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1.
BMC Plant Biol ; 19(1): 243, 2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31174472

RESUMO

BACKGROUND: Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. The genetic network regulating green flesh formation has been studied in tomato, melon and watermelon. However, little is known about the inheritance and molecular basis of green flesh in cucumber. This study sought to determine the main genomic regions associated with green flesh. Three F2 and two BC1 populations derived from the 9110Gt (cultivated cucumber, green flesh color) and PI183967 (wild cucumber, white flesh color) were used for the green flesh genetic analysis. Two F2 populations of them were further employed to do the map construction and quantitative trait loci (QTL) study. Also, a core cucumber germplasms population was used to do the GWAS analysis. RESULTS: We identified three indexes, flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in three environments. Genetic analysis indicated that green flesh color in 9110Gt is controlled by a major-effect QTL. We developed two genetic maps with 192 and 174 microsatellite markers respectively. Two novel inversions in Chr1 were identified between cultivated and wild cucumbers. The major-effect QTL, qgf5.1, was identified using FC, FEC and FCC index in all different environments used. In addition, the same qgf5.1, together with qgf3.1, was identified via GWAS. Further investigation of two candidate regions using pairwise LD correlations, combined with genetic diversity of qgf5.1 in natural populations, it was found that Csa5G021320 is the candidate gene of qgf5.1. Geographical distribution revealed that green flesh color formation could be due to the high latitude, which has longer day time to produce the photosynthesis and chlorophyll synthesis during cucumber domestication and evolution. CONCLUSIONS: We first reported the cucumber green flesh color is a quantitative trait. We detected two novel loci qgf5.1 and qgf3.1, which regulate the green flesh formation in cucumber. The QTL mapping and GWAS approaches identified several candidate genes for further validation using functional genomics or forward genetics approaches. Findings from the present study provide a new insight into the genetic control of green flesh in cucumber.


Assuntos
Cucumis sativus/fisiologia , Estudo de Associação Genômica Ampla , Fenótipo , Pigmentação/genética , Locos de Características Quantitativas/genética , Mapeamento Cromossômico , Cor , Cucumis sativus/genética , Redes Reguladoras de Genes/fisiologia
2.
BMC Plant Biol ; 19(1): 277, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31234776

RESUMO

BACKGROUND: The Asia lotus (Nelumbo nucifera Gaertn.) is an ornamental aquatic plant with high economic value. Flower colour is an important ornamental trait, with much of N. nucifera breeding focusing on its yellow flowers. To explore the yellow flower colouration mechanism in N. nucifera, we analysed its pigment constituents and content, as well as gene expression in the flavonoid pathway, in two N. nucifera cultivars. RESULTS: We performed metabolomic and gene expression analyses in two N. nucifera cultivars with yellow and white flowers, Molinqiuse (MLQS) and Yeguangbei (YGB), respectively, at five stages of flower colouration. Based on phenotypic observation and metabolite analyses, the later stages of flower colouration (S3-S5) were determined to be key periods for differences between MLQS and YGB, with dihydroflavonols and flavonols differing significantly between cultivars. Dihydroquercetin, dihydrokaempferol, and isorhamnetin were significantly higher in MLQS than in YGB, whereas kaempferol was significantly higher in YGB. Most of the key homologous structural genes in the flavonoid pathway were significantly more active in MLQS than in YGB at stages S1-S4. CONCLUSION: In this study, we performed the first analyses of primary and secondary N. nucifera metabolites during flower colouration, and found that isorhamnetin and kaempferol shunting resulted in petal colour differences between MLQS and YGB. Based on our data integration analyses of key enzyme expression in the putative flavonoid pathways of the two N. nucifera cultivars, NnFLS gene substrate specificity and differential expression of NnOMTs may be related to petal colour differences between MLQS and YGB. These results will contribute to determining the mechanism of yellow flower colouration in N. nucifera, and will improve yellow petal colour breeding in lotus species.


