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 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 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 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 Temporospatial Flavonoids Metabolism Variation in Ginkgo biloba Leaves

2020 ◽  
Vol 11 ◽  
Author(s):  
Ying Guo ◽  
Tongli Wang ◽  
Fang-Fang Fu ◽  
Yousry A. El-Kassaby ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Early Stage ◽  
Sunshine Duration ◽  
Flavonoid Biosynthesis ◽  
Flavonoid Glycosides ◽  
Biosynthesis Pathway ◽  
Flavonoids Biosynthesis ◽  
Flavonoid Biosynthesis Pathway

Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.

Natural Polymorphisms in a Pair of NSP2 Homoeologs Can Cause Loss of Nodulation in Peanut

2020 ◽  
Author(s):  
Ze Peng ◽  
Huiqiong Chen ◽  
Lubin Tan ◽  
Hongmei Shu ◽  
Rajeev K Varshney ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Root Nodules ◽  
Germplasm Collection ◽  
Mendelian Inheritance ◽  
Legume Crop ◽  
Arachis Hypogaea L ◽  
Transcription Factor Genes ◽  
Cultivated Peanut ◽  
Microbial Symbiosis

Abstract Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, which is important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3 ~ 1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings provided the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results provided implications and insights into the evolution of homoeologous genes in allopolyploid species.

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