Temporal transcriptome profiling reveals candidate genes involved in cold acclimation of Camellia japonica (Naidong)

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.

Download Full-text

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

Poultry Science ◽

10.1016/j.psj.2021.101310 ◽

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

Download Full-text

Genome-wide transcriptome profiling of black poplar ( Populus nigra L.) under boron toxicity revealed candidate genes responsible in boron uptake, transport and detoxification

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2016.09.015 ◽

2016 ◽

Vol 109 ◽

pp. 146-155 ◽

Cited By ~ 10

Author(s):

Kubilay Yıldırım ◽

Senem Uylaş

Keyword(s):

Candidate Genes ◽

Transcriptome Profiling ◽

Populus Nigra ◽

Boron Toxicity ◽

Boron Uptake ◽

Black Poplar ◽

Genome Wide

Download Full-text

Transcriptome profiling in Camellia japonica var. decumbens for the discovery of genes involved in chilling tolerance under cold stress

Annals of Forest Research ◽

10.15287/afr.2018.1311 ◽

2019 ◽

Vol 62 (1) ◽

Author(s):

Yawen Wu ◽

Markus Müller ◽

Tian Bai ◽

Shunyang Yao ◽

Oliver Gailing ◽

...

Keyword(s):

Cold Stress ◽

Transcriptome Profiling ◽

Chilling Tolerance ◽

Camellia Japonica

Download Full-text

Transcriptome profiling of cold acclimation in bermudagrass (Cynodon dactylon)

Scientia Horticulturae ◽

10.1016/j.scienta.2015.08.024 ◽

2015 ◽

Vol 194 ◽

pp. 230-236 ◽

Cited By ~ 11

Author(s):

Huisen Zhu ◽

Xiuju Yu ◽

Tao Xu ◽

Tailiang Wang ◽

Lixia Du ◽

...

Keyword(s):

Cold Acclimation ◽

Cynodon Dactylon ◽

Transcriptome Profiling

Download Full-text

Transcriptome Analysis Reveals Key Genes and Pathways Associated with Mummify Piglets

Genome ◽

10.1139/gen-2021-0026 ◽

2021 ◽

Author(s):

Shujie Wang ◽

Pingxian Wu ◽

Kai Wang ◽

Xiang Ji ◽

Dong Chen ◽

...

Keyword(s):

Candidate Genes ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Reproductive Capacity ◽

Signal Pathways ◽

Comparative Transcriptome ◽

Rna Seq ◽

Promising Candidate ◽

Pork Consumption ◽

Differential Genes

China is the country with the largest pork consumption in the world. However, the incidence of high mummify piglets (3-5%) is one of the important factors that cause the slow improvement of pig reproductive capacity, and the genetic mechanism is still unclear. This study aimed to identify candidate genes related to high mummify piglets. RNA-seq technology was used to comparative transcriptome profiling of blood from high piglets mummified and healthy sow at different stages of pregnancy (35d, 56d, 77d and 98d). A total of 137 to 420 DEGs were detected in each stage. Seven differentially expressed genes were significantly differentially expressed at various stages. IL-9R, TLR8, ABLIM3, FSH-α, ASCC1, PRKCZ, and GCK may play an important role in course of mummify piglets. The differential genes we identified between the groups were mainly enriched in immune and inflammation regulation, and others were mainly enriched in reproduction. Considering the function of candidate genes, IL-9R and TLR8 were suggested as the most promising candidate genes involved in mummify piglet traits. We speculate that during pregnancy, it may be the combined effects of the above-mentioned inflammation, immune response, and reproduction-related signal pathways that affect the occurrence of mummifying piglets, and further affect pig reproduction.

Download Full-text

A Computational Pipeline for Functional Gene Discovery

10.21203/rs.3.rs-770297/v1 ◽

2021 ◽

Author(s):

Aolani Colon ◽

Rishabh Hirday ◽

Ami Patel ◽

Amrita Poddar ◽

Emma Tuberty-Vaughan ◽

...

Keyword(s):

Candidate Genes ◽

Outer Segment ◽

Gene Discovery ◽

Immunohistochemical Analysis ◽

Transcriptome Profiling ◽

Photoreceptor Cells ◽

Functional Gene ◽

Mouse Retina ◽

Computational Pipeline ◽

Photoreceptor Outer Segment

Abstract Many computational pipelines exist for the detection of differentially expressed genes. However, computational pipelines for functional gene detection are rarely exist. We developed a new computational pipeline for functional gene identification from transcriptome profiling data. Key features of the pipeline include clustering optimization by gap statistics, gene ontology analysis for each cluster, and literature analysis for functional gene discovery. By leveraging this pipeline on RNA-seq datasets of mouse retinal development studies, we identified 14 candidate genes involved in the formation of the photoreceptor outer segment. The expression of top three candidate genes (Pde8b, Laptm4b, and Nr1h4) in the outer segment of the developing mouse retina were experimentally validated by immunohistochemical analysis. This computational pipeline can accurately predict novel functional gene for a specific biological process, e.g., the outer segment development of the photoreceptor cells in the mouse retina. This pipeline is also applicable to functional gene discovery for any other biological processes and in any other organs and tissues.

Download Full-text

Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.)

10.21203/rs.2.16981/v4 ◽

2020 ◽

Author(s):

Haishan An ◽

Jiaying Zhang ◽

Fangjie Xu ◽

Shuang Jiang ◽

Xueying Zhang

Keyword(s):

Candidate Genes ◽

Transcriptome Analysis ◽

Adventitious Root ◽

Root Formation ◽

Transcriptome Profiling ◽

Vaccinium Corymbosum ◽

Adventitious Root Formation ◽

Root Characteristics ◽

Indole Butyric Acid ◽

Root Primordium

Abstract Background: Propagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation.Results: Rooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation.Conclusions: The transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.

Download Full-text