Assuntos
Flavonoides/metabolismo , Flores/genética , Nelumbo/metabolismo , Pigmentação/genética , Perfilação da Expressão Gênica , Genes de Plantas , Quempferóis/metabolismo , Metaboloma , Metiltransferases/genética , Nelumbo/enzimologia , Nelumbo/genética , Quercetina/análogos & derivados , Quercetina/metabolismo , Especificidade da Espécie
3.
BMC Plant Biol ; 19(1): 228, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146678

RESUMO

BACKGROUND: Some broccoli (Brassica oleracea L. italic) accessions have purple sepals and cold weather would deepen the purple color, while the sepals of other broccoli lines are always green even in cold winter. The related locus or gene is still unknown. In this study, a high-density genetic map was constructed based on specific locus amplified fragment (SLAF) sequencing in a doubled-haploid segregation population with 127 individuals. And mapping of the purple sepal trait in flower heads based on phenotypic data collected during three seasons was performed. RESULTS: A genetic map was constructed, which contained 6694 SLAF markers with an average sequencing depth of 81.37-fold in the maternal line, 84-fold in the paternal line, and 15.76-fold in each individual population studied. In all of the annual data recorded, three quantitative trait loci (QTLs) were identified that were all distributed within the linkage group (LG) 1. Among them, a major locus, qPH.C01-2, located at 36.393 cM LG1, was consistently detected in all analysis. Besides this locus, another two minor loci, qPH.C01-4 and qPH.C01-5, were identified near qPH.C01-2, based on the phenotypic data from spring of 2018. CONCLUSION: The purple sepal trait could be controlled by a major single locus and two minor loci. The genetic map and location of the purple sepal trait of flower heads provide an important foundation for mapping other compound traits and the identification of the genes related to purple sepal trait in broccoli.


Assuntos
Brassica/fisiologia , Inflorescência/fisiologia , Pigmentação/genética , Locos de Características Quantitativas , Brassica/genética , Mapeamento Cromossômico , Inflorescência/genética
4.
BMC Plant Biol ; 19(1): 240, 2019 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-31170934

RESUMO

BACKGROUND: Red maple (Acer rubrum L.) is one of the most common and widespread trees with colorful leaves. We found a mutant with red, yellow, and green leaf phenotypes in different branches, which provided ideal materials with the same genetic relationship, and little interference from the environment, for the study of complex metabolic networks that underly variations in the coloration of leaves. We applied a combination of NGS and SMRT sequencing to various red maple tissues. RESULTS: A total of 125,448 unigenes were obtained, of which 46 and 69 were thought to be related to the synthesis of anthocyanins and carotenoids, respectively. In addition, 88 unigenes were presumed to be involved in the chlorophyll metabolic pathway. Based on a comprehensive analysis of the pigment gene expression network, the mechanisms of leaf color were investigated. The massive accumulation of Cy led to its higher content and proportion than other pigments, which caused the redness of leaves. Yellow coloration was the result of the complete decomposition of chlorophyll pigments, the unmasking of carotenoid pigments, and a slight accumulation of Cy. CONCLUSIONS: This study provides a systematic analysis of color variations in the red maple. Moreover, mass sequence data obtained by deep sequencing will provide references for the controlled breeding of red maple.


Assuntos
Acer/fisiologia , Perfilação da Expressão Gênica/instrumentação , Pigmentação/genética , Transcriptoma , Acer/genética , Acer/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/fisiologia
5.
Zoology (Jena) ; 134: 66-68, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31146908

RESUMO

Color patterns are a fascinating organismal feature and play key roles in several fundamental ecological and evolutionary processes. They give important insights into the process of phenotypic divergence. Color patterns also provide striking examples of convergence, the independent evolution of phenotypic similarities. In the era of genome sequencing and editing it is now increasingly possible to study divergence and convergence from a molecular perspective. Recent work in cichlid fishes suggests independent genetic changes at the same genomic locus as the cause for the parallel losses and gains of stripe color patterns. Together with evidence from other animal groups, a picture emerges whereby independent mutations at genomic hotspots associate with both the divergent and convergent evolution of genetically and physiologically distinct color pattern phenotypes such as stripe patterns and countershading.


Assuntos
Ciclídeos/fisiologia , Pigmentação/genética , Animais , Ciclídeos/genética , Genômica , Lagos , Mutação , Pigmentos Biológicos , Especificidade da Espécie
6.
Plant Mol Biol ; 100(6): 647-658, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31154655

RESUMO

KEY MESSAGE: Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development. Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3' region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development.


