scholarly journals Transcriptomic and Metabolomic Joint Analysis Reveals Distinct Flavonoid Biosynthesis Regulation for Variegated Testa Color Development in Peanut (Arachis Hypogaea L.)

2020 ◽  
Author(s):  
Mengdie Hu ◽  
Jiawei Li ◽  
Mingyu Hou ◽  
Xiaoqing Liu ◽  
Shunli Cui ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Molecular Mechanisms ◽  
Color Difference ◽  
Flavonoid Biosynthesis ◽  
Joint Analysis ◽  
Anthocyanin Synthesis ◽  
Pigment Synthesis ◽  
Comparison Groups ◽  
Liquid Chromatography Tandem Mass ◽  
Testa Color

Abstract Peanut (Arachis hypogaea L.) is one of the important oil and economic crops, among which the variegated testa peanut is a unique member. But the molecular mechanisms underlying the pigment synthesis in variegated testa are still unclear. Differentially expressed genes (DEGs) in pigment metabolism pathway in colored area indicated there were 27 DEGs highly related to the synthesis of variegated testa color among 1,050 DEGs,which were 13 up-regulated and 14 down-regulated,consisting of 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs and 9 MYBs. GO analysis indicated DEGs were similarly enriched in 3 branches.KEGG analysis suggested flavonoid biosynthesis is the most direct metabolic pathway for the synthesis of testa variegation. The liquid chromatography tandem mass spectrometry (LC-MS/MS) results showed that cyanidin and delphinidin were the main metabolites that caused the color difference between the colored area and the non-colored area. Through the verification of 20 DEGs via qPCR, the results were consistent with that of transcriptome sequencing in 4 comparison groups. The results in this study lay the foundation for revealing the molecular regulation mechanisms of anthocyanin synthesis in variegated testa peanut.

scholarly journals Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.)

2020 ◽  
Author(s):  
Mengdie Hu ◽  
Jiawei Li ◽  
Mingyu Hou ◽  
Xiaoqing Liu ◽  
Shunli Cui ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Molecular Mechanisms ◽  
Color Difference ◽  
Flavonoid Biosynthesis ◽  
Joint Analysis ◽  
Anthocyanin Synthesis ◽  
Pigment Synthesis ◽  
Comparison Groups ◽  
Liquid Chromatography Tandem Mass ◽  
Testa Color

Abstract Peanut (Arachis hypogaea L.) is one of the important oil and economic crops, among which the variegated testa peanut is a unique member. But the molecular mechanisms underlying the pigment synthesis in variegated testa are still unclear. Differentially expressed genes (DEGs) in pigment metabolism pathway in colored area indicated there were 27 DEGs highly related to the synthesis of variegated testa color among 1,050 DEGs,which were 13 up-regulated and 14 down-regulated,consisting of 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs and 9 MYBs. GO analysis indicated DEGs were similarly enriched in 3 branches.KEGG analysis suggested flavonoid biosynthesis is the most direct metabolic pathway for the synthesis of testa variegation.The liquid chromatography tandem mass spectrometry (LC-MS/MS) results showed that cyanidin and delphinidin were the main metabolites that caused the color difference between the colored area and the non-colored area. Through the verification of 20 DEGs via qPCR, the results were consistent with that of transcriptome sequencing in 4 comparison groups. The results in this study lay the foundation for revealing the molecular regulation mechanisms of anthocyanin synthesis in variegated testa peanut.

scholarly journals Transcriptomic and metabolomic joint analysis reveals distinct flavonoid biosynthesis regulation for variegated testa color development in peanut (Arachis hypogaea L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mengdie Hu ◽  
Jiawei Li ◽  
Mingyu Hou ◽  
Xiaoqing Liu ◽  
Shunli Cui ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Flavonoid Biosynthesis ◽  
Joint Analysis ◽  
Pigment Synthesis ◽  
Color Development ◽  
Arachis Hypogaea L ◽  
Comparison Groups ◽  
Liquid Chromatography Tandem Mass ◽  
Regulation Mechanisms ◽  
Testa Color

