scholarly journals Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shuaifei Feng ◽  
Xiaoyong Du ◽  
Chao Wang ◽  
Dengdeng Ye ◽  
Guanjun Ma ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Comparison Group ◽  
Bone Development ◽  
Expression Patterns ◽  
Osteoclast Differentiation ◽  
Economic Losses ◽  
Mineral Absorption ◽  
Cartilage Development

Cartilage dysplasia is one of the important reasons for the weakness of pig limbs and hooves. Porcine rickets with weak limbs and hooves bring huge economic losses to the pig industry. However, research on the development of pig cartilage is lacking. This study investigated the key genes and molecular mechanisms involved in cartilage development via an RNA-seq technique. Samples of proximal tibia cartilage were collected from three normal piglets with 1 day, 14 days, and 28 days of age, respectively, and then these samples were divided into two comparison groups (1-day vs. 14-day group, 14-day vs. 28-day group). Through the transcriptome analysis, 108 differentially expressed genes (DEGs), such as FORL2, were obtained from 1-day vs. 14-day comparison group, and 3602 DEGs were obtained from 14-day vs. 28-day comparison group, including SOX9, BMP6, and MMP13. The gene ontology (GO) functional and KEGG pathway enrichment revealed that many functions of DEGs were related to bone development. The pathways of DEGs from Day 1 vs. Day 14 were mainly enriched in mineral absorption, but the DEGs of Day 14 vs. Day 28 were enriched in osteoclast differentiation. Then, the expression patterns of six candidate genes were verified via qPCR. In conclusion, candidate genes affecting cartilage development in Yorkshire pigs were obtained by transcriptome analysis, and the clues showed that Day 14 to Day 28 is a more active and extensive period in cartilage developments, which played a key role in revealing the molecular mechanism of pig cartilage development basis, also compensating for vacancies in cartilage research.

scholarly journals Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zihan Liu ◽  
Sha Li ◽  
Wei Li ◽  
Qi Liu ◽  
Lingli Zhang ◽  
...  
Keyword(s):  
Male Sterility ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Interaction Mechanism ◽  
Outer Wall ◽  
Comparative Transcriptome ◽  
Male Sterile ◽  
Comparative Transcriptome Analysis ◽  
The Impact

Abstract Background Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular mechanisms related to anther abortion in wheat, which remain unclear at present. Results In this study, five isonuclear alloplasmic male sterile lines (IAMSLs) and their maintainer were investigated. Cytological analysis indicated that the abortion type was identical in IAMSLs, typical and stainable abortion, and the key abortive period was in the binucleate stage. Most of the 1,281 core shared differentially expressed genes identified by transcriptome sequencing compared with the maintainer in the vital abortive stage were involved in the metabolism of sugars, oxidative phosphorylation, phenylpropane biosynthesis, and phosphatidylinositol signaling, and they were downregulated in the IAMSLs. Key candidate genes encoding chalcone--flavonone isomerase, pectinesterase, and UDP-glucose pyrophosphorylase were screened and identified. Moreover, further verification elucidated that due to the impact of downregulated genes in these pathways, the male sterile anthers were deficient in sugar and energy, with excessive accumulations of ROS, blocked sporopollenin synthesis, and abnormal tapetum degradation. Conclusions Through comparative transcriptome analysis, an intriguing core transcriptome-mediated male-sterility network was proposed and constructed for wheat and inferred that the downregulation of genes in important pathways may ultimately stunt the formation of the pollen outer wall in IAMSLs. These findings provide insights for predicting the functions of the candidate genes, and the comprehensive analysis of our results was helpful for studying the abortive interaction mechanism in CMS wheat.

scholarly journals Transcriptome Analysis of Watermelon Leaves Reveals Candidate Genes Responsive to Cucumber green mottle mosaic virus Infection

2019 ◽  
Vol 20 (3) ◽  
pp. 610 ◽  
Author(s):  
Yuyan Sun ◽  
Min Fan ◽  
Yanjun He
Keyword(s):  
Mosaic Virus ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Pcr Analysis ◽  
Whole Plant ◽  
Plant Pathogen Interactions ◽  
Differently Expressed Genes

Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, which cause diseases in cucurbits, especially watermelon. In watermelon, symptoms develop on the whole plant, including leaves, stems, peduncles, and fruit. To better understand the molecular mechanisms of watermelon early responses to CGMMV infection, a comparative transcriptome analysis of 24 h CGMMV-infected and mock-inoculated watermelon leaves was performed. A total of 1641 differently expressed genes (DEGs) were identified, with 886 DEGs upregulated and 755 DEGs downregulated after CGMMV infection. A functional analysis indicated that the DEGs were involved in photosynthesis, plant–pathogen interactions, secondary metabolism, and plant hormone signal transduction. In addition, a few transcription factor families, including WRKY, MYB, HLH, bZIP and NAC, were responsive to the CGMMV-induced stress. To confirm the high-throughput sequencing results, 15 DEGs were validated by qRT-PCR analysis. The results provide insights into the identification of candidate genes or pathways involved in the responses of watermelon leaves to CGMMV infection.

