scholarly journals Differential Regulation of Anthocyanins in Cerasus humilis Fruit Color Revealed by Combined Transcriptome and Metabolome Analysis

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1065
Author(s):  
Xiaolong Ji ◽  
Jing Ren ◽  
Shaoyu Lang ◽  
Di Wang ◽  
Liwei Zhu ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Fruit Color ◽  
Metabolome Analysis ◽  
Appearance Quality ◽  
Regulation Network ◽  
Cerasus Humilis ◽  
The Relationship

Coloring is an important appearance quality of fruit. In order to evaluate the relationship between metabolites and fruit color, we analyzed the metabolites and transcriptional profiles of two different Cerasus humilis cultivars: “RF” (cv. Zhangwu, red fruit) and “YF” (cv. Nongda No.5, yellow fruit). The results of identification and quantification of metabolites showed that there were significant differences in the contents of 11 metabolites between RF and YF. Transcriptomics was used to analyze the expression patterns of genes related to the anthocyanin biosynthesis pathway, and subsequently, the regulation network of anthocyanin biosynthesis was established to explore their relationship with color formation. QRT-PCR, performed for 12 key genes, showed that the expression profiles of the differentially expressed genes were consistent with the results of the transcriptome data. A co-expression analysis revealed that the late genes were significantly positively correlated with most of the different metabolites. The results of the study provide a new reference for improving the fruit color of Cerasus humilis in the future.

scholarly journals Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1154
Author(s):  
Hongjia Zhang ◽  
Seong-Gyu Jang ◽  
San Mar Lar ◽  
Ah-Rim Lee ◽  
Fang-Yuan Cao ◽  
...  
Keyword(s):  
Gene Family ◽  
Catalytic Domain ◽  
Amylose Content ◽  
Expression Patterns ◽  
Starch Synthase ◽  
Eating Quality ◽  
Segmental Duplications ◽  
Genome Wide ◽  
The Relationship

Starch is a major ingredient in rice, and the amylose content of starch significantly impacts rice quality. OsSS (starch synthase) is a gene family related to the synthesis of amylose and amylopectin, and 10 members have been reported. In the present study, a synteny analysis of a novel family member belonging to the OsSSIV subfamily that contained a starch synthase catalytic domain showed that three segmental duplications and multiple duplications were identified in rice and other species. Expression data showed that the OsSS gene family is involved in diverse expression patterns. The prediction of miRNA targets suggested that OsSS are possibly widely regulated by miRNA functions, with miR156s targeted to OsSSII-3, especially. Haplotype analysis exhibited the relationship between amylose content and diverse genotypes. These results give new insight and a theoretical basis for the improved amylose content and eating quality of rice.

scholarly journals Dynamic Changes of the Anthocyanin Biosynthesis Mechanism During the Development of Heading Chinese Cabbage (Brassica rapa L.) and Arabidopsis Under the Control of BrMYB2

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiong He ◽  
Qianqian Lu ◽  
Yuting He ◽  
Yaxiu Wang ◽  
Ninan Zhang ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Anthocyanin Accumulation ◽  
Total Anthocyanin ◽  
Head Development ◽  
Whole Plant ◽  
Heading Chinese Cabbage ◽  
Upregulated Genes

