Genome-scale mRNA transcriptomic insights into the responses of oilseed rape (Brassica napus L.) to varying boron availabilities

Hua, Yingpeng; Feng, Yifei; Zhou, Ting; Xu, Fangsen

doi:10.1007/s11104-017-3204-2

Cited by 29 publications

(30 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA-seq was performed on an Illumina Hiseq X Ten platform (Illumina Inc., San Diego, CA, USA), which generated approximate 6.0-Gb of sequencing data with 150-bp paired-end (PE) reads for each sample. Transcript abundances (FPKM values) were determined from the RNA-seq data with the method described by Hua et al (2017) . For the gene co-expression network performed by CYTOSCAPE v. 3.2.1, cycle nodes represent genes, and the size of the nodes represents the power of the interrelation among the nodes by degree value.…”

Section: Resultsmentioning

confidence: 99%

“…A total of 27 RNA samples were subjected to an Illumina Hiseq X Ten platform (Illumina Inc., San Diego, CA, USA), which generated approximate 6.0-Gb of sequencing data with 150-bp paired-end (PE) reads for each sample. Transcript abundances (FPKM values) were determined from the RNA-seq data with the method described by Hua et al (2017) . Three independent biological replicates for each treatment were prepared for the high-throughput transcriptomic profiling.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

Hua

Zhou

Liao

et al. 2018

G3 Genes|Genomes|Genetics

Self Cite

View full text Add to dashboard Cite

Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (AnAnCnCn, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype “XY15” and an N-inefficient (lower NUE) genotype “814” of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50× depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the An and Cn subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

Hua

Zhou

Liao

et al. 2018

G3 Genes|Genomes|Genetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Considering the rapeseed cultivar of Zhongshuang 11 (a winter cultivar), having well-known information on genome sequences, is an elite genotype with high oil quality, seed production, and strong stress resistance [ 19 ], we used Zhongshuang 11 as the rapeseed lines studied in the following experiments. Rapeseed seedlings, which was originally obtained from Prof. Jin-yong Huang (jinyhuang@zzu.edu.cn, Zhengzhou University, Zhengzhou, 450,001, Henan Province, China), were hydroponically grown with Hoagland nutrient solution in an illuminated growth chamber [ 52 ]. The cultivated conditions were set according to the report by Hua et al [ 52 ].…”

Section: Methodsmentioning

confidence: 99%

“…Rapeseed seedlings, which was originally obtained from Prof. Jin-yong Huang (jinyhuang@zzu.edu.cn, Zhengzhou University, Zhengzhou, 450,001, Henan Province, China), were hydroponically grown with Hoagland nutrient solution in an illuminated growth chamber [ 52 ]. The cultivated conditions were set according to the report by Hua et al [ 52 ].…”

Section: Methodsmentioning

confidence: 99%

Comprehensive dissection into morpho-physiologic responses, ionomic homeostasis, and transcriptomic profiling reveals the systematic resistance of allotetraploid rapeseed to salinity

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background Salinity severely inhibit crop growth, yield, and quality worldwide. Allotetraploid rapeseed (Brassica napus L.), a major glycophyte oil crop, is susceptible to salinity. Understanding the physiological and molecular strategies of rapeseed salinity resistance is a promising and cost-effective strategy for developing highly resistant cultivars. Results First, early leaf senescence was identified and root system growth was inhibited in rapeseed plants under severe salinity conditions. Electron microscopic analysis revealed that 200 mM NaCl induced fewer leaf trichomes and stoma, cell plasmolysis, and chloroplast degradation. Primary and secondary metabolite assays showed that salinity led to an obviously increased anthocyanin, osmoregulatory substances, abscisic acid, jasmonic acid, pectin, cellulose, reactive oxygen species, and antioxidant activity, and resulted in markedly decreased photosynthetic pigments, indoleacetic acid, cytokinin, gibberellin, and lignin. ICP-MS assisted ionomics showed that salinity significantly constrained the absorption of essential elements, including the nitrogen, phosphorus, potassium, calcium, magnesium, iron, mangnese, copper, zinc, and boron nutrients, and induced the increase in the sodium/potassium ratio. Genome-wide transcriptomics revealed that the differentially expressed genes were involved mainly in photosynthesis, stimulus response, hormone signal biosynthesis/transduction, and nutrient transport under salinity. Conclusions The high-resolution salt-responsive gene expression profiling helped the efficient characterization of central members regulating plant salinity resistance. These findings might enhance integrated comprehensive understanding of the morpho-physiologic and molecular responses to salinity and provide elite genetic resources for the genetic modification of salinity-resistant crop species.

show abstract

“…A total of 30 RNA samples (~ 2.0 μg) with the RIN values > 8.0 were used to construct strand-specific cDNA libraries, which were used for the high-throughput transcriptomic sequencing on a lane of an Illumina Hiseq 4000 platform (read length = 150 bp, paired end). The gene expression were normalized using the Fragments Per Kilobase of exon model per Million mapped reads (FPKM) values, and the criteria for false discovery rate ≤ 0.05 and absolute values of log 2 (fold-change) ≥1 were used to characterize gene differential expression [ 49 ]. Analyses of gene ontology (GO) and metabolic route enrichment for the differentially expressed genes (DEGs) were performed using PANTHER ( http://www.pantherdb.org/ ) [ 50 ] and Kyoto Encyclopedia of Genes and Genomes (KEGG) ( http://www.kegg.jp/ ) [ 51 ], respectively.…”

Section: Methodsmentioning

confidence: 99%

Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation

et al. 2018

Self Cite

View full text Add to dashboard Cite

BackgroundNitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (AnAnCnCn, 2n = 4x = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes.ResultsIn this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO3−) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance.ConclusionsWe identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1507-y) contains supplementary material, which is available to authorized users.

show abstract

Genome-scale mRNA transcriptomic insights into the responses of oilseed rape (Brassica napus L.) to varying boron availabilities

Cited by 29 publications

References 73 publications

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

Comprehensive dissection into morpho-physiologic responses, ionomic homeostasis, and transcriptomic profiling reveals the systematic resistance of allotetraploid rapeseed to salinity

Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation

Contact Info

Product

Resources

About