scholarly journals Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1066
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Temperature ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gossypium Barbadense ◽  
Fiber Development ◽  
Potential Candidate ◽  
Fiber Initiation

Gossypium barbadense is an important source of natural textile fibers, as is Gossypium hirsutum. Cotton fiber development is often affected by various environmental factors, such as abnormal temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation. In this study, we reveal that high temperatures (HT) accelerate fiber development, improve fiber quality, and induced fuzz initiation of a thermo-sensitive G. barbadense variety L7009. It was proved that fuzz initiation was inhibited by low temperature (LT), and 4 dpa was the stage most susceptible to temperature stress during the fuzz initiation period. A total of 43,826 differentially expressed genes (DEGs) were identified through comparative transcriptome analysis. Of these, 9667 were involved in fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were potentially involved in fuzz initiation induced by high temperature. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barbadense.

scholarly journals Genomic architecture of biomass heterosis inArabidopsis

2017 ◽  
Vol 114 (30) ◽  
pp. 8101-8106 ◽  
Author(s):  
Mei Yang ◽  
Xuncheng Wang ◽  
Diqiu Ren ◽  
Hao Huang ◽  
Miqi Xu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Expression Patterns ◽  
Natural Populations ◽  
Genome Wide Association Studies ◽  
Genomic Architecture ◽  
Genome Wide ◽  
Stimulus Responsive ◽  
Abiotic Stimuli

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200Arabidopsishybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates includeWUSCHEL,ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representativeArabidopsishybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis inArabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.

scholarly journals Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules

2018 ◽  
Vol 19 (10) ◽  
pp. 2924 ◽  
Author(s):  
Yingbin Xue ◽  
Qingli Zhuang ◽  
Shengnan Zhu ◽  
Bixian Xiao ◽  
Cuiyue Liang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Transcriptional Regulatory Network ◽  
Phosphorus Deficiency ◽  
Expression Patterns ◽  
P Deficiency ◽  
Pi Homeostasis ◽  
Genome Wide ◽  
Pi Starvation ◽  
Soybean Nodule

Phosphorus (P) deficiency is a major limitation for legume crop production. Although overall adaptations of plant roots to P deficiency have been extensively studied, only fragmentary information is available in regard to root nodule responses to P deficiency. In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis in soybean nodules grown under P-sufficient (500 μM KH2PO4) and P-deficient (25 μM KH2PO4) conditions to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of (differentially expressed genes) DEGs appeared to be involved in maintaining Pi homeostasis in soybean nodules, including eight Pi transporters (PTs), eight genes coding proteins containing the SYG1/PHO81/XPR1 domain (SPXs), and 16 purple acid phosphatases (PAPs). The results suggest that a complex transcriptional regulatory network participates in soybean nodule adaption to Pi starvation, most notable a Pi signaling pathway, are involved in maintaining Pi homeostasis in nodules.

scholarly journals Transcriptome Analysis of Tailfins From Grass-Goldfish And Egg-Goldfish to Identify Genes Involved in Artificial Selection for Ornamental Purposes

2021 ◽  
Author(s):  
Shu-yan Wang ◽  
Nai-yi Liu ◽  
Jie Fang
Keyword(s):  
Artificial Selection ◽  
Transcriptome Analysis ◽  
Target Genes ◽  
Expression Patterns ◽  
Osteoclast Differentiation ◽  
Signalling Pathway ◽  
Axis Formation ◽  
Dorsal Fin ◽  
Homeobox Protein ◽  
Selection For

Abstract Goldfish, one of the first animals domesticated for ornamental purposes, experience huge morphological variation, of which the number changes in tailfins and the loss of dorsal fins is the most impressive due to their important functions in fish. In the present study, a transcriptome analysis of the tailfins of Grass- (with complete dorsal fin and a single tailfin), and Egg-goldfish (loss of dorsal fin and double tail fins) was carried out to determine the sequence variants, to detect differential gene expression patterns in transcriptomes, and to characterize the effects of selection and identify target genes under selection. In total, 124,808,475 and 101,965,939 high quality reads were obtained from the tailfins of Grass- and Egg-goldfish, respectively, and 114,796 unigenes were further assembled from over 33.48 Gb nucleotides. A large portion of unigenes related to various primary and secondary metabolite pathways were identified, and the differentially expressed genes (DEGs) between the tailfins from Grass- and Egg-goldfish were also generally enriched in the metabolite pathways, for instant, the PI3K−Akt signalling pathway, the MAPK signalling pathway, osteoclast differentiation, and the dorso-ventral axis formation, all relating to cell proliferation, growth, and differentiation. These identified DEGs (HOXA2b, HOXB13a, paired mesoderm homeobox protein 1-like isoform X2 (PRRX2), zinc finger E-box-binding homeobox 1-like isoform X3 (ZEB1), and homeobox protein (Meis1), presumably played an important role in the development of the double tail fins during the artificial selection for ornamental purposes.

