scholarly journals Transcriptome profiling and comparison of Rhinanthus major and Rhinanthus minor reciprocal F1 hybrids during seed stratification and germination

2021 ◽  
Author(s):  
Khaled Mirzaei ◽  
Renate A. Wesselingh
Keyword(s):  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
F1 Hybrids ◽  
Rna Seq ◽  
Seed Formation ◽  
Maternal Parent ◽  
Expression Of Genes ◽  
Fitness Consequences ◽  
Hybrid Seeds ◽  
Rhinanthus Minor

Germination is a vital stage in a plants life cycle, and a different germination behavior of offspring in comparison to their parents can have fitness consequences. In studies on hybridization between Rhinanthus minor and R. major, low germination rates of F1 hybrids with R. major as the maternal parent have often been reported. In contrast, the F1m hybrid, with R. minor as the maternal parent, germinates readily and rapidly. In order to find the cause of this difference, we used RNA-Seq to obtain transcriptome profiles of F1a and F1m seeds during stratification at 4C and just after germination, after 40 days of stratification for the F1m seeds and 60 days for the F1a seeds. A comparison of the transcriptome of F1a seeds that had just germinated (60 days) with non-germinated F1a seeds after 40 and 60 days revealed 2918 and 1349 differentially expressed (DE) genes, respectively. For F1m seeds, 958 genes showed differential expression in germinated and non-germinated seeds after 40 days. The DE genes of F1a and F1m hybrids clustered into two separate groups, even though they had the same parents, and no differentially expression was found for plastid genes. Non-germinated F1a seeds had an abundance of enzymes and proteins associated with peroxidase activity, peroxiredoxin activity and nutrient reservoir activity. Expression of genes related to seed germination and seed development increased in non-germinated F1a hybrid seeds between 40 and 60 days of cold stratification. F1a seeds that had germinated showed an upregulation of genes related to the gibberellic acid-mediated signaling pathway and response to gibberellin, along with a low expression of DELLA superfamily. Although the results demonstrated strong differences in gene expression during stratification between the reciprocal hybrids, we could not identify its cause, since no plastid genes were differentially expressed. It is possible that differences in embryo development after seed formation and before stratification play a role, including epigenetic imprinting.

scholarly journals Transcriptome profiling provides new insights into florets number difference of inflorescence in lavandula angustifolia

2020 ◽  
Author(s):  
haiping hao ◽  
xiao pei zhu ◽  
Hui Li ◽  
Jian Gong ◽  
Amjad Farooq ◽  
...  
Keyword(s):  
Essential Oil ◽  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Extraction Methods ◽  
Essential Oil Composition ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Composition ◽  
Aba Metabolism ◽  
Aba Content

Abstract Background Lavender flowers essential oil had been for a variety of therapeutic and cosmetic purposes, and had been popular for centuries. The previous studies of lavender mainly focused on essential oil composition and extraction methods, ignoring the factors which affected the production of essential oils, such as the floret number. This study aims to get a deeper insight into florets number difference mechanism. Results Hormone profile showed positive correlation between ABA content and the number of florets while IAA was negatively correlated. RNA-Seq results showed that 2848 differentially expressed genes screened by comparing different florets samples in one plant. By analyzing dynamic changes of differentially expressed genes, many potentially interesting genes were identified that encoded putative regulators or key components of ABA metabolism and signaling transduction, such as NCED, PYL, PP2C, SnRK2. These genes were highlighted to reveal their importance in regulation of florets numbers. Conclusions 1. The different ABA concentrations lead to florets difference in the Lavandula angustifolia “JX-2” clusters; 2. ABA may affect the florets number by regulating IAA transport and accumulation. The results will be useful for a better understanding of the molecular mechanism on florets number difference that could be laid the foundation for molecular breeding of muti-flortes varieties.

scholarly journals Transcriptome Analysis Reveals Key Genes and Pathways Associated with Mummify Piglets

Genome ◽  
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.

scholarly journals Transcriptome Profiling of the Retained Fetal Membranes—An Insight in the Possible Pathogenesis of the Disease