Chinese cabbage is an important vegetable mainly planted in Asian countries, and mining the molecular mechanism responsible for purple coloration in Brassica crops is fast becoming a research hotspot. In particular, the anthocyanin accumulation characteristic of purple heading Chinese cabbage, along with the plant’s growth and head developing, is still largely unknown. To elucidate the dynamic anthocyanin biosynthesis mechanism of Chinese cabbage during its development processes, here we investigated the expression profiles of 86 anthocyanin biosynthesis genes and corresponding anthocyanin accumulation characteristics of plants as they grew and their heads developed, between purple heading Chinese cabbage 11S91 and its breeding parents. Anthocyanin accumulation of 11S91 increased from the early head formation period onward, whereas the purple trait donor 95T2-5 constantly accumulated anthocyanin throughout its whole plant development. Increasing expression levels of BrMYB2 and BrTT8 together with the downregulation of BrMYBL2.1, BrMYBL2.2, and BrLBD39.1 occurred in both 11S91 and 95T2-5 plants during their growth, accompanied by the significantly continuous upregulation of a phenylpropanoid metabolic gene, BrPAL3.1; a series of early biosynthesis genes, such as BrCHSs, BrCHIs, BrF3Hs, and BrF3’H; as well as some key late biosynthesis genes, such as BrDFR1, BrANS1, BrUF3GT2, BrUF5GT, Br5MAT, and Brp-Cout; in addition to the transport genes BrGST1 and BrGST2. Dynamic expression profiles of these upregulated genes correlated well with the total anthocyanin contents during the processes of plant growth and leaf head development, and results supported by similar evidence for structural genes were also found in the BrMYB2 transgenic Arabidopsis. After intersubspecific hybridization breeding, the purple interior heading leaves of 11S91 inherited the partial purple phenotypes from 95T2-5 while the phenotypes of seedlings and heads were mainly acquired from white 94S17; comparatively in expression patterns of investigated anthocyanin biosynthesis genes, cotyledons of 11S91 might inherit the majority of genetic information from the white type parent, whereas the growth seedlings and developing heading tissues of 11S91 featured expression patterns of these genes more similar to 95T2-5. This comprehensive set of results provides new evidence for a better understanding of the anthocyanin biosynthesis mechanism and future breeding of new purple Brassica vegetables.

scholarly journals HUBUNGAN PERSENTASE SERANGAN HAMA PENGGEREK BUAH KOPI (Hypothenemus hampei Ferr.(Coleoptera: Scolytidae)) dengan DUGAAN KEHILANGAN HASIL di KECAMATAN BETARA TANJUNG JABUNG BARAT

2016 ◽  
Vol 1 (2) ◽  
pp. 85 ◽  
Author(s):  
Hayata Hayata
Keyword(s):  
Skin Color ◽  
Linear Regression Analysis ◽  
Strong Relationship ◽  
Fruit Color ◽  
Survey Method ◽  
Production Loss ◽  
Hypothenemus Hampei ◽  
Green Beans ◽  
The Relationship

AbstractHypothenemus hampei is one of the main causes of the decrease in production and quality of coffee. The fenomena of this damage can be indicted by dwarfing fruit color changing to a reddish yellow, and finally the fall resulted in a decrease in the quantity and quality of production. This production loss was affected by the attack level of coffe pest. Symptoms of coffe pest attack (PBKo) can be identicated by its attacting form where PBKo can destroy both the unripe and ripe coffe. This research aims to know the relationship attacks Percentage the production loss due to the pest attack. Hypothenemus hampei Ferr. (Coleoptera: Scolytidae) in Betara subdistrict of Tanjung Jabung Barat regency. This research has been conducted in July–August 2016. This research using survey method with linear regression analysis i.e. regression between the percentage of attacks and the percentage of production loss. The attack percentage of PBKo pests in the Parit Panglong Betara village range between 8.20 – 17.76%. The percentage highest production loss results on red skin color coffee 7.11% and low on coffee colored skin green beans 3.95%. The percentage of PBKo pest attack had not showed a very strong relationship with the level of production loss. Keywords: Hypothenemus hampei, coffee AbstrakHypothenemus hampei merupakan salah satu penyebab utama penurunan produksi dan mutu kopi. Kerusakan yang ditimbulkannya berupa buah menjadi tidak berkembang, berubah warna menjadi kuning kemerahan dan akhirnya gugur mengakibatkan penurunan jumlah dan mutu hasil. Kehilangan hasil dipengaruhi oleh tingkat serangan hama penggerek buah kopi. Gejala serangan hama penggerek buah kopi (PBKo) dapat diketahui dari bentuk  serangan dimana PBKo dapat menggerek buah kopi yang masih muda sampai dengan yang masak. Penelitian ini bertujuan untuk mengetahui hubungan Persentase serangan dengan dugaan kehilangan hasil akibat serangan hama penggerek buah kopi Hypothenemus hampei Ferr.(Coleoptera:Scolytidae) di Kecamatan Betara Kabupaten Tanjung Jabung Barat. Penelitian dilaksanakan pada bulan Juli–Agustus 2016. Penelitian ini menggunakan metode survei dengan analisis regresi linier yaitu regresi antara persentase serangan dengan persentase kehilangan hasil. Persentase serangan hama PBKo di Desa Parit Panglong Betara berkisar antara 8,20 – 17,76 %. Persentase kehilangan hasil yang tertinggi didapatkan pada kopi yang warna kulit merah 7,11 % dan terendah pada kopi  yang berwarna kulit biji hijau 3,95 %.  Persentase serangan hama PBKo tidak memperlihatkan hubungan yang kuat dengan tingkat kehilangan hasil Kata kunci : Hypothenemus hampei, kopi

