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Transcriptomic Diversity of Solanum tuberosum Varieties: A Drive towards Future Analysis of Its Polyploidy Genome
* 1 , 1 , 1 , 1 , 1 , 2 , 1 , 1 , 3 , 1 , 1 , * 1
1  Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka
2  Department of Chemistry Education, Ekiti State University, Ado-Ekiti, 362103, Nigeria
3  Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka
Academic Editor: Carmen Arena


Despite the significance of potatoes in combating hunger and ensuring global food security, their potential for fostering a sustainable society has not been fully exploited due to its complex biological system as a polyploid. Therefore, there is a need for a more gene-informed potato breeding program to improve yields, nutrient content and other market characteristics. This study aimed at analysing the RNA-seq data from leaf samples of four potato varieties annotated as HJ, HL, LS and V7, to understand the transcriptomic diversity among the varieties. A pipeline was developed and used for the analyses of the fragments reads from each potato variety. A significant amount (>85%) of fragment reads in all samples were mapped to the reference genome. Out of 27,356 gene features obtained from this study, 65.93% were expressed in all samples, and 4.5% were unique to individual potato species. Although all potato varieties' top 10 expressed genes were associated with chloroplastic proteins/enzymes, other highly unique genes are yet to be fully annotated. Furthermore, the result from fold-change analysis, hierarchical-cluster plot and heatmap showed potato varieties HJ as the most distant species, while potato varieties HL and V7 are most similar. More so, the heatmap showed that genes expressed in HJ had the most similar cluster among themselves. Although limited by the unavailability of phenotype information and sample replicates, this study has shown that potato varieties, even with the same polyploid number, express a significant level of diversity in their transcriptome under the same condition.

Keywords: Polyploidy; Potatoes; RNA-seq; chloroplastic proteins; transcriptomic diversity; potato breeding program