scholarly journals Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Huini Tang ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Genetic Constitution ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

scholarly journals Comparative Transcriptome Analysis of Alpinia oxyphylla reveals Tissue-specific Expression of Flavonoid Biosynthesis Genes

2020 ◽  
Author(s):  
Bingmiao Gao
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Genetically Engineered ◽  
Flavonoid Biosynthesis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Alpinia Oxyphylla

Abstract Background: Alpinia oxyphylla is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla ; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. Methods: We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results: In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3,110 differentially expressed genes and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes (such as CHS, CHI, F3H, FLS, ANS ) associated with flavonoid biosynthesis. Conclusion: The tissue-specific expression of the genes corresponds to accumulation of flavonoids in these tissues.These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla .

Transcriptome Analysis of Low- and High-Sucrose Pear Cultivars Identifies Key Regulators of Sucrose Biosynthesis in Fruits

2020 ◽  
Vol 61 (8) ◽  
pp. 1493-1506
Author(s):  
Jiahong Lü ◽  
Xin Tao ◽  
Gaifang Yao ◽  
Shaoling Zhang ◽  
Huping Zhang
Keyword(s):  
Transcriptome Analysis ◽  
Fruit Development ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Linear Regression Analysis ◽  
Sucrose Phosphate Synthase ◽  
Sucrose Accumulation ◽  
Sucrose Content ◽  
Sucrose Biosynthesis ◽  
High Sucrose

Abstract Sucrose accumulation is one of the important factors that determine fruit enlargement and quality. Evaluation of the sugar profile of 105 pear cultivars revealed low-sucrose and high-sucrose (HS) types of pear fruits. To better understand the molecular mechanisms governing the sucrose content of pear fruits, this study performed transcriptome analysis during fruit development using low-sucrose ‘Korla’ fragrant pear and HS ‘Hosui’ pear, and a coexpression module uniquely associated with the control of high-sucrose accumulation was identified by weighted gene coexpression network analysis. These results suggested that there are seven candidate genes encoding key enzymes (fructokinase, glucose-6-phosphate isomerase, sucrose phosphate synthase and sucrose synthase) involved in sucrose biosynthesis and several transcription factors (TFs) whose expression patterns correlate with those of genes associated with sucrose biosynthesis. This correlation was confirmed by linear regression analysis between predicted gene expression and sucrose content in different pear cultivars during fruit development. This study provides insight into the molecular mechanism underlying differences in sucrose content across pear cultivars and presents candidate structural genes and TFs that could play important roles in regulating carbohydrate partitioning and sucrose accumulation.

scholarly journals Transcriptome Analysis Reveals Genes of Flooding-Tolerant and Flooding-Sensitive Rapeseeds Differentially Respond to Flooding at the Germination Stage

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 693
Author(s):  
Jijun Li ◽  
Sidra Iqbal ◽  
Yuting Zhang ◽  
Yahui Chen ◽  
Zengdong Tan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Flooding Stress ◽  
Go Enrichment ◽  
The Common ◽  
Go Enrichment Analysis ◽  
Insight Into ◽  
Germination Stage

Flooding results in significant crop yield losses due to exposure of plants to hypoxic stress. Various studies have reported the effect of flooding stress at seedling establishment or later stages. However, the molecular mechanism prevailing at the germination stage under flooding stress remains enigmatic. The present study highlights the comparative transcriptome analysis in two rapeseed lines, i.e., flooding-tolerant (Santana) and -sensitive (23651) lines under control and 6-h flooding treatments at the germination stage. A total of 1840 up-regulated and 1301 down-regulated genes were shared by both lines in response to flooding. There were 4410 differentially expressed genes (DEGs) with increased expression and 4271 DEGs with reduced expression shared in both control and flooding conditions. Gene ontology (GO) enrichment analysis revealed that “transcription regulation”, “structural constituent of cell wall”, “reactive oxygen species metabolic”, “peroxidase”, oxidoreductase”, and “antioxidant activity” were the common processes in rapeseed flooding response. In addition, the processes such as “hormone-mediated signaling pathway”, “response to organic substance response”, “motor activity”, and “microtubule-based process” are likely to confer rapeseed flooding resistance. Mclust analysis clustered DEGs into nine modules; genes in each module shared similar expression patterns and many of these genes overlapped with the top 20 DEGs in some groups. This work provides a comprehensive insight into gene responses and the regulatory network in rapeseed flooding stress and provides guidelines for probing the underlying molecular mechanisms in flooding resistance.

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