AbstractPeanut is one of the important oil and economic crops, among which the variegated testa peanut is a unique member. The molecular mechanisms underlying the pigment synthesis in variegated testa are still unclear. Differentially expressed genes (DEGs) in the flavonoid metabolism pathway in pigmented areas indicated that there were 27 DEGs highly related to the synthesis of variegated testa color among 1,050 DEGs. Of these 27, 13 were up-regulated and 14 were down-regulated, including 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs, and 9 MYBs. GO (Gene Ontology) analysis indicated that DEGs were similarly enriched in three branches. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis suggested flavonoid biosynthesis is the most direct metabolic pathway for the synthesis of testa variegation. The liquid chromatography–tandem mass spectrometry (LC–MS/MS) results showed that cyanidin and delphinidin were the primary metabolites that caused the color differences between the pigmented and the non-pigmented areas. Through the verification of 20 DEGs via qPCR, the results were consistent with transcriptome sequencing in four comparison groups. The results in this study lay the foundation for revealing the molecular regulation mechanisms of flavonoid synthesis in variegated testa peanut.

scholarly journals Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 341
Author(s):  
Lei Zhang ◽  
Haoyun Sun ◽  
Tao Xu ◽  
Tianye Shi ◽  
Zongyun Li ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Morphological Analysis ◽  
Molecular Mechanisms ◽  
Flavonoid Biosynthesis ◽  
Phenotypic Characterization ◽  
Comparative Transcriptome ◽  
Hub Genes ◽  
Breeding Programs ◽  
Comparative Transcriptome Analysis ◽  
Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

scholarly journals Gene Expressing and sRNA Sequencing Show That Gene Differentiation Associates with a YellowAcer palmatumMutant Leaf in Different Light Conditions

2015 ◽  
Vol 2015 ◽  
pp. 1-10
Author(s):  
Shu-Shun Li ◽  
Qian-Zhong Li ◽  
Li-Ping Rong ◽  
Ling Tang ◽  
Bo Zhang
Keyword(s):  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Light Condition ◽  
Low Density ◽  
Physiological Changes ◽  
Potential Mechanism ◽  
Light Conditions ◽  
Pigment Synthesis ◽  
Leaf Coloration ◽  
Gene Expressing

Acer palmatumThunb., like other maples, is a widely ornamental-use small woody tree for leaf shapes and colors. Interestingly, we found a yellow-leaves mutant “Jingling Huangfeng” turned to green when grown in shade or low-density light condition. In order to study the potential mechanism, we performed high-throughput sequencing and obtained 1,082 DEGs in leaves grown in different light conditions that result inA. palmatumsignificant morphological and physiological changes. A total of 989 DEGs were annotated and clustered, of which many DEGs were found associating with the photosynthesis activity and pigment synthesis. The expression of CHS and FDR gene was higher while the expression of FLS gene was lower in full-sunlight condition; this may cause more colorful substance like chalcone and anthocyanin that were produced in full-light condition, thus turning the foliage to yellow. Moreover, this is the first available miRNA collection which contains 67 miRNAs ofA. palmatum, including 46 conserved miRNAs and 21 novel miRNAs. To get better understanding of which pathways these miRNAs involved, 102 Unigenes were found to be potential targets of them. These results will provide valuable genetic resources for further study on the molecular mechanisms ofAcer palmatumleaf coloration.

scholarly journals Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9859
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

2020 ◽  
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Abstract BackgroundLight plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. ResultsA total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. ConclusionsOur study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

scholarly journals PbCOP1.1 Contributes to the Negative Regulation of Anthocyanin Biosynthesis in Pear

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 39 ◽  
Author(s):  
Meng Wu ◽  
Min Si ◽  
Xieyu Li ◽  
Linyan Song ◽  
Jianlong Liu ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Pcr Analysis ◽  
Anthocyanin Synthesis ◽  
Light Signaling ◽  
Pear Fruit ◽  
Phylogenetic Tree Analysis ◽  
Expression Levels ◽  
Protein Sequence Alignment

