scholarly journals Hypothalamic and Ovarian Transcriptome Profiling Reveals Potential Candidate Genes in Low and High Egg Production of White Muscovy Ducks (Cairina Moschata)

2021 ◽  
pp. 101310
Author(s):  
Bello Semiu Folaniyi ◽  
Haiping Xu ◽  
Lijin Guo ◽  
Li Kan ◽  
Zheng Ming ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Egg Production ◽  
Transcriptome Profiling ◽  
Potential Candidate ◽  
Cairina Moschata ◽  
Muscovy Ducks

scholarly journals Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Meat Quality ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Protein Protein Interaction ◽  
Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Transcriptome Profiling Analysis of Muscle Tissue Reveals Potential Candidate Genes Affecting Water Holding Capacity in Chinese Simmental Beef Cattle

2021 ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Rna Seq ◽  
Protein Protein Interaction ◽  
Water Holding

Abstract Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were subjected to RNA sequencing (RNA-seq), among which eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 1256 genes were identified as differentially expressed genes (DEGs) between two groups, of which 948 genes were up-regulated and 308 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 24 GO terms and 78 pathways. Additionally, based on protein-protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARg, MYH10, MYL2, MYPN, and TPI1) influenced WHC in accordance with previous studies, but also identified six genes (ITGAV, FGF2, THBS1, DCN, COL4A1, and TGFBR1) as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Hehe Liu ◽  
Lei Wang ◽  
Zhanbao Guo ◽  
Qian Xu ◽  
Wenlei Fan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Intake ◽  
Egg Production ◽  
Production Efficiency ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Production Traits ◽  
Pekin Ducks ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks. Results Feed conversation ratio (FCR) was positively correlated with feed intake but negatively correlated with egg-related traits, including egg weight and egg production, both phenotypically and genetically. Estimates of pedigree-based heritability were higher than 0.2 for all traits investigated, except hip-width. Based on whole-genome sequencing data, we conducted genome-wide association studies to identify genomic regions associated with these traits. In total, 11 genomic regions were associated with FCR. No genomic regions were identified as significantly associated with hip-width, total feed intake, average daily feed intake, and total egg production. Analysis of selective sweeps between mallard and Pekin ducks confirmed three of these genomic regions on chromosomes 13, 3 and 6. Within these three regions, variants in candidate genes that were in linkage disequilibrium with the GWAS leader single nucleotide polymorphisms (SNPs) (Chr13:2,196,728, P = 7.05 × 10–14; Chr3:76,991,524, P = 1.06 × 10–12; Chr6:20,356,803, P = 1.14 × 10–10) were detected. Thus, we identified 31 potential candidate genes associated with FCR, among which the strongest candidates are those that are highly expressed in tissues involved in reproduction and nervous system functions of ducks: CNTN4, CRBR, GPR63, KLHL32, FHL5, TRNT1, MANEA, NDUFAF4, and SCD. Conclusions For the first time, we report the identification of genomic regions that are associated with FCR in ducks and our results illustrate the genomic changes that occurred during their domestication and are involved in egg production efficiency.

scholarly journals Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raju Bheemanahalli ◽  
Montana Knight ◽  
Cherryl Quinones ◽  
Colleen J. Doherty ◽  
S. V. Krishna Jagadish
Keyword(s):  
Grain Size ◽  
Candidate Genes ◽  
Gene Network ◽  
Genome Wide Association ◽  
Potential Candidate ◽  
Genetic Loci ◽  
Stay Green ◽  
Yield And Quality ◽  
Genome Wide ◽  
Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

scholarly journals Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation

2016 ◽  
Vol 33 (8) ◽  
pp. 1017-1025 ◽  
Author(s):  
Erika M. Munch ◽  
Amy E. Sparks ◽  
Jesus Gonzalez Bosquet ◽  
Lane K. Christenson ◽  
Eric J. Devor ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Human Embryos ◽  
Potential Candidate ◽  
Blastocyst Formation

An Outbreak of Duck Viral Enteritis (Duck Plague) in Domestic Muscovy Ducks (Cairina moschata domesticus) in Illinois

2001 ◽  
Vol 45 (2) ◽  
pp. 522 ◽  
Author(s):  
Enzo R. Campagnolo ◽  
Monty Banerjee ◽  
Brundaban Panigrahy ◽  
Rick L. Jones
Keyword(s):  
Cairina Moschata ◽  
Viral Enteritis ◽  
Muscovy Ducks

scholarly journals SARS-CoV-2 Infection-Induced Promoter Hypomethylation as an Epigenetic Modulator of Heat Shock Protein A1L (HSPA1L) Gene

2021 ◽  
Vol 12 ◽  
Author(s):  
Jibran Sualeh Muhammad ◽  
Narjes Saheb Sharif-Askari ◽  
Zheng-Guo Cui ◽  
Mawieh Hamad ◽  
Rabih Halwani
Keyword(s):  
Epithelial Cells ◽  
Mrna Expression ◽  
Candidate Genes ◽  
Epigenetic Regulation ◽  
Dna Methyltransferases ◽  
Lung Epithelial Cells ◽  
Potential Candidate ◽  
Blood Samples ◽  
Lung Epithelial

Numerous researches have focused on the genetic variations affecting SARS-CoV-2 infection, whereas the epigenetic effects are inadequately described. In this report, for the first time, we have identified potential candidate genes that might be regulated via SARS-CoV-2 induced DNA methylation changes in COVID-19 infection. At first, in silico transcriptomic data of COVID-19 lung autopsies were used to identify the top differentially expressed genes containing CpG Islands in their promoter region. Similar gene regulations were also observed in an in vitro model of SARS-CoV-2 infected lung epithelial cells (NHBE and A549). SARS-CoV-2 infection significantly decreased the levels of DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B) in lung epithelial cells. Out of 14 candidate genes identified, the expression of 12 genes was upregulated suggesting promoter hypomethylation, while only two genes were downregulated suggesting promoter hypermethylation in COVID-19. Among those 12 upregulated genes, only HSPA1L and ULBP2 were found to be upregulated in AZA-treated lung epithelial cells and immune cells, suggesting their epigenetic regulation. To confirm the hypomethylation of these two genes during SARS-CoV-2 infection, their promoter methylation and mRNA expression levels were determined in the genomic DNA/RNA obtained from whole blood samples of asymptomatic, severe COVID-19 patients and equally matched healthy controls. The methylation level of HSPA1L was significantly decreased and the mRNA expression was increased in both asymptomatic and severe COVID-19 blood samples suggesting its epigenetic regulation by SARS-CoV-2 infection. Functionally, HSPA1L is known to facilitate host viral replication and has been proposed as a potential target for antiviral prophylaxis and treatment.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

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