Transcriptome analysis reveals genes commonly responding to multiple abiotic stresses in rapeseed

Zhang, Yuting; Ali, Usman; Zhang, Guofang; Yu, Liangqian; Fang, Shuai; Iqbal, Sidra; Li, Hehuan; Lu, Shaoping; Guo, Liang

doi:10.1007/s11032-019-1052-x

Cited by 31 publications

(51 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The RNA-seq datasets of Zhang et al [ 47 ] were analyzed to identify differentially expressed ATG genes in roots, stems, leaves, flowers, seeds, and siliques in B. napus under normal and stress conditions ( Figure 10 A). Most of the BnATGs were induced in the flowering development, while BnATG8b, BnATG8s , BnATG18n, BnATGd, BnATGb , and BnATG101c were repressed in this stage.…”

Section: Resultsmentioning

confidence: 99%

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Eshkiki

Hajiahmadi

Abedi

et al. 2020

Plants

View full text Add to dashboard Cite

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

show abstract

Section: Resultsmentioning

confidence: 99%

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Eshkiki

Hajiahmadi

Abedi

et al. 2020

Plants

View full text Add to dashboard Cite

show abstract

“…The GATA family genes were systematically investigated in A. thaliana and O. sativa (Reyes et al, 2004), Solanum lycopersicum (Yuan et al, 2018), Vitis vinifera (Zhang et al, 2018), Phyllostachys edulis and Gossypium genues (Zhang et al, 2019). According to these studies, the GATA genes from dicotyledons, but not from monocots, could be strictly divided into four subfamilies.…”

Section: Discussionmentioning

confidence: 99%

“…The DNA binding domains of GATA proteins contain a type IV zinc nger structure C-X 2 -C-X 17-20 -C-X 2 -C and a conserved basic follow region, and most of them featured with C-X 2 -C-X 18 -C-X 2 -C or C-X 2 -C-X 20 -C-X 2 -C zinc nger domains (Lowry et al, 1999;Reyes et al, 2004;Yuan et al, 2017;. Generally, the GATA family genes could be divided into four subfamilies as subfamily I, II, III and IV in plant species such as Arabidopsis thaliana based on phylogenetic relationships, DNA binding domains and intron-exon structures (Reyes et al, 2004;Yuan et al, 2017;Zhang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Zhu

Guo

Chen

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: GATA transcription factors are involved in plant developmental processes, which also respond to environmental stresses through binding DNA regulatory regions to regulate the downstream genes. However, little information of GATA genes is available in Brassica napus, one of important oil crops. The release of B. napus genome sequences provides a good opportunity to perform a genome-wide characterization of GATA family genes in the rapeseed genome. Results: In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus. They were classified into four subfamilies on the basis of phylogenetic analysis and the domain structures. The sequences of BnGATAs were obvious divergence among four subfamilies based on their GATA domains, structures and motif compositions. Gene duplication and the synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into the evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distribution analysis suggests functional disparity of GATA family genes in different genotypes of a core collection germplasm.Conclusion: This study examined genomic structures, evolution features, expression patterns and SNP distribution of 96 BnGATAs. The results enriched our knowledge of the GATA genes in rapeseed.

show abstract

“…Transcriptome data of 12 different B.napus tissues were obtained from a previous study by Sun et al (2017) under the project ID of PRJNA394926 in the NCBI. Moreover, transcriptome data of B.napus under dehydration, salt, ABA induce and cold stress condition were described in Zhang et al (2019). The data was available at (https://bigd.big.ac.cn/) under the project ID of CRA001775.…”

Section: Expression Patterns Of Bnsnrksmentioning

confidence: 99%

“…The expression pattern of BnSnRK genes under various abiotic stress were studied using the published transcriptome data of B.napus under drought, salinity, ABA induction and cold stresses (Zhang et al, 2019). Overall, BnSnRK genes signi cantly changed the expression level under different abiotic stresses (Figure8 , Table S8).…”

Section: Expression Pro Les Of Bnsnrks Under Different Abiotic Stressesmentioning

confidence: 99%

Genome-wide identification and characterization of SnRK family genes in Brassica napus

Zhu

Jiang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.Results: Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.Conclusion: We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.

show abstract

Transcriptome analysis reveals genes commonly responding to multiple abiotic stresses in rapeseed

Cited by 31 publications

References 67 publications

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Genome-Wide Identification and Characterization of GATA Family Genes in Brassica Napus

Genome-wide identification and characterization of SnRK family genes in Brassica napus

Contact Info

Product

Resources

About