Methylome and transcriptome analysis reveals candidate genes for tuber shape variation in tissue culture-derived potato

Plant Growth Regulation - Tập 93 - Trang 319-332 - 2021
Jagesh Kumar Tiwari1, Tanuja Buckseth1, Rajesh Kumar Singh1, Rasna Zinta1, Aastha Saraswati1, Manoj Kumar1,2, Swarup Kumar Chakrabarti1
1Indian Council of Agricultural Research - Central Potato Research Institute, Shimla, India
2Indian Council of Agricultural Research - Central Potato Research Institute, Regional Station, Meerut, India

Tóm tắt

We investigated genome-wide DNA methylation and transcriptome (RNA-seq) profiling for tuber shape variation in potato. Mother plant (M1, round) and tissue culture-derived clonal variant plant (M2, elongated) were used. Total number of DNA methylation sites at cytosine contexts (CpG, CHG and CHH) was higher in M2 than M1, where CHH was the highest followed by CHG and CpG. Differential methylation regions (DMRs) analysis in M1 (control) and M2 revealed maximum DMRs number on chromosome 5 in CHG context and hypo-methylation was higher than hyper-methylation. Further, transcriptome analysis revealed that a total of 20,747 genes were differentially expressed between M1 (control) and M2, of which 280 (over-expressed) and 612 (under-expressed) genes were statistically significant (p ≤ 0.05). The gene ontology (GO) annotation showed predominance of molecular function, whereas signal transduction and carbohydrate metabolism were major KEGG (Kyoto encyclopedia of genes and genomes) pathways. RNA-seq gene expression was validated for the ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on the comparative analysis, we observed a few candidate genes associated with tuber developmental processes such as phytohormones-related (e.g. SAUR family protein, abscisic acid environmental stress-inducible protein TAS14), sugar metabolism (e.g. UDP-glucosyltransferase, glycosyltransferase family GT8 protein), transcription factors (e.g. F-box family protein, MYB, WRKY, MADS-box), stress-responsive proteins (e.g. early-responsive to dehydration 3, cytochrome P450, proline-rich protein) and cell wall modifying genes (e.g. endo-1,4-beta-glucanase, glycine-rich cell wall structural protein 1.8, 3-ketoacyl-CoA synthase 10). Our study suggests that these candidate genes probably play key roles in tuber shape variation in potato.

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