scholarly journals Differential Expression of Two Expansin Genes in Developing Fruit of Cracking-susceptible and -resistant Litchi Cultivars

2006 ◽  
Vol 131 (1) ◽  
pp. 118-121 ◽  
Author(s):  
Wang Yong ◽  
Lu Wangjin ◽  
Li Jianguo ◽  
Jiang Yueming
Keyword(s):  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Fruit Growth ◽  
Base Pairs ◽  
Fruit Cracking ◽  
Rapid Amplification ◽  
Race Pcr ◽  
The Relationship ◽  
Days After Anthesis

To understand the relationship between fruit cracking and gene expression patterns, we identified two expansin genes from litchi (Litchi chinensis Sonn.) fruit and then examined their expression profiles in pericarp and aril at different stages of fruit development, using the cracking-resistant cultivar Huaizhi and the cracking-susceptible cultivar Nuomici. Two full-length cDNAs of 1087 and 1010 base pairs encoding expansin, named LcExp1 and LcExp2, were isolated from expanding fruit using RT-PCR and RACE-PCR (rapid amplification of cDNA ends) methods. LcExp1 mRNA could be detected from the early stage of fruit rapid growth (59 days after anthesis). The LcExp1 mRNA increased and reached to the highest level at the end of growth phase (80 days after anthesis) in pericarp of `Huaizhi', while the mRNA could be detected at the stage of rapid fruit growth, then increased slightly and finally kept remained almost constant in the pericarp of `Nuomici'. Similar accumulation of LcExp2 mRNA was observed in fruit aril of `Nuomici' and `Huaizhi', whereas LcExp2 accumulated only in pericarp of `Huaizhi' but did not appear in pericarp of `Nuomici'. The results indicate that expression of two expansin genes in litchi pericarp are closely associated with fruit growth and cracking.

scholarly journals Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhao ◽  
Yonghui Liu ◽  
Lin Li ◽  
Haijun Meng ◽  
Ying Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Developmental Stage ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

scholarly journals Artificial Neural Network to Predict Varicocele Impact on Male Fertility through Testicular Endocannabinoid Gene Expression Profiles

2018 ◽  
Vol 2018 ◽  
pp. 1-15
Author(s):  
Davide Perruzza ◽  
Nicola Bernabò ◽  
Cinzia Rapino ◽  
Luca Valbonetti ◽  
Ilaria Falanga ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Artificial Neural Network ◽  
Male Fertility ◽  
Cannabinoid Receptors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Artificial Neural ◽  
The Relationship

