Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jul 10;14(7):1421.
doi: 10.3390/genes14071421.

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

Ming Hu  1   2 , Meili Xie  2 , Xiaobo Cui  2 , Junyan Huang  2 , Xiaohui Cheng  2 , Lijiang Liu  2 , Shunping Yan  1 , Shengyi Liu  2 , Chaobo Tong  2
Affiliations

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

Ming Hu et al. Genes (Basel). .

Abstract

SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.

Keywords: Brassica napus; SRS gene family; agronomic traits; expression pattern.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The pipeline for BnSRS gene family analysis.
Figure 2
Figure 2
A phylogenetic tree was constructed using the ML method to analyze the relationship between SRS genes. The BnSRS genes were found to be clustered into four distinct subgroups, distinguishable by different colors in the tree.
Figure 3
Figure 3
The distribution and collinearity of the BnSRS genes. Different color represents different subgroups, the red lines indicated the duplicated gene pairs of BnSRS.
Figure 4
Figure 4
The phylogenetic tree, conserved motifs, and gene structure for the BnSRS genes. (A) The phylogenetic tree for the BnSRS genes was constructed. (B) The conserved motifs identified in the BnSRS genes. Different color represents different motif. (C) The gene structure of the BnSRS genes. The green, purple, and red box represent the CDS, UTR, and DUF702 domains, respectively. The red box is above the green box, and it covers part of the green box.
Figure 5
Figure 5
The sequence logos of conversed motifs in the BnSRS proteins. Each letter’s height depicts the occurrence frequency of the corresponding base or amino acid residue at that position.
Figure 6
Figure 6
Cis-element analysis of the BnSRS genes. The different color boxes represent different cis-elements.
Figure 7
Figure 7
The expression levels of the BnSRS genes in 32 tissues. The red and blue represent high and low expressions, respectively. DAP represents days after pollination.
Figure 8
Figure 8
The expression pattern of the BnSRS genes under different biotic and abiotic stresses. (A) The number of BnSRS genes simultaneously expressed under different stresses. The ‘de’ represents dehydration and “S.s” represents S. sclerotiorum. The yellow bar represented the number of genes with expression in the tissue, the black dot indicated expression in the corresponding tissues, and the black bar indicated the number of genes expressed in the corresponding tissues. (B) The expression levels of the BnSRS genes under different stresses. The red and blue represent high and low expressions, respectively.
Figure 9
Figure 9
Protein-protein interaction analysis of BnSRS gene family members. (A) The network of protein-protein interaction analysis. The red points represent the BnSRS proteins, the blue points represent the proteins that interacted with the BnSRS proteins, the green lines represent the interactions between the BnSRS proteins, and the grey lines represent the interactions between the BnSRS proteins and the other proteins. (B) The KEGG pathway analysis of the genes encoding the proteins interacted with BnSRS genes.
Figure 10
Figure 10
The association analysis between BnSRR1 and agronomic traits in B. napus. (A) Manhattan plot with protein content, final flowering time (FFT), and thousand seeds weight (TSW). (B–D) Phenotypic analysis of different genotypic groups at significant loci for protein content, FFT, and TSW. There were 106 and 203 B. napus accessions in Hap1 and Hap2 populations, respectively.
See this image and copyright information in PMC

References

    1. Chalhoub B., Denoeud F., Liu S., Parkin I.A., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345:950–953. doi: 10.1126/science.1253435. - DOI - PubMed
    1. Singh S., Yadav S., Singh A., Mahima M., Singh A., Gautam V., Sarkar A.K. Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis. Plant J. 2020;101:87–100. doi: 10.1111/tpj.14520. - DOI - PubMed
    1. Smith D.L., Fedoroff N.V. LRP1, a gene expressed in lateral and adventitious root primordia of arabidopsis. Plant Cell. 1995;7:735–745. - PMC - PubMed
    1. De Rybel B., Audenaert D., Xuan W., Overvoorde P., Strader L.C., Kepinski S., Hoye R., Brisbois R., Parizot B., Vanneste S., et al. A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nat. Chem. Biol. 2012;8:798–805. doi: 10.1038/nchembio.1044. - DOI - PMC - PubMed
    1. Eklund D.M., Cierlik I., Ståldal V., Claes A.R., Vestman D., Chandler J., Sundberg E. Expression of Arabidopsis SHORT INTERNODES/STYLISH family genes in auxin biosynthesis zones of aerial organs is dependent on a GCC box-like regulatory element. Plant Physiol. 2011;157:2069–2080. doi: 10.1104/pp.111.182253. - DOI - PMC - PubMed

Publication types

LinkOut - more resources