4.6 Article

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

Journal

PLANT GROWTH REGULATION
Volume 93, Issue 3, Pages 319-332

Publisher

SPRINGER
DOI: 10.1007/s10725-020-00690-5

Keywords

Potato; Transcriptome; Methylome; Tuber shape variation; Genes

Categories

Funding

  1. seed research of the Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, India
  2. institute biotechnology programme of the Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, India

Ask authors/readers for more resources

By investigating DNA methylation and transcriptome profiling in potato, our study identified several candidate genes associated with tuber shape variation, including those involved in phytohormone regulation, sugar metabolism, transcription factors, stress responses, and cell wall modification. These candidate genes are suggested to play key roles in shaping potato tubers.
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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available