-based approach and 115 metabolites differentially produced by the mutation cultivars were identified. KEGG enrichment indicated that the most metabolites differentially produced by the mutation cultivars were involved in glycerophospholipid metabolism, tryptophan metabolism, isoflavonoid biosynthesis, flavone and flavonol biosynthesis. Integrated analysis of the metabolomic and transcriptomic data showed that there were four significant enrichment pathways between the two cultivars, including phenylalanine metabolism, phenylpropanoid biosynthesis, flavone and flavonol biosynthesis and flavonoid biosynthesis. CONCLUSION: The results of this study revealed the mechanism of metabolites changes in C. tortisepalum foliage colour mutation cultivars, which provides a new reference for breeders to improve the foliage color of C. tortisepalum.

Flower color modification in Torenia fournieri by genetic engineering of betacyanin pigments.

BACKGROUND: Betalains are reddish and yellow pigments that accumulate in a few plant species of the order Caryophyllales. These pigments have antioxidant and medicinal properties and can be used as functional foods. They also enhance resistance to stress or disease in crops. Several plant species belonging to other orders have been genetically engineered to express betalain pigments. Betalains can also be used for flower color modification in ornamental plants, as they confer vivid colors, like red and yellow. To date, betalain engineering to modify the color of Torenia fournieri-or wishbone flower-a popular ornamental plant, has not been attempted. RESULTS: We report the production of purple-reddish-flowered torenia plants from the purple torenia cultivar "Crown Violet."  Three betalain-biosynthetic genes encoding CYP76AD1, dihydroxyphenylalanine (DOPA) 4,5-dioxygenase (DOD), and cyclo-DOPA 5-O-glucosyltransferase (5GT) were constitutively ectopically expressed under the cauliflower mosaic virus (CaMV) 35S promoter, and their expression was confirmed by quantitative real-time PCR (qRT-PCR) analysis. The color traits, measured by spectrophotometric colorimeter and spectral absorbance of fresh petal extracts, revealed a successful flower color modification from purple to reddish. Red pigmentation was also observed in whole plants. LC-DAD-MS and HPLC analyses confirmed that the additional accumulated pigments were betacyanins-mainly betanin (betanidin 5-O-glucoside) and, to a lesser extent, isobetanin (isobetanidin 5-O-glucoside). The five endogenous anthocyanins in torenia flower petals were also detected. CONCLUSIONS: This study demonstrates the possibility of foreign betacyanin accumulation in addition to native pigments in torenia, a popular garden bedding plant. To our knowledge, this is the first report presenting engineered expression of betalain pigments in the family Linderniaceae. Genetic engineering of betalains would be valuable in increasing the flower color variation in future breeding programs for torenia.

Identification and Characterization of the miRNA Transcriptome Controlling Green Pigmentation of Chicken Eggshells.

Green eggs are mainly caused by inserting an avian endogenous retrovirus (EVA-HP) fragment into the SLCO1B3 gene. Although the genotypes for this insertion allele are consistent, eggshell color (ESC) may vary after a peak laying period; light-colored eggs are undesired by consumers and farmers and result in financial loss, so it is necessary to resolve this problem. miRNAs are small non-coding RNAs that exert essential functions in animal development and diseases. However, the regulatory miRNAs and detailed molecular mechanisms regulating eggshell greenness remain unclear. In the present study, we determined the genotype of green-eggshell hens through the detection of a homozygous allele insertion in the SLCO1B3 gene. The shell gland epithelium was obtained from green-eggshell hens that produced white and green shell eggs to perform transcriptome sequencing and investigate the important regulatory mechanisms that influence the ESC. Approximately 921 miRNAs were expressed in these two groups, which included 587 known miRNAs and 334 novel miRNAs, among which 44 were differentially expressed. There were 22 miRNAs that were significantly upregulated in the green and white groups, respectively, which targeted hundreds of genes, including KIT, HMOX2, and several solute carrier family genes. A Gene Ontology enrichment analysis of the target genes showed that the differentially expressed miRNA-targeted genes mainly belonged to the functional categories of homophilic cell adhesion, gland development, the Wnt signaling pathway, and epithelial tube morphogenesis. A KEGG enrichment analysis showed that the Hedgehog signaling pathway was significantly transformed in this study. The current study provides an overview of the miRNA expression profiles and the interaction between the miRNAs and their target genes. It provides valuable insights into the molecular mechanisms underlying green eggshell pigmentation, screening more effective hens to produce stable green eggs and obtaining higher economic benefits.

