scholarly journals Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e36442 ◽  
Author(s):  
Feng Cheng ◽  
Jian Wu ◽  
Lu Fang ◽  
Silong Sun ◽  
Bo Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Dominant Gene ◽  
Gene Fractionation

Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

2010 ◽  
Vol 4 (2) ◽  
pp. 123-128 ◽  
Author(s):  
ChangKug Kim ◽  
SungHan Park ◽  
Shoshi Kikuchi ◽  
SooJin Kwon ◽  
Suhyoung Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

2020 ◽  
Author(s):  
Alexander Calderwood ◽  
Jo Hepworth ◽  
Shannon Woodhouse ◽  
Lorelei Bilham ◽  
D. Marc Jones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Detailed Comparison ◽  
Developmental Time ◽  
Floral Transition ◽  
Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

Phytochemical and Gene Expression Reveals the Antioxidant Responses to Copper Ions in Brassica rapa

2019 ◽  
Vol 39 (1) ◽  
pp. 313-323
Author(s):  
Yanan Ruan ◽  
Guangsi Ji ◽  
Jianshuang Gao ◽  
Long Ling ◽  
Hongyan Wang
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Copper Ions ◽  
Antioxidant Responses

scholarly journals Identification of Differential Gene Expression in Brassica rapa Nectaries through Expressed Sequence Tag Analysis

PLoS ONE ◽  
2010 ◽  
Vol 5 (1) ◽  
pp. e8782 ◽  
Author(s):  
Marshall Hampton ◽  
Wayne W. Xu ◽  
Brian W. Kram ◽  
Emily M. Chambers ◽  
Jerad S. Ehrnriter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Brassica Rapa ◽  
Expressed Sequence Tag ◽  
Differential Gene ◽  
Expressed Sequence Tag Analysis ◽  
Expressed Sequence

scholarly journals Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

2020 ◽  
Author(s):  
Kathleen Greenham ◽  
Ryan C. Sartor ◽  
Stevan Zorich ◽  
Ping Lou ◽  
Todd C. Mockler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Regulatory Network ◽  
Time Course ◽  
Expression Patterns ◽  
Time Of Day ◽  
Circadian Regulation ◽  
Genome Wide ◽  
Circadian Control ◽  
Gene Regulatory

AbstractAn important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Gene expression is one method for determining the activity of paralogs; however, the majority of transcript abundance data represents a static point that does not consider the spatial and temporal dynamics of the transcriptome. Studies in Arabidopsis have estimated up to 90% of the transcriptome to be under diel or circadian control depending on the condition. As a result, time of day effects on the transcriptome have major implications on how we characterize gene activity. In this study, we aimed to resolve the circadian transcriptome in the polyploid crop Brassica rapa and explore the fate of multicopy orthologs of Arabidopsis circadian regulated genes. We performed a high-resolution time course study with 2 h sampling density to capture the genes under circadian control. Strikingly, more than two-thirds of expressed genes exhibited rhythmicity indicative of circadian regulation. To compare the expression patterns of paralogous genes, we developed a program in R called DiPALM (Differential Pattern Analysis by Linear Models) that analyzes time course data to identify transcripts with significant pattern differences. Using DiPALM, we identified genome-wide divergence of expression patterns among retained paralogs. Cross-comparison with a previously generated diel drought experiment in B. rapa revealed evidence for differential drought response for these diverging paralog pairs. Using gene regulatory network models we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal additional evidence for divergence in expression between B. rapa paralogs that may be driven in part by variation in conserved non coding sequences. These findings provide new insight into the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new method for assessing paralog activity at the transcript level.SignificanceThe circadian regulation of the transcriptome leads to time of day changes in gene expression that coordinates environmental conditions with physiological responses. Brassica rapa, a morphologically diverse crop species, has undergone whole genome triplication since diverging from Arabidopsis resulting in an expansion of gene copy number. To examine how this expansion has influenced the circadian transcriptome we developed a new method for comparing gene expression patterns. This method facilitated the discovery of genome-wide expansion of expression patterns for genes present in multiple copies and divergence in temporal abiotic stress response. We find support for conserved sequences outside the gene body contributing to these expression pattern differences and ultimately generating new connections in the gene regulatory network.

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