The relationship between varicocele and fertility has always been a matter of debate because of the absence of predictive clinical indicators or molecular markers able to define the severity of this disease. Even though accumulated evidence demonstrated that the endocannabinoid system (ECS) plays a central role in male reproductive biology, particularly in the testicular compartment, to date no data point to a role for ECS in the etiopathogenesis of varicocele. Therefore, the present research has been designed to investigate the relationship between testicular ECS gene expression and fertility, using a validated animal model of experimental varicocele (VAR), taking advantage of traditional statistical approaches and artificial neural network (ANN). Experimental induction of VAR led to a clear reduction of spermatogenesis in left testes ranging from a mild (Johnsen score 7: 21%) to a severe (Johnsen score 4: 58%) damage of the germinal epithelium. However, the mean number of new-borns recorded after two sequential matings was quite variable and independent of the Johnsen score. While the gene expression of biosynthetic and degrading enzymes of AEA (NAPE-PLD and FAAH, respectively) and of 2-AG (DAGLα and MAGL, respectively), as well as their binding cannabinoid receptors (CB1 and CB2), did not change between testes and among groups, a significant downregulation of vanilloid (TRPV1) expression was recorded in left testes of VAR rats and positively correlated with animal fertility. Interestingly, an ANN trained by inserting the left and right testicular ECS gene expression profiles (inputs) was able to predict varicocele impact on male fertility in terms of mean number of new-borns delivered (outputs), with a very high accuracy (average prediction error of 1%). The present study provides unprecedented information on testicular ECS gene expression patterns during varicocele, by developing a freely available predictive ANN model that may open new perspectives in the diagnosis of varicocele-associated infertility.

scholarly journals Integrated Analysis of the Metabolome and Transcriptome on Anthocyanin Biosynthesis in Four Developmental Stages of Cerasus humilis Peel Coloration

2021 ◽  
Vol 22 (21) ◽  
pp. 11880
Author(s):  
Xiaolong Ji ◽  
Jing Ren ◽  
Yixin Zhang ◽  
Shaoyu Lang ◽  
Di Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Syringic Acid ◽  
Integrated Analysis ◽  
Fruit Peel ◽  
Cerasus Humilis ◽  
Important Trait ◽  
Anthocyanin Biosynthetic Genes

Cerasus humilis is a unique dwarf shrub and fruit color is an important trait in the species. In this study, we evaluated the transcriptomic and metabolomic profiles of the plant at different developmental stages to elucidate the mechanism underlying color formation. In a metabolomics analysis, 16 anthocyanin components were identified at four developmental stages, and high levels of cyanidin O-syringic acid and pelargonidin 3-O-beta-d-glucoside (callitephin chloride) were correlated with the reddening of the fruit peel. A co-expression analysis revealed that ANS and UFGT play key roles in pigmentation (PCC > 0.82). Additionally, transcriptome data showed that most anthocyanin biosynthetic genes and two MYB transcription factors were significantly up-regulated. QRT-PCR results for these differentially expressed genes were generally consistent with the high-throughput sequencing. Moreover, the overexpression of ChMYB1 (TRINITY_DN21536_c0_g1) in apple calli could contribute to the accumulation of anthocyanin. It was also found that UFGT (TRINITY_DN19893_c1_g5) and ChMYB1 (TRINITY_DN21536_c0_g1) have similar expression patterns. These findings provide insight into the mechanisms underlying anthocyanin accumulation and coloration during fruit peel development, providing a basis for the breeding of anthocyanin-rich C. humilis cultivars.

scholarly journals Genome-wide Identification, Evolutionary and Functional Analyses of Kfb Family Members in Potato

2022 ◽  
Author(s):  
Ruimin Tang ◽  
Haitao Dong ◽  
Liheng He ◽  
Peng Li ◽  
Yuanrui Shi ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Family Members ◽  
Structure Evolution ◽  
Duplicated Genes ◽  
Physiological Processes ◽  
Localization Analysis ◽  
And Function ◽  
Functional Mechanisms

Abstract Background: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but this family members have not been systematically identified and analyzed in potato. Results: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the KFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups according to their structural and phylogenetic features. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses. Transcriptomic and qRT-PCR analyses of StKFBs deciphered that multiple StKFB genes were differentially expressed in three colored potato tubers. Genes that were highly expressed in yellow fleshed tubers (Jin-16) and were lowly expressed in the red- (Red Rose-2) or purple-fleshed (Xisen-8) tubers, such as StKFB07, StKFB15, StKFB23, StKFB29 and StKFB44, may negatively regulate anthocyanin biosynthesis.Conclusions: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings set the stage for further study of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.