A Network of Circular RNA and MicroRNA Sequencing Provides Insights into Pigment Deposition of Changshun Blue Eggshell Chickens.

Eggshell color plays important biological roles and attracts the attention of both egg retailers and researchers. However, whether non-coding RNAs are involved in pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was used to analyse the uterine gland transcriptome (CircRNA and miRNA) of Changshun chicken blue-shell hens producing four different eggshell color eggs including dark blue PK(DB) and light blue (LB), dark brown and greenish (between blue and pink, DP) and pink (p). We found that miR-192-x, targeting SLC16a7, was expressed in DB, DP, and LB groups compared with the PK group, which indicates that miR-192-x may play a role in the blue eggshell color. KEGG and GO analyses showed that the "metabolic pathways" with targeted genes such BLVRA and HMOX1 were detected in dark and light blue color eggshell chickens, which confirms the different ratios of biliverdin and HO-1 involved in the deposition of blue color. As annotated by connectivity analysis, RASGRF1 and RASGRF2, belonging to the RASGRF family, are involved in the Ras signaling pathway, which plays an important role in cell growth, differentiation, metastasis and apoptosis. Our findings enrich the database of circRNA, miRNAs and genes for chicken uterine tissue, which will be useful in accelerating molecular selection for blue eggshell color layers.

Integrative Analysis of Metabolome and Transcriptome of Carotenoid Biosynthesis Reveals the Mechanism of Fruit Color Change in Tomato (Solanum lycopersicum).

Tomato fruit ripening is accompanied by carotenoid accumulation and color changes. To elucidate the regulatory mechanisms underlying carotenoid synthesis during fruit ripening, a combined transcriptomic and metabolomic analysis was conducted on red-fruited tomato (WP190) and orange-fruited tomato (ZH108). A total of twenty-nine (29) different carotenoid compounds were identified in tomato fruits at six different stages. The abundance of the majority of the carotenoids was enhanced significantly with fruit ripening, with higher levels of lycopene; (E/Z)-lycopene; and α-, ß- and γ-carotenoids detected in the fruits of WP190 at 50 and 60 days post anthesis (DPA). Transcriptome analysis revealed that the fruits of two varieties exhibited the highest number of differentially expressed genes (DEGs) at 50 DPA, and a module of co-expressed genes related to the fruit carotenoid content was established by WGCNA. qRT-PCR analysis validated the transcriptome result with a significantly elevated transcript level of lycopene biosynthesis genes (including SlPSY2, SlZCIS, SlPDS, SlZDS and SlCRTSO2) observed in WP190 at 50 DPA in comparison to ZH108. In addition, during the ripening process, the expression of ethylene biosynthesis (SlACSs and SlACOs) and signaling (SlEIN3 and SlERF1) genes was also increased, and these mechanisms may regulate carotenoid accumulation and fruit ripening in tomato. Differential expression of several key genes in the fruit of two tomato varieties at different stages regulates the accumulation of carotenoids and leads to differences in color between the two varieties of tomato. The results of this study provide a comprehensive understanding of carotenoid accumulation and ethylene biosynthesis and signal transduction pathway regulatory mechanisms during tomato fruit development.

The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates.

The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation.

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery.