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 675
Author(s):  
Joanna Jaworska ◽  
Katarzyna Ropka-Molik ◽  
Katarzyna Piórkowska ◽  
Tomasz Szmatoła ◽  
Ilona Kowalczyk-Zięba ◽  
...  
Keyword(s):  
Post Partum ◽  
Transcriptome Profiling ◽  
Biological Pathways ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Fetal Membranes ◽  
Gene Ontology Analysis ◽  
Rna Seq ◽  
Matrix Metabolism ◽  
Profound Insight

Retained fetal membranes (RFM) is one of the most common post-partum diseases of a complex etiology. Moreover, its pathogenesis is still not elucidated. Detailed transcriptomic analysis of physiological and retained placenta may bring profound insight in the pathogenesis of the disease. The aim of the study was to compare the transcriptome of the retained and physiologically released placenta as well as biological pathways and processes in order to determine the possible pathogenesis of the disease. Samples of the endometrium and the allantochorion were taken within 2 h after parturition from control mares (n = 3) and mares with RFM (n = 3). RNA sequencing was performed with the use of all samples and mRNA expression of chosen genes was validated with Real Time PCR. Analysis of RNA-seq identified 487 differentially expressed genes in the allantochorion and 261 in the endometrium of control and RFM mares (p < 0.0001). Within genes that may be important in the release of fetal membranes and were differentially expressed, our report pinpointed BGN, TIMP1, DRB, CD3E, C3, FCN3, CASP3, BCL2L1. Gene ontology analysis showed possible processes which were altered in RFM that are apoptosis, inflammatory-related processes, and extracellular matrix metabolism and might be involved in the pathogenesis of RFM. This is the first report on the transcriptome of RFM and physiologically released placenta in mares.

195 TRANSCRIPTOME PROFILING OF BOVINE ENDOMETRIUM BASED ON THE PREGNANCY OUTCOME AFTER TRANSFER OF IN VIVO-DERIVED EMBRYOS

2009 ◽  
Vol 21 (1) ◽  
pp. 196
Author(s):  
D. Salilew-Wondim ◽  
N. Ghanem ◽  
C. Grosse-Brinkhaus ◽  
A. Becker ◽  
F. Rings ◽  
...  
Keyword(s):  
Estrous Cycle ◽  
Pregnancy Outcome ◽  
Embryo Transfer ◽  
Transcriptome Profiling ◽  
R Package ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Protein Amino Acid ◽  
Expression Of Genes

Transcriptome profiling of pre-transfer cycle endometrium in relation to its ability to sustain the upcoming pregnancy may pave the way to develop or identify molecular markers that can be utilized to detect and select receptive endometrium before embryo transfer. Here, we aim to show differential expression of genes between endometrium biopsies derived from recipients during pre-transfer cycle based on the pregnancy successes after embryo transfer. For this, endometrium biopsies were taken from 56 Simmental cyclic heifers of the same age at day 7 and 14 of the estrous cycle. On the next cycle, in vivo-produced day 7 blastocysts were transferred to all animals at day 7 of the estrous cycle. Pregnancy diagnosis was done at 28, 42, and 56 days of gestation. Thirty-two cows were returned to heat after 21 days, 7 were pregnant until day 42 but no pregnancy after that, and 15 resulted in calf delivery. Subsequently, the endometrium biopsies sampled during the pre-transfer period were categorized based on the pregnancy outcome. Those endometrial biopsies taken at days 7 and 14 during the pre-transferred period from those that resulted in successful calf delivery were named as d7CD and d14CD, respectively, and those endometrial samples collected at days 7 and 14 during pre-transferred period from those groups that resulted in no pregnancy were named as d7NP and d14NP, respectively. Total RNA was extracted from 3 pools of each experimental group in 3 replicates using RNeasy mini kit (Qiagen, Hilden, Germany). A total of 12 biotin-labeled cRNA samples were hybridized on 12 bovine Affymetrix arrays (Affymetrix, Santa Clara, CA, USA) consisting of 24128 probe sets. The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis, and the data analysis was performed using LIMMA written on R package, which maintained the bioconductor. The results showed that 1130 transcripts were differentially expressed between d7CD and d7NP, of which 626 and 504 were up- and down-regulated, respectively, in d7CD. Genes that involve in regulation of transcription (PPARA, NR2F1, MYB, MYB, and CHF2) and the collagen families (COL1A1 and COL1A2) were enriched in d7CD. A total of 234 transcripts were differentially expressed between d14CD and d14NP, of which 94 and 140 were up- and down-regulated, respectively, in d14CD compared to d14NP. Transcripts involved in protein amino acid phosphorylation (MA2K6, GATM, AK3L1, and MAPK10) were found to be enriched in d14CD compared to d14NP. In conclusion, pre-transfer endometrium biopsies showed significant differences in transcriptome profile depending on the pregnancy outcome after transfer of in vivo-derived blastocysts and enable to identify transcripts related to pregnancy establishment.

Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach (Spinacia oleracea L.)

Genome ◽  
2021 ◽  
Author(s):  
Zhiyuan Liu ◽  
Haoying Wang ◽  
Zhaosheng Xu ◽  
Helong Zhang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Spinacia Oleracea ◽  
Transcriptome Profiling ◽  
Vital Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Spinacia Oleracea L

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA-sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2,278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.

scholarly journals Differentially Expressed Genes Associated with the Cabbage Yellow-Green-Leaf Mutant in the ygl-1 Mapping Interval with Recombination Suppression

2018 ◽  
Vol 19 (10) ◽  
pp. 2936 ◽  
Author(s):  
Xiaoping Liu ◽  
Hailong Yu ◽  
Fengqing Han ◽  
Zhiyuan Li ◽  
Zhiyuan Fang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Genomic Region ◽  
Differentially Expressed ◽  
Green Leaf ◽  
Rna Seq ◽  
Recombination Suppression ◽  
Leaf Mutant ◽  
Positional Mapping ◽  
Two Populations

Although the genetics and preliminary mapping of the cabbage yellow-green-leaf mutant YL-1 has been extensively studied, transcriptome profiling associated with the yellow-green-leaf mutant of YL-1 has not been discovered. Positional mapping with two populations showed that the yellow-green-leaf gene ygl-1 is located in a recombination-suppressed genomic region. Then, a bulk segregant RNA-seq (BSR) was applied to identify differentially expressed genes (DEGs) using an F3 population (YL-1 × 11-192) and a BC2 population (YL-1 × 01-20). Among the 37,286 unique genes, 5730 and 4118 DEGs were detected between the yellow-leaf and normal-leaf pools from the F3 and BC2 populations. BSR analysis with four pools greatly reduced the number of common DEGs from 4924 to 1112. In the ygl-1 gene mapping region with suppressed recombination, 43 common DEGs were identified. Five of the DEGs were related to chloroplasts, including the down-regulated Bo1g087310, Bo1g094360, and Bo1g098630 and the up-regulated Bo1g059170 and Bo1g098440. The Bo1g098440 and Bo1g098630 genes were excluded by qRT-PCR. Hence, we inferred that these three DEGs (Bo1g094360, Bo1g087310, and Bo1g059170) in the mapping interval may be tightly associated with the development of the yellow-green-leaf mutant phenotype.

scholarly journals Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 395 ◽  
Author(s):  
Yaokun Li ◽  
Lingxuan Kong ◽  
Ming Deng ◽  
Zhiquan Lian ◽  
Yinru Han ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanism ◽  
Stress Responses ◽  
Animal Health ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Ppar Signaling ◽  
Hu Sheep

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses.

scholarly journals Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260017
Author(s):  
Kai Ma ◽  
Xiang Luo ◽  
Liqun Han ◽  
Yu Zhao ◽  
Aisajan Mamat ◽  
...  
Keyword(s):  
Clock Genes ◽  
Transcriptome Profiling ◽  
Female Flower ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Flower Bud ◽  
Bud Development ◽  
Developmental Gradient ◽  
Alternatively Spliced ◽  
Flower Bud Development

Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.

scholarly journals Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

2020 ◽  
Vol 21 (3) ◽  
pp. 1080
Author(s):  
Jawahar Lal Katara ◽  
Ram Lakhan Verma ◽  
Madhuchhanda Parida ◽  
Umakanta Ngangkham ◽  
Kutubuddin Ali Molla ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Carbon Fixation ◽  
Reference Genome ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Grain Filling ◽  
Rna Seq ◽  
Kegg Pathway Analysis ◽  
Expression Of Genes ◽  
Differential Expression Of Genes

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

Sign in / Sign up

Export Citation Format

Share Document