Assuntos
Lycopersicon esculentum/metabolismo , Pigmentação/genética , Proteínas de Plantas/metabolismo , Processamento Alternativo , Carotenoides/metabolismo , Mapeamento Cromossômico , Clonagem Molecular , Cor , DNA Complementar/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genes Recessivos , Teste de Complementação Genética , Genótipo , Lycopersicon esculentum/genética , Mutação , Proteínas de Plantas/genética , Trans-Splicing
7.
Appl Microbiol Biotechnol ; 103(12): 4889-4897, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31037381

RESUMO

Conidia are asexual spores and play a crucial role in fungal dissemination. Conidial pigmentation is important for tolerance against UV radiation and contributes to survival of fungi. The molecular basis of conidial pigmentation has been studied in several fungal species. In spite of sharing the initial common step of polyketide formation, other steps for pigment biosynthesis appear to be species-dependent. In this study, we isolated an Aspergillus flavus spontaneous mutant that produced yellow conidia. The underlying genetic defect, a three-nucleotide in-frame deletion in the gene, AFLA_051390, that encodes a copper-transporting ATPase, was identified by a comparative genomics approach. This genetic association was confirmed by disruption of the wild-type gene. When yellow mutants were grown on medium supplemented with copper ions or chloride ions, green conidial color was partially and nearly completely restored, respectively. Further disruption of AFLA_045660, an orthologue of Aspergillus nidulans yA (yellow pigment) that encodes a multicopper oxidase, in wild type and a derived strain producing dark green conidia showed that it yielded mutants that produced gold conidia. The results placed formation of the gold pigment after that of the yellow pigment and before that of the dark green pigment. Using reported inhibitors of DHN-melanin (tricyclazole and phthalide) and DOPA-melanin (tropolone and kojic acid) pathways on a set of conidial color mutants, we investigated the involvement of melanin biosynthesis in A. flavus conidial pigment formation. Results imply that both pathways have no bearing on conidial pigment biosynthesis of A. flavus.


Assuntos
Aspergillus flavus/enzimologia , ATPases Transportadoras de Cobre/metabolismo , Proteínas Fúngicas/metabolismo , Pigmentos Biológicos/biossíntese , Esporos Fúngicos/enzimologia , Aspergillus flavus/genética , ATPases Transportadoras de Cobre/genética , Proteínas Fúngicas/genética , Deleção de Genes , Genômica , Melaninas/biossíntese , Mutação , Oxirredutases/metabolismo , Pigmentação/genética , Esporos Fúngicos/genética
8.
Genet Sel Evol ; 51(1): 12, 2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30987584

RESUMO

BACKGROUND: In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn-2/beige mutation (assumed to be caused by a different structural modification). RESULTS: For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the ASIP gene. Thus, we hypothesize that the 5' region of the ITCH-ASIP fusion gene leads to a higher transcription level than the 5' region of the ASIP gene. CONCLUSIONS: We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the ASIP locus. Both of the associated mutations fawn-2/beige and yellow lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of ASIP depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5' region of the ASIP gene itself has additional impacts, especially for the fawn-2/beige mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the ASIP coding sequences has been reported, which supports our hypothesis that repressors in the 5' region of ASIP are absent in the fawn-2/beige mutant.


Assuntos
Proteína Agouti Sinalizadora/genética , Pigmentação/genética , Codorniz/genética , Proteína Agouti Sinalizadora/metabolismo , Alelos , Animais , Cor , Éxons/genética , Plumas/metabolismo , Genótipo , Mutação/genética , Fenótipo , Regiões não Traduzidas/genética
9.
Nat Commun ; 10(1): 1852, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-31015412

RESUMO

Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-ß superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.


Assuntos
Tentilhões/fisiologia , Pigmentação/genética , Seleção Genética/fisiologia , Caracteres Sexuais , Cromossomos Sexuais/genética , Animais , Cor , Feminino , Folistatina/genética , Perfilação da Expressão Gênica , Loci Gênicos/fisiologia , Especiação Genética , Estudo de Associação Genômica Ampla , Genômica , Haplótipos/genética , Masculino , Preferência de Acasalamento Animal/fisiologia , Polimorfismo Genético , Sequenciamento Completo do Genoma
10.
Genome Biol ; 20(1): 64, 2019 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-30935422

RESUMO

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.


Assuntos
Evolução Molecular , Genoma de Inseto , Hemípteros/genética , Sequência de Aminoácidos , Animais , Dedos de Zinco CYS2-HIS2 , Comportamento Alimentar , Dosagem de Genes , Perfilação da Expressão Gênica , Transferência Genética Horizontal , Genes Homeobox , Hemípteros/crescimento & desenvolvimento , Hemípteros/metabolismo , Pigmentação/genética , Olfato , Fatores de Transcrição/genética
11.
Plant Physiol Biochem ; 138: 130-139, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30870763