The synthesis of anthocyanin in pear (Pyrus bretschneideri) fruit is regulated by light. However, little is known about the molecular mechanisms of pear fruit coloring mediated by upstream light-signaling regulators. Here, the photoresponse factors CONSTITUTIVE PHOTOMORPHOGENIC (COP) 1.1 and 1.2 were cloned from ‘Red Zaosu’ peel to study their functions in pear fruit coloring. The overexpression vectors pBI121-PbCOP1.1 and pBI121-PbCOP1.2 were constructed to analyze their effects on anthocyanin synthesis in pear fruit. A protein sequence alignment and phylogenetic tree analysis revealed that PbCOP1 proteins are highly homologous with those of other species. An analysis of tissue differential expression showed that the greatest expression levels of PbCOP1s occurred in the leaves. Their expression levels increased in the leaves during development, when the leaves changed from red to green. The overexpression of PbCOP1s in the peel resulted in reduced anthocyanin synthesis at the injection sites. A quantitative PCR analysis of the injection sites showed that PbCOP1.1 significantly inhibited the expression of the anthocyanin synthesis-related genes CHI, DFR, UFGT2, bHLH3, HY5 and GST. Based on the above results, we hypothesize that PbCOP1.1 is an anthocyanin synthetic inhibitory factor of pear coloration.

scholarly journals Genetic Studies Involving Wine Testa Color in Peanut1

1997 ◽  
Vol 24 (1) ◽  
pp. 60-62 ◽  
Author(s):  
W. D. Branch
Keyword(s):  
Arachis Hypogaea ◽  
Genetic Study ◽  
Genetic Studies ◽  
Arachis Hypogaea L ◽  
True Breeding ◽  
Cultivated Peanut ◽  
Testa Color ◽  
New Cultivars

Abstract A better understanding of peanut (Arachis hypogaea L.) testa color genetics would be helpful to breeders in developing new cultivars to meet U.S. market acceptability. Wine is one of the least understood of all basic testa colors in peanut. The objective of this genetic study was to gain further knowledge on the inheritance of wine testa color and possible allelic interactions. Crosses were made using two true-breeding wine testa color genotypes (Wine-Frr and PI 264549) as females with the tan testa and recessive red testa male parents Krinkle-Leaf and Makulu Red, respectively. F1, F2, and F3 data suggest no difference between the two wine testa color genotypes. Inheritance of wine testa color was found to be recessive with a one gene difference between wine and the tan testa color of Krinkle-Leaf, and with two gene differences between wine and the recessive red testa color of Makulu Red. Inheritance of wine seems to closely parallel that for recessive red testa color in the cultivated peanut.

scholarly journals Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

2019 ◽  
Vol 20 (18) ◽  
pp. 4335 ◽  
Author(s):  
Ju Gao ◽  
Gaoxing Dai ◽  
Weiyong Zhou ◽  
Haifu Liang ◽  
Juan Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Bulked Segregant Analysis ◽  
Recessive Gene ◽  
Leaf Traits ◽  
Anthocyanin Synthesis ◽  
Genetic Characteristics ◽  
Specific Organ ◽  
Flower Organs ◽  
Purple Leaf

The anthocyanin biosynthesis of rice is a major concern due to the potential nutritional value. Purple appears in various organs and tissues of rice such as pericarp, flower organs, leaves, leaf sheaths, internodes, ligules, apex, and stigma. At present, there are many studies on the color of rice pericarp, but the gene and mechanism of other organs such as leaves are still unclear, and the gene regulatory network of specific organ coloring has not been systematically understood. In this study, genetic analysis demonstrated that the purple leaf traits of rice were regulated by a recessive gene. The green leaf cultivar Y58S and purple leaf cultivar XianHongB were used to construct the mapping population. A set of near isogenicline (NIL) (BC3F1) was bred via crossing and back-crossing. The generations of BC3F2 appeared to separate four phenotypes, pl1, pl2, pl3, and pl4, due to the occurrence of a purple color in different organs. We constructed three bulked segregant analysis (BSA) pools (pl1–pl2, pl1–pl3, and pl1–pl4) by using the separated generations of BC3F5 and mapped the purple leaf gene plr4 to the vicinity of 27.9–31.1 Mb on chromosome 4. Subsequently, transcriptome sequencing (RNA-Seq) for pl3 and pl2 was used to analyze the differentially expressed genes in the localization interval, where 12 unigenes exhibited differential expression in which two genes (Os04g0577800, Os04g0616400) were downregulated. The two downregulated genes (Os04g0577800 and Os04g0616400) are possible candidate genes because of the recessive genetic characteristics of the purple leaf genes. These results will facilitate the cloning of plr4 and illustrate the molecular mechanisms of the anthocyanin synthesis pathway.

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