scholarly journals Global insights into homoeolog gene expression in upland cotton under intraspecific hybridization

2021 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Upland Cotton ◽  
Expression Patterns ◽  
Yield Potential ◽  
World Cotton ◽  
Intraspecific Hybridization ◽  
Genome Doubling ◽  
Gene Pairs ◽  
Agronomic Crops ◽  
Metabolic Genes

Abstract Background: Hybridization is useful to enhance yield potential of agronomic crops in the world. Cotton has genome doubling due to alloteraploidy process and hybridization process in coordinate with duplicated genome can produce more yield and adaptability. Therefore, expression of homoeolog gene pairs between hybrids and inbred parents are vital to characterize genetic source of heterosis in cotton.Results: Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (An average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. Conclusions: These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.

Abstract 18584: Decoding the Regulatory LncRNAs in Neonatal Heart During Perinatal Circulatory Transition

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Marlin Touma ◽  
Ashley Cass ◽  
Xuedong Kang ◽  
Yan Zhao ◽  
Reshma Biniwale ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Regulatory Function ◽  
Newborn Mouse ◽  
Protein Coding ◽  
Congenital Diseases ◽  
Gene Pairs ◽  
Neonatal Heart

Background: Fetal to neonatal transition of heart is an elaborate process, during which, neonatal cardiomyocytes undergo functional maturation and terminal exit from the cell cycle. However, transcriptome programming in neonatal cardiac chambers during perinatal stages is understudied. In particular, the changes in long non-coding RNAs (lncRNAs) in neonatal heart have not been explored. Objective: To achieve transcriptome-wide analysis of lncRNAs in neonatal left ventricle (LV) and right ventricle (RV) during maturation stages using deep RNA-Sequencing Methods: Deep RNA-sequencing was performed on male newborn mouse (C57 BL) LV and RV at 3 time points of perinatal circulatory transition: P0, P3 and P7. Reads were mapped to mouse genome (mm10). The lncRNAs annotated in NONCODE database were identified. Differentially expressed lncRNAs were defined as those with coefficient of variation ≥0.2, at a false discovery rate ≤0.05, and expressed at ≥3 RPKM in at least one sample. Correlated lncRNAs/ gene pairs were identified using Pearson’s (r2≥0.8, P≤0.05). A subset of LncRNAs/gene expression was validated using qRT-PCR. Results: Out of the 70, 983 observed unique lncRNAs, approximately 7000 were identified exhibiting significant variation during maturation windows with highly spatial-temporal dependent expression patterns, including approximately 5000 known and 2000 novel lncRNAs. Notably, 20% of these lncRNAs were located within 50 KB of a protein coding gene. Out of a total of 2400 lncRNAs/gene pairs, 10 % exhibited significantly concordant (lncRNA/gene) expression patterns. These correlated genes were significantly enriched in metabolism, cell cycle and contractility functional ontology. Interestingly, some of these lncRNAs exhibited concordance with their neighboring gene in human tissues with congenital heart defects, suggesting conserved, potentially significant, regulatory function. Conclusions: Transcriptome programming during neonatal heart maturation involves global changes in lncRNAs. Their expression concordance with neighboring protein coding genes implicates potential important regulatory role of lncRNAs in neonatal heart chamber specification and congenital diseases.

scholarly journals Differential gene expression patterns in vein regions susceptible versus resistant to neointimal hyperplasia

2018 ◽  
Vol 50 (8) ◽  
pp. 615-627
Author(s):  
Sun Hyung Kwon ◽  
Li Li ◽  
Christi M. Terry ◽  
Yan-Ting Shiu ◽  
Philip J. Moos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vein Graft ◽  
Expression Profiles ◽  
Neointimal Hyperplasia ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Yield Potential ◽  
Microarray Gene Expression ◽  
Graft Placement ◽  
Time Points

Arteriovenous hemodialysis graft (AVG) stenosis results in thrombosis and AVG failure, but prevention of stenosis has been unsuccessful due in large part to our limited understanding of the molecular processes involved in neointimal hyperplasia (NH) formation. AVG stenosis develops chiefly as a consequence of highly localized NH formation in the vein-graft anastomosis region. Surprisingly, the vein region just downstream of the vein-graft anastomosis (herein termed proximal vein region) is relatively resistant to NH. We hypothesized that the gene expression profiles of the NH-prone and NH-resistant regions will be different from each other after graft placement, and analysis of their genomic profiles may yield potential therapeutic targets to prevent AVG stenosis. To test this, we evaluated the vein-graft anastomosis (NH-prone) and proximal vein (NH-resistant) regions in a porcine model of AVG stenosis with a porcine microarray. Gene expression changes in these two distinct vein regions, relative to the gene expression in unoperated control veins, were examined at early (5 days) and later (14 days) time points following graft placement. Global genomic changes were much greater in the NH-prone region than in the NH-resistant region at both time points. In the NH-prone region, genes related to regulation of cell proliferation and osteo-/chondrogenic vascular remodeling were most enriched among the significantly upregulated genes, and genes related to smooth muscle phenotype were significantly downregulated. These results provide insights into the spatial and temporal genomic modulation underlying NH formation in AVG and suggest potential therapeutic strategies to prevent and/or limit AVG stenosis.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

scholarly journals Integrative Pan-Cancer Analysis Reveals Decreased Melatonergic Gene Expression in Carcinogenesis and RORA as a Prognostic Marker for Hepatocellular Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Yi Zou ◽  
Huaqin Sun ◽  
Yating Guo ◽  
Yidan Shi ◽  
Zhiyu Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Prognostic Marker ◽  
Nuclear Receptor ◽  
Expression Patterns ◽  
Cancer Development ◽  
Metabolic Genes ◽  
Intracellular Receptor ◽  
Cancer Types ◽  
The Relationship

