Abstract
Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
Highlights
Potato is the third most important food crop after rice and wheat, the average yield of potatoes around the world is far below its physiological potential of 120 tons/ha [1]
There are 249,457 potato Expressed Sequence Tags (ESTs) in the National Center for Biotechnology Information EST database, which have been a valuable resource for gene discovery and expression in several potato genotypes, tissues, and environmental stress responses [4,5,6,7,8]
Approaches to quantitative gene expression profiling include the development of cDNA and oligonucleotide-based microarrays, for which 26 experiments and 506 assays exist in the National Center for Biotechnology Information Gene Expression Omnibus and the European Bioinformatics Institute ArrayExpress [9,10]
Summary
Potato is the third most important food crop after rice and wheat (http://faostat.fao.org), the average yield of potatoes around the world is far below its physiological potential of 120 tons/ha [1]. Tissues sampled and sequencing metrics Here, we analyzed gene expression patterns in a set of 32 tissues from DM plants that represent major organs, developmental stages, and stress-related conditions (Tables 1 and 2).
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