scholarly journals Integrated miRNA-mRNA analysis reveals the roles of miRNAs in the replanting benefit of Achyranthes bidentata roots

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yan Hui Yang ◽  
Ming Jie Li ◽  
Yan Jie Yi ◽  
Rui Fang Li ◽  
Cui Xiang Li ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
First Year ◽  
Achyranthes Bidentata ◽  
Yield And Quality ◽  
Post Transcriptional Regulation

AbstractThe yield and quality of the medicinal plant Achyranthes bidentata can be increased when it is replanted into a field cultivated previously with the same crop, however, fundamental aspects of its biology (so-called “replanting benefit”) still remain to be elucidated. miRNAs are sRNA molecules involved in the post-transcriptional regulation of gene expression in plant biological processes. Here, 267 conserved and 36 novel miRNAs were identified in A. bidentata roots. We compared the miRNA content of the roots (R1) from first-year planting with that of the roots (R2) of second-year replanting, and screened 21 differentially expressed (DE) miRNAs. Based on in silico functional analysis, integrated miRNA-mRNA datasets allowed the identification of 10 miRNA-target family modules, which might participate in the benefit. The expression profiles of the miRNA-target modules were potentially correlated with the presence of the replanting benefit. The indication was that the miRNA-responsive continuous monoculture could reprogram miRNA-mRNA expression patterns, which possibly promote the root growth and development, enhance its transport activity and strengthen its tolerance to various stresses, thereby improving A. bidentata productivity as observed in the replanting benefit. Our study provides basic data for further research on the molecular mechanisms of the benefit in A. bidentata.

scholarly journals Hyperglycemia Affects miRNAs Expression Pattern during Adipogenesis of Human Visceral Adipocytes—Is Memorization Involved?

Nutrients ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1774 ◽  
Author(s):  
Justyna Strycharz ◽  
Ewa Świderska ◽  
Adam Wróblewski ◽  
Marta Podolska ◽  
Piotr Czarny ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Expression Profiles ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Receptor Interaction ◽  
Cell Cycles ◽  
Chronic Hyperglycemia ◽  
Three Stages ◽  
Mirnas Expression ◽  
The Relationship

microRNAs are increasingly analyzed in adipogenesis, whose deregulation, especially visceral, contributes to the development of diabetes. Hyperglycemia is known to affect cells while occurring acutely and chronically. Therefore, we aimed to evaluate the effect of hyperglycemia on human visceral pre/adipocytes from the perspective of microRNAs. The relative expression of 78 microRNAs was determined by TaqMan Low Density Arrays at three stages of HPA-v adipogenesis conducted under normoglycemia, chronic, and intermittent hyperglycemia (30 mM). Hierarchical clustering/Pearson correlation revealed the relationship between various microRNAs’ expression profiles, while functional analysis identified the genes and signaling pathways regulated by differentially expressed microRNAs. Hyperglycemia affected microRNAs’ expression patterns during adipogenesis, and at the stage of pre-adipocytes, differentiated and matured adipocytes compared to normoglycemia. Interestingly, the changes that were evoked upon hyperglycemic exposure during one adipogenesis stage resembled those observed upon chronic hyperglycemia. At least 15 microRNAs were modulated during normoglycemic and/or hyperglycemic adipogenesis and/or upon intermittent/chronic hyperglycemia. Bioinformatics analysis revealed the involvement of these microRNAs in cell cycles, lipid metabolism, ECM–receptor interaction, oxidative stress, signaling of insulin, MAPK, TGF-β, p53, and more. The obtained data suggests that visceral pre/adipocytes exposed to chronic/intermittent hyperglycemia develop a microRNAs’ expression pattern, which may contribute to further visceral dysfunction, the progression of diabetic phenotype, and diabetic complications possibly involving “epi”-memory.

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