BackgroundMelatonin has been shown to play a protective role in the development and progression of cancer. However, the relationship between alterations in the melatonergic microenvironment and cancer development has remained unclear.MethodsWe performed a comprehensive investigation on 12 melatonergic genes and their relevance to cancer occurrence, progression and survival by integrating multi-omics data from microarray analysis and RNA sequencing across 11 cancer types. Specifically, the 12 melatonergic genes that we investigated, which reflect the melatonergic microenvironment, included three membrane receptor genes, three nuclear receptor genes, two intracellular receptor genes, one synthetic gene, and three metabolic genes.ResultsWidely coherent underexpression of nuclear receptor genes, intracellular receptor genes, and metabolic genes was observed in cancerous samples from multiple cancer types compared to that in normal samples. Furthermore, genomic and/or epigenetic alterations partially contributed to these abnormal expression patterns in cancerous samples. Moreover, the majority of melatonergic genes had significant prognostic effects in predicting overall survival. Nevertheless, few corresponding alterations in expression were observed during cancer progression, and alterations in expression patterns varied greatly across cancer types. However, the association of melatonergic genes with one specific cancer type, hepatocellular carcinoma, identified RORA as a tumor suppressor and a prognostic marker for patients with hepatocellular carcinoma.ConclusionsOverall, our study revealed decreased melatonergic gene expression in various cancers, which may help to better elucidate the relationship between melatonin and cancer development. Taken together, our findings highlight the potential prognostic significance of melatonergic genes in various cancers.

scholarly journals Screening and analysis on the differentially expression genes between diploid and autotetraploid watermelon by using of digital gene expression profile

2019 ◽  
Vol 79 (2) ◽  
pp. 180-190 ◽  
Author(s):  
Y. L. Long ◽  
F. Qiao ◽  
X. F. Jiang ◽  
H. Q. Cong ◽  
M. L. Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Digital Gene Expression ◽  
Background Level ◽  
Global Gene Expression ◽  
Gene Expression Patterns ◽  
Protein Signaling ◽  
Genome Doubling ◽  
Digital Gene Expression Profile ◽  
Stress Related Genes

Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in ‘metabolic process’, ‘cell’ and ‘catalytic activity’. KEGG analysis revealed that these DEGs mainly cover ‘metabolic pathways’, ‘secondary metabolites’ and ‘ribosome’. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.

scholarly journals A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chao Zhou ◽  
Xiaoyun Liu ◽  
Xinglei Li ◽  
Hanlin Zhou ◽  
Sijia Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Duplication ◽  
Chromatin Condensation ◽  
Expression Patterns ◽  
Rice Genome ◽  
Genome Doubling ◽  
Autotetraploid Rice ◽  
A Genome ◽  
Ideal System ◽  
Accessible Chromatin

AbstractEvolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus. Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2019 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Comparison Groups ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background:Allopolyploids are widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger growth vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploidBrassica napus(AnAnCnCn) relative to its two diploid progenitors, B. rapa(ArAr) and B. oleracea(CoCo), after approximately7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach. Results:The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napusafter approximately7,500 years of natural domestication, andmost differentially expressed genes (DEGs) in B. napuswere downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCnvs ArArand AnAnCnCnvs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, the homoeolog expression bias and expression level dominance (ELD) inB. napuswere thoroughly studied through analysis of the expression levels of 27609 B. rapa-B. oleraceaorthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napusmaintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additivity expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulationexpression, rather than downregulationexpression,was observedin gene pairs of B. napus. Conclusions:In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napusafter approximately 7,500 years of evolution and domestication and mayenhance our understanding of allopolyploids.

scholarly journals QTL Mapping of Agronomic and Economic Traits for Four F2 Populations of Upland Cotton

2020 ◽  
Author(s):  
Hongge Li ◽  
Zhaoe Pan ◽  
Shoupu He ◽  
Yinhua Jia ◽  
Xiaoli Geng ◽  
...  
Keyword(s):  
Complex Traits ◽  
Upland Cotton ◽  
Genetic Basis ◽  
Fiber Quality ◽  
Genetic Maps ◽  
Yield Potential ◽  
High Yield ◽  
World Cotton ◽  
Economic Traits ◽  
High Yield Potential

Abstract Background: Upland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of unland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04-3 and J02-247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs). Results: Extensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 cM, 752.45 cM, 752.45 cM and 1 163.66 cM, one for each of the four F2 populations.. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B×Suyuan04-3 population. Conclusions: These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

scholarly journals Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus

2020 ◽  
Author(s):  
Mengdi Li ◽  
Ruihua Wang ◽  
Xiaoming Wu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Expression Patterns ◽  
Expression Level ◽  
Gene Expression Patterns ◽  
Homologous Gene ◽  
Gene Pairs ◽  
Expression Bias ◽  
Homoeolog Expression Bias ◽  
Expression Level Dominance

Abstract Background: Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7,500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach.Results: The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7,500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48%, 29.7% and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus.Conclusions: In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7,500 years of evolution and domestication and may enhance our understanding of allopolyploidy.

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