RESUMO

The flower color of Paeonia 'Coral Sunset' and 'Pink Hawaiian Coral' changes from coral to pink to pale yellow during flowering, which confers high ornamental value to these two cultivars. However, the molecular mechanism underlying flower color change is still unclear. In this study, flavonoids in petals of Paeonia 'Coral Sunset' and 'Pink Hawaiian Coral' at seven flowering stages were analyzed to explore the effects of the flavonoid component on changes in flower color. In addition, four cDNA libraries of 'Coral Sunset' during the critical blooming stages were constructed and the transcriptome was sequenced to investigate the molecular mechanism underlying changes to flower color. Two anthocyanins (cyanidin-3,5-di-O-glucoside and peonidin-3,5-di-O-glucoside) were detected in both cultivars. Total anthocyanin content in both cultivars accumulated continuously from stages 1-3 and then decreased sharply. Correlation analysis showed that the change in flower color from coral to pink to pale yellow is due to a significant decrease in anthocyanin content. A total of 91,583 Unigenes were obtained in 'Coral Sunset', 33,962 (37.08%) of which were annotated to major databases. Based on the enrichment analysis of differentially expressed genes, eight structural genes (CHS, F3H, F3'H, FLS, DRF, ANS, ANR and UFGT) and 13 transcription factors (five MYB, three bHLH, one WD40, one HY5, one PIF3, one COP1 and two PHY) related to flavonoid biosynthesis were screened. The qRT-PCR results were generally consistent with the high-throughput sequencing results. This research will provide a foundation to clarify the mechanisms underlying changes in flower color of herbaceous peony.


Assuntos
Antocianinas , Flores , Perfilação da Expressão Gênica , Genes de Plantas , Paeonia , Pigmentação/genética , Pigmentos Biológicos , Antocianinas/biossíntese , Antocianinas/genética , Flores/genética , Flores/metabolismo , Paeonia/genética , Paeonia/metabolismo , Pigmentos Biológicos/biossíntese , Pigmentos Biológicos/genética
12.
Arch Insect Biochem Physiol ; 101(1): e21546, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30908737

RESUMO

The gene vermilion encodes tryptophan 2,3-dioxygenase, part of the ommochrome pathway, and is responsible for the dark pigmented eyes in some insects, including beetles. Using RNA interference, we targeted the vermilion gene ortholog in embryos and pupae of the yellow mealworm, Tenebrio molitor, resulting in larvae and adults, respectively, that lacked eye pigment. RNA-Seq was used to analyze the impact of vermilion-specific RNA interference on gene expression. There was a 425-fold reduction in vermilion gene expression (p = 0.0003), as well as significant (p < 0.05) differential expression of 109 other putative genes, most of which were downregulated. Enrichment analysis of Gene Ontology terms found in the differentially expressed data set included genes known to be involved in the ommochrome pathway. However, enrichment analysis also revealed the influence of vermilion expression on genes involved in protein translocation to the endoplasmic reticulum, signal transduction, G-protein-coupled receptor signaling, cell-cycle arrest, mannose biosynthesis, and vitamin transport. These data demonstrate that knockdown of vermilion in T. molitor results in complete loss of eye color (white-eyed phenotype) and identify other interrelated genes in the vermilion metabolic pathway. Therefore, a dominant marker system based on eye color can be developed for the genetic manipulation of T. molitor to increase the value of mealworms as an alternative food source by decreasing negative traits, such as disease susceptibility, and increasing desired traits, such as protein content and vitamin production.


Assuntos
Tenebrio/genética , Triptofano Oxigenase/genética , Criação de Animais Domésticos , Animais , Cor de Olho/genética , Expressão Gênica , Marcadores Genéticos , Proteínas de Insetos/genética , Proteínas de Insetos/metabolismo , Larva/genética , Pigmentação/genética , Pupa/genética , Interferência de RNA , Tenebrio/enzimologia , Tenebrio/crescimento & desenvolvimento
13.
Genetics ; 212(1): 343-360, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30842209

RESUMO

Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5' intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.


