Abstract
BackgroundThe tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development.ResultsHere, as a first step toward understanding these networks, we analyzed and characterized the genome-wide transcriptional profiling and dynamics of sweetpotato root in seven distinct developmental stages using a customized microarray containing 39,724 genes. Analysis of these genes identified temporal programs of gene expression, including hundreds of transcription factor (TF) genes. We found that most genes active in roots were shared across all developmental stages, although significant quantitative changes in gene abundance were observed for 5,368 (including 435 TFs) genes. Clustering analysis of these differentially expressed genes pointed out six distinct expression patterns during root development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that genes involved in different processes were enriched at specific stages of root development. In contrast with the large number of shared expressed genes in root development, each stage or period of root development has only a small number of specific genes. In total, 712 (including 27 TFs) and 1,840 (including 115 TFs) genes were identified as root-stage and root-period specific, respectively at the level of microarray. Several of the specific TF genes are known regulators of root development, including DA1-related protein, SHORT-ROOT and BEL1-like. The remaining TFs with unknown roles would also play critical regulatory roles during sweetpotato tuberous root formation and development.ConclusionsThe results generated in this study provided spatiotemporal patterns of root gene expression in support of future efforts for understanding the underlying molecular mechanism that control sweetpotato yield and quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0567-5) contains supplementary material, which is available to authorized users.
Highlights
The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives
Sweetpotato unigene assembly, microarray design and gene annotation An oligonucleotide microarray containing 39, 724 unique genes was created based on a large EST collection from publicly available database and in-house sequences
The data set can be accessed at the Gene Expression Omnibus (GEO) database as platform GPL17440 and series GSE48834
Summary
The tuberous root of sweetpotato is undisputedly an important organ from agronomic and biological perspectives. Little is known regarding the regulatory networks programming tuberous root formation and development. Sweetpotato (Ipomoea batatas), one of the most important food crops in the world, is mainly cultivated for its underground tuberous roots, which are rich in starch and other nutrients. The sweetpotato tuberous root, involved in carbohydrate storage and vegetative propagation, is a unique organ, which has the value of biological research for organogenesis and evolution. Understanding the processes regulating the tuberous root formation and development is of particular importance [2]. The formation of tuberous root depends mainly on two biological processes.
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