BACKGROUND: Gangba sheep as a famous breed of Tibetan sheep, its wool color is mainly white and black. Gangba wool is economically important as a high-quality raw material for Tibetan blankets and Tibetan serge. However, relatively few studies have been conducted on the wool color of Tibetan sheep. RESULTS: To fill this research gap, this study conducted an in-depth analysis of two populations of Gangba sheep (black and white wool color) using whole genome resequencing to identify genetic variation associated with wool color. Utilizing PCA, Genetic Admixture, and N-J Tree analyses, the present study revealed a consistent genetic relationship and structure between black and white wool colored Gangba sheep populations, which is consistent with their breed history. Analysis of selection signatures using multiple methods (FST, π ratio, Tajima's D), 370 candidate genes were screened in the black wool group (GBB vs GBW); among them, MC1R, MLPH, SPIRE2, RAB17, SMARCA4, IRF4, CAV1, USP7, TP53, MYO6, MITF, MC2R, TET2, NF1, JAK1, GABRR1 genes are mainly associated with melanin synthesis, melanin delivery, and distribution. The enrichment results of the candidate genes identified 35 GO entries and 19 KEGG pathways associated with the formation of the black phenotype. 311 candidate genes were screened in the white wool group (GBW vs GBB); among them, REST, POU2F1, ADCY10, CCNB1, EP300, BRD4, GLI3, and SDHA genes were mainly associated with interfering with the differentiation of neural crest cells into melanocytes, affecting the proliferation of melanocytes, and inhibiting melanin synthesis. 31 GO entries and 22 KEGG pathways were associated with the formation of the white phenotype. CONCLUSIONS: This study provides important information for understanding the genetic mechanism of wool color in Gangba, and provides genetic knowledge for improving and optimizing the wool color of Tibetan sheep. Genetic improvement and selective breeding to produce wool of specific colors can meet the demand for a diversity of wool products in the Tibetan wool textile market.

Ecological drivers of ultraviolet colour evolution in snakes.

Ultraviolet (UV) colour patterns invisible to humans are widespread in nature. However, research bias favouring species with conspicuous colours under sexual selection can limit our assessment of other ecological drivers of UV colour, like interactions between predators and prey. Here we demonstrate widespread UV colouration across Western Hemisphere snakes and find stronger support for a predator defence function than for reproduction. We find that UV colouration has evolved repeatedly in species with ecologies most sensitive to bird predation, with no sexual dichromatism at any life stage. By modelling visual systems of potential predators, we find that snake conspicuousness correlates with UV colouration and predator cone number, providing a plausible mechanism for selection. Our results suggest that UV reflectance should not be assumed absent in "cryptically coloured" animals, as signalling beyond human visual capacities may be a key outcome of species interactions in many taxa for which UV colour is likely underreported.

Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini (Cucurbita pepo).

KEY MESSAGE: A large fragment deletion of CpAPRR2, encoding a two-component response regulator-like protein, which influences immature white rind color formation in zucchini (Cucurbita pepo). Fruit rind color is an important agronomic trait that affects commodity quality and consumer choice in zucchini (Cucurbita pepo). However, the molecular mechanism controlling rind color is unclear. We characterized two zucchini inbred lines: '19' (dark green rind) and '113' (white rind). Genetic analysis revealed white immature fruit rind color to be controlled by a dominant locus (CpW). Combining bulked segregant analysis sequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) markers, we mapped the CpW locus to a 100.4 kb region on chromosome 5 and then narrow down the candidate region to 37.5 kb using linkage analysis of 532 BC1 and 1613 F2 individuals, including 6 coding genes. Among them, Cp4.1LG05g02070 (CpAPRR2), encoding a two-component response regulator-like protein, was regarded to be a promising candidate gene. The expression level of CpAPRR2 in dark green rind was significantly higher than that in white rind and was induced by light. A deletion of 2227 bp at the 5' end of CpAPRR2 in '113' might explain the white phenotype. Further analysis of allelic diversity in zucchini germplasm resources revealed rind color to be associated with the deletion of CpAPRR2. Subcellular localization analysis indicated that CpAPRR2 was a nuclear protein. Transcriptome analysis using near-isogenic lines with dark green (DG) and white (W) rind indicated that genes involved in photosynthesis and porphyrin metabolism pathways were enriched in DG compared with W. Additionally, chlorophyll synthesis-related genes were upregulated in DG. These results identify mechanisms of zucchini rind color and provide genetic resources for breeding.

Painted flowers: Eluta generates pigment patterning in Antirrhinum.

In the early 1900s, Erwin Baur established Antirrhinum majus as a model system, identifying and characterising numerous flower colour variants. This included Picturatum/Eluta, which restricts the accumulation of magenta anthocyanin pigments, forming bullseye markings on the flower face. We identified the gene underlying the Eluta locus by transposon-tagging, using an Antirrhinum line that spontaneously lost the nonsuppressive el phenotype. A candidate MYB repressor gene at this locus contained a CACTA transposable element. We subsequently identified plants where this element excised, reverting to a suppressive Eluta phenotype. El alleles inhibit expression of anthocyanin biosynthetic genes, confirming it to be a regulatory locus. The modes of action of Eluta were investigated by generating stable transgenic tobacco lines, biolistic transformation of Antirrhinum petals and promoter activation/repression assays. Eluta competes with MYB activators for promoter cis-elements, and also by titrating essential cofactors (bHLH proteins) to reduce transcription of target genes. Eluta restricts the pigmentation established by the R2R3-MYB factors, Rosea and Venosa, with the greatest repression on those parts of the petals where Eluta is most highly expressed. Baur questioned the origin of heredity units determining flower colour variation in cultivated A. majus. Our findings support introgression from wild species into cultivated varieties.

Assessment of macro, trace and toxic element intake from rice: differences between cultivars, pigmented and non-pigmented rice.

Pigmented and non-pigmented rice varieties (grown in different areas) were collected in China, Yunnan, to investigate the content of macro-, trace elements and potentially toxic elements (PTEs), and to assess the health risk associated with dietary intake. The order of elemental concentrations in rice was Mn > Zn > Fe > Cu > Se for trace elements, P > K > Mg > Ca > Na for macro elements, and Cr > As > Cd for PTEs. Rice with a high concentration of essential elements also associated with a high content of PTEs. In addition, higher content of Cr, Mn and Na were found in pigmented rice. The health risk assessment showed that the daily intake of all elements was below the tolerable limit (UL). Moreover the intake of Fe, Zn and Se was far from sufficient for the nutrient requirement. The PTEs in rice dominated the health risk. Of concern is that this rice consumption is likely to contribute to carcinogenic risks in the long term and that adults are at higher health risk from pigmented rice compared to non-pigmented rice. This study confirms that the lack of essential micronutrients in rice and the health risk associated with rice diets should remain a concern.

Integrative analysis of transcriptome and target metabolites uncovering flavonoid biosynthesis regulation of changing petal colors in Nymphaea 'Feitian 2'.

BACKGROUND: Nymphaea (waterlily) is known for its rich colors and role as an important aquatic ornamental plant globally. Nymphaea atrans and some hybrids, including N. 'Feitian 2,' are more appealing due to the gradual color change of their petals at different flower developmental stages. The petals of N. 'Feitian 2' gradually change color from light blue-purple to deep rose-red throughout flowering. The mechanism of the phenomenon remains unclear. RESULTS: In this work, flavonoids in the petals of N. 'Feitian 2' at six flowering stages were examined to identify the influence of flavonoid components on flower color changes. Additionally, six cDNA libraries of N. 'Feitian 2' over two blooming stages were developed, and the transcriptome was sequenced to identify the molecular mechanism governing petal color changes. As a result, 18 flavonoid metabolites were identified, including five anthocyanins and 13 flavonols. Anthocyanin accumulation during flower development is the primary driver of petal color change. A total of 12 differentially expressed genes (DEGs) in the flavonoid biosynthesis pathway were uncovered, and these DEGs were significantly positively correlated with anthocyanin accumulation. Six structural genes were ultimately focused on, as their expression levels varied significantly across different flowering stages. Moreover, 104 differentially expressed transcription factors (TFs) were uncovered, and three MYBs associated with flavonoid biosynthesis were screened. The RT-qPCR results were generally aligned with high-throughput sequencing results. CONCLUSIONS: This research offers a foundation to clarify the mechanisms underlying changes in the petal color of waterlilies.

A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L.

Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships. We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size. Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits. We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.

Transcriptomic Analysis of Green Leaf Plants and White-Green Leaf Mutants in Haworthia cooperi var. pilifera.

Haworthia cooperi var. pilifera is a succulent plant with ornamental value. The white-green leaf mutant (wl) showed a significant difference in leaf color from the wild-type plant (WT). In this study, we integrated the transcriptomes of wl and WT plants to screen differentially expressed genes related to leaf color variation. The results of transcriptome analysis showed that 84,163 unigenes were obtained after de novo assembly and the NR database annotated the largest number of unigenes, which accounted for 57.13%, followed by NT (43.02%), GO (39.84%), Swiss-Prot (39.25%), KEGG (36.06%), and COG (24.88%). Our finding showed that 2586 genes were differentially expressed in the two samples, including 1996 down-regulated genes and 590 up-regulated genes. GO analysis predicted that these differentially expressed genes (DEGs) participate in 12 cellular components, 20 biological processes, and 13 molecular function terms and KEGG analysis showed that metabolic pathways, plant-pathogen interaction, glycerophospholipid metabolism, endocytosis, plant hormone signal transduction, and ether lipid metabolism were enriched among all identified pathways. Through functional enrichment analysis of DEGs, we found that they were involved in chloroplast division and the biosynthesis of plant pigments, including chlorophyll, carotenoids, anthocyanin, and transcription factor families, which might be related to the formation mechanism of leaf color. Taken together, these results present insights into the difference in gene expression characteristics in leaves between WT and wl mutants and provide a new insight for breeding colorful leaf phenotypes in succulent plants.

Complex petal spot formation in the Beetle Daisy (Gorteria diffusa) relies on spot-specific accumulation of malonylated anthocyanin regulated by paralogous GdMYBSG6 transcription factors.

Gorteria diffusa has elaborate petal spots that attract pollinators through sexual deception, but how G. diffusa controls spot development is largely unknown. Here, we investigate how pigmentation is regulated during spot formation. We determined the anthocyanin composition of G. diffusa petals and combined gene expression analysis with protein interaction assays to characterise R2R3-MYBs that likely regulate pigment production in G. diffusa petal spots. We found that cyanidin 3-glucoside pigments G. diffusa ray floret petals. Unlike other petal regions, spots contain a high proportion of malonylated anthocyanin. We identified three subgroup 6 R2R3-MYB transcription factors (GdMYBSG6-1,2,3) that likely activate the production of spot pigmentation. These genes are upregulated in developing spots and induce ectopic anthocyanin production upon heterologous expression in tobacco. Interaction assays suggest that these transcription factors regulate genes encoding three anthocyanin synthesis enzymes. We demonstrate that the elaboration of complex spots in G. diffusa begins with the accumulation of malonylated pigments at the base of ray floret petals, positively regulated by three paralogous R2R3-MYB transcription factors. Our results indicate that the functional diversification of these GdMYBSG6s involved changes in the spatial control of their transcription, and modification of the duration of GdMYBSG6 gene expression contributes towards floral variation within the species.

Unravelling the metabolomic diversity of pigmented and non-pigmented traditional rice from Tamil Nadu, India.

Rice metabolomics is widely used for biomarker research in the fields of pharmacology. As a consequence, characterization of the variations of the pigmented and non-pigmented traditional rice varieties of Tamil Nadu is crucial. These varieties possess fatty acids, sugars, terpenoids, plant sterols, phenols, carotenoids and other compounds that plays a major role in achieving sustainable development goal 2 (SDG 2). Gas-chromatography coupled with mass spectrometry was used to profile complete untargeted metabolomics of Kullkar (red colour) and Milagu Samba (white colour) for the first time and a total of 168 metabolites were identified. The metabolite profiles were subjected to data mining processes, including principal component analysis (PCA), Orthogonal Partial Least Square Discrimination Analysis (OPLS-DA) and Heat map analysis. OPLS-DA identified 144 differential metabolites between the 2 rice groups, variable importance in projection (VIP) ≥ 1 and fold change (FC) ≥ 2 or FC ≤ 0.5. Volcano plot (64 down regulated, 80 up regulated) was used to illustrate the differential metabolites. OPLS-DA predictive model showed good fit (R2X = 0.687) and predictability (Q2 = 0.977). The pathway enrichment analysis revealed the presence of three distinct pathways that were enriched. These findings serve as a foundation for further investigation into the function and nutritional significance of both pigmented and non-pigmented rice grains thereby can achieve the SDG 2.