Assuntos
Proteínas de Drosophila/genética , Drosophila/genética , Elementos Facilitadores Genéticos , Evolução Molecular , Animais , Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Pigmentação/genética , Especificidade da Espécie
14.
Molecules ; 24(6)2019 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-30889908

RESUMO

Almost all flowers of the tea plant (Camellia sinensis) are white, which has caused few researchers to pay attention to anthocyanin accumulation and color changing in tea flowers. A new purple-leaf cultivar, Baitang purple tea (BTP) was discovered in the Baitang Mountains of Guangdong, whose flowers are naturally pink, and can provide an opportunity to understand anthocyanin metabolic networks and flower color development in tea flowers. In the present study, twelve anthocyanin components were identified in the pink tea flowers, namely cyanidin O-syringic acid, petunidin 3-O-glucoside, pelargonidin 3-O-beta-d-glucoside, which marks the first time these compounds have been found in the tea flowers. The presence of these anthocyanins seem most likely to be the reason for the pink coloration of the flowers. Twenty-one differentially expressed genes (DEGs) involved in anthocyanin pathway were identified using KEGG pathway functional enrichment, and ten of these DEG's screened using venn and KEGG functional enrichment analysis during five subsequent stages of flower development. By comparing DEGs and their expression levels across multiple flower development stages, we found that anthocyanin biosynthesis and accumulation in BTP flowers mainly occurred between the third and fourth stages (BTP3 to BTP4). Particularly, during the period of peak anthocyanin synthesis 17 structural genes were upregulated, and four structural genes were downregulated only. Ultimately, eight critical genes were identified using weighted gene co-expression network analysis (WGCNA), which were found to have direct impact on biosynthesis and accumulation of three flavonoid compounds, namely cyanidin 3-O-glucoside, petunidin 3-O-glucoside and epicatechin gallate. These results provide useful information about the molecular mechanisms of coloration in rare pink tea flower of anthocyanin-rich tea, enriching the gene resource and guiding further research on anthocyanin accumulation in purple tea.


Assuntos
Antocianinas/metabolismo , Camellia sinensis/genética , Camellia sinensis/metabolismo , Flores/metabolismo , Metaboloma/genética , Pigmentação/genética , Análise de Sequência de RNA , Transcriptoma/genética , Vias Biossintéticas/genética , Análise Discriminante , Flores/genética , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Genes de Plantas , Análise dos Mínimos Quadrados , Anotação de Sequência Molecular , Análise de Componente Principal , Reprodutibilidade dos Testes
15.
Mar Biotechnol (NY) ; 21(3): 384-395, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30863905

RESUMO

Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.


Assuntos
Pigmentação/genética , Locos de Características Quantitativas/genética , Tilápia/genética , Animais , Aquicultura , Cruzamento , Estudo de Associação Genômica Ampla , Fenótipo
16.
Nat Ecol Evol ; 3(4): 657-667, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30833758

RESUMO

Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets-a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.


Assuntos
Peixes/genética , Pigmentação/genética , Visão Ocular/genética , Animais , Cromossomos , Cor , Especiação Genética , Genoma
17.
Proc Natl Acad Sci U S A ; 116(12): 5633-5642, 2019 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-30819892

RESUMO

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.


Assuntos
Lagartos/genética , Pigmentação da Pele/genética , Oxirredutases do Álcool/genética , Oxirredutases do Álcool/fisiologia , Animais , Carotenoides/genética , Carotenoides/metabolismo , Cor , Dioxigenases/genética , Lagartos/metabolismo , Pigmentação/genética , Polimorfismo Genético/genética , Pterinas/metabolismo
18.
Int J Mol Sci ; 20(3)2019 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-30704122

RESUMO

Ornamental kale is a popular decorative plant. We identified a peculiar bicolor leaf double haploid line, with green margins and red centers. The development of bicolor leaves can be divided into three stages: S1, S2, and S3. To probe the reason for bicolor formation, we analyzed the anthocyanin and chlorophyll contents, detected the changes in indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellin 3 (GA3), sugar, and starch contents, and identified the differentially expressed genes (DEGs) using RNA-seq. Results showed that the bicolor leaf phenotype is gradually formed with anthocyanin degrading and chlorophyll accumulation. Anthocyanin content is lower in the green margin (S3_S) than in the red center (S3_C) part at S3. IAA content was positively correlated with anthocyanin content during the bicolor leaf development. During anthocyanin degrading from S1 to S2, cinnamate-4-hydroxylase (C4H) and transport inhibitor response 1 (TIR1) were downregulated, while lateral organ boundaries domain 39 (LBD39) was upregulated. Two peroxidases, two ß-glucosidases (BGLU), LBD39, LBD37, detoxifying efflux carrier 35 (DTX35), three no apical meristem (NAC) transcription factors (TFs), and 15 WRKY DNA-binding protein (WRKY) TFs were downregulated in S3_S vs. S3_C. The bicolor phenotype was mainly linked to anthocyanin degrading and chlorophyll accumulation, and that anthocyanin degrading resulted from reduced anthocyanin biosynthesis and increased anthocyanin degradation.


Assuntos
Antocianinas/metabolismo , Brassica/metabolismo , Clorofila/metabolismo , Pigmentação/fisiologia , Folhas de Planta/metabolismo , Brassica/genética , Brassica/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Pigmentação/genética , Proteínas de Plantas/metabolismo , Transcriptoma/genética , Transcriptoma/fisiologia
19.
Molecules ; 24(3)2019 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-30744185

RESUMO

Sampling for DUS test of flower colors should be fixed at the stages and sites that petals are fully colored, and besides, flower colorations are uniform among individuals and stable for a period of time to allow testers to get consistent results. It remains a problem since spatial and temporal flower colorations are reported a lot but their change traits are little discussed. In this study, expression state, uniformity and stability of color phenotypes, anthocyanin contents, and gene expression levels were taken into account based on measurements at 12 development stages and three layers (inner, middle, and outer petals) of two varieties of Ranunculus asiaticus L. to get their best sampling. Our results showed that, outer petals of L9⁻L10 (stage 9⁻stage 10 of variety 'Jiaoyan zhuanhong') and C5⁻C6 (stage 5⁻stage 6 of variety 'Jiaoyan yanghong') were the best sampling, respectively. For DUS test, it is suggested to track flower colorations continuously to get the best sampling as well as representative colors since different cultivars had different change traits, and moreover, full expression of color phenotypes came later and lasted for a shorter duration than those of anthocyanin contents and gene expressions. Our innovation exists in following two points. Firstly, a model of change dynamic was introduced to illustrate the change traits of flower colorations, anthocyanin contents, and gene expressions. Secondly, genes used for expression analysis were screened on account of tentative anthocyanins, which were identified based on comparison between liquid chromatography⁻mass spectrometry (LC⁻MS) results and molecular mass and mass fragment pattern (M²) of each putative anthocyanin and their fragments deduced in our previous study. Gene screening in this regard may also be interest for other non-model plant genera with little molecular background.


Assuntos
Flores/genética , Regulação da Expressão Gênica de Plantas , Pigmentação/genética , Ranunculus/genética , Antocianinas/metabolismo , Cromatografia Líquida de Alta Pressão , Metabolismo Energético , Flores/metabolismo , Perfilação da Expressão Gênica , Humanos , Espectrometria de Massas , Fenótipo , Característica Quantitativa Herdável , Ranunculus/metabolismo
20.
BMC Genomics ; 20(1): 117, 2019 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-30732560

RESUMO

BACKGROUND: Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and its mutants. RESULTS: Using bisulfite sequencing (BS-Seq) and RNA-sequencing (RNA-Seq), we analysed three deep-red-skinned apple (Malus × domestica) mutants (Yanfu 3, YF3; Yanfu 8, YF8; Shannonghong, SNH) and their lighter-skinned parents (Nagafu 2, NF2; Yanfu 3, YF3; Ralls, RL) to explore the different changes in methylation patterns associated with anthocyanin concentrations. We identified 13,405, 13,384, and 10,925 differentially methylated regions (DMRs) and 1987, 956, and 1180 differentially expressed genes (DEGs) in the NF2/YF3, YF3/YF8, and RL/SNH comparisons, respectively. And we found two DMR-associated DEGs involved in the anthocyanin pathway: ANS (MD06G1071600) and F3H (MD05G1074200). These genes exhibited upregulated expression in apple mutants, and differences were observed in the methylation patterns of their promoters. These results suggested that both the regulatory and structural genes may be modified by DNA methylation in the anthocyanin pathway. However, the methylation of structural genes was not the primary reason for expression-level changes. The expression of structural genes may be synergistically regulated by transcription factors and methylation changes. Additionally, the expression of the transcription factor gene MYB114 (MD17G1261100) was upregulated in the deep-red-skinned apple. CONCLUSION: Through the analysis of global methylation and transcription, we did not find the correlation between gene expression and the DNA methylation. However, we observed that the upregulated expression of ANS (MD06G1071600) and F3H (MD05G1074200) in apple mutants results in increased anthocyanin contents. Moreover, MYB114 (MD17G1261100) is likely another regulatory gene involved in apple coloration. Our data provided a new understanding about the differences in formation of apple colour mutants.


Assuntos
Metilação de DNA/genética , Frutas/metabolismo , Perfilação da Expressão Gênica , Malus/genética , Mutação , Fenótipo , Pigmentação/genética , Antocianinas/metabolismo , Frutas/genética , Genômica , Malus/metabolismo
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