The potential role of short internodes/stylish (SHI/STY) and SHI related sequence (SRS) in potato tuberization

Abstract

BACKGROUND SRS: (Short Internodes/Stylish/SHI-Related Sequence) genes play a crucial role in plant developments, encompassing organ morphogenesis. However, at present, the biological significance of potato StSRS genes remains unknown. This study comprehensively identified and analysed the potential functions of StSRS genes in potato tuberization. RESULTS: Through phylogenetic and conserved motif analyses, eight members of the StSRS family were successfully identified and classified into five distinct subfamilies. The intraspecies and interspecies collinearity analyses offered insights into the evolutionary clues of the StSRS family, showing closer homology to tomato and tobacco. High-quality RNA-sequencing (Q30 > 97.16%) revealed dynamic gene expression profiles, with 146 to 997 differentially expressed transcription factors (DETFs), particularly from the MYB-related, GATA, and bHLH families. Among them, the expression of two StSRS genes, StSRS1 and StSRS8, were dramatically changed during potato tuber formation. Weighted Gene Co-expression Network Analysis (WGCNA) uncovered stage-specific gene modules and spotlighted hub genes. Specifically, StSRS8 was strongly associated with the Stolon stage, while StSRS1 was evidently linked to the Tuber stage. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the transcripts of both StSRS1 and StSRS8 were predominantly expressed during potato tuberization, as compared to those in other tissues. However, it is scarcely detectable for other six StSRS genes. Furthermore, the transcripts of StSRS8 were repressed under short-day (SD) conditions. CONCLUSION: These findings yield critical insights into the potato StSRS gene family and furnish essential information for further function investigation of StSRS genes, particularly StSRS1 and StSRS8, in the context of potato tuberization.

Keywords: Potato tuberization; Short internodes/Stylish (SHI/STY) and SHI-related sequence (SRS) family; Transcriptome; Weighted gene co-expression network analysis (WGCNA).

Fig. 1

Chromosomal distribution of StSRS genes. Chromosomal information for the StSRS genes was obtained from the S. tuberosum genome annotation file and TBtools was used to generate this figure

Fig. 2

StSRS gene structure and conserved motifs analysis. Conserved motifs were detected using MEME and are represented by boxes of different colors

Fig. 3

Phylogenetic analysis of SRS gene family from Solanum tuberosum, Arabidopsis thaliana, Solanum lycopersicum, Nicotiana benthamiana, and Capsicum annuum. Phylogenetic tree was constructed by MEGA11 using Neighbour-Joining method with 1,000, bootstrap values

Fig. 4

Intraspecific and interspecific collinearity analysis of potato SRS gene family. (A) Duplication status of the StSRS gene family within the potato genome; (B) Duplication status of the SRS gene family between potato and tobacco, tomato, and pepper

Fig. 5

Transcriptomic analysis of four potato tuerization stages. A The images of four key stages of potato tuberization (Stolon, Swelling, Initiation, and Tuber), bar = 1 cm; B Principal component analysis of 12 samples; C Correlation analysis of 12 samples

Fig. 6

Comparative analysis of DEGs and DETFs. A Volcano plot of up-regulated and down-regulated genes for each comparison combination; B Venn plot for each comparison combination; C Heat map of DETFs for each comparison combination; D GO enrichment of DETFs for each comparison combination analysis

Fig. 7

WGCNA analysis of four different stages of potato tuber formation. A Sample clustering tree and trait heat map between each sample; B Correlation analysis of tissues and modules; C Scatter plot of correlation results between gene MM in MEbule module and gene GS in Stolon; D Scatter plot of correlation results between gene MM in MEdarkseagreen4 module and gene GS in Tuber

Fig. 8

Co-expression network diagram. A Co-expression network diagram of MEblue module related to potato Stolon stage. B Co-expression network diagram of MEdarkseagreen4 module related to potato small tuber stage. C qRT-PCR verification of the WGCNA data. Statistical significance of differential expression was determined using a Student’s t-test, with p < 0.05

Fig. 9

Expression analysis of StSRS gene family in different tissues of potato. A Heatmap analysis of expression levels of the StSRS gene family in the four stages of tuber formation; B The schematic diagram outlining the proposed mode of action. GA, gibberellin; ABA, abscisic acid, JA, jasmonic acid; TFs, transcription factors; TFBS, transcription factor binding sites; C, D qRT-PCR analysis of the StSRS1 and StSRS8 in different tissues of potato. Statistical significance of differential expression was determined using a Student’s t-test, with p < 0.05