Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

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.

Effect of Pot Volume on the Growth of Sweetpotato Cultivated in the New Hydroponic System

“…Differentiation of tuberous roots from adventitious roots coincides with an increase in the activity of primary cambium and a decrease in the lignification of stele (Togari, 1950). Consistent with this observation, genes involved in lignin biosynthesis are down-regulated during the initiation of tuberous root development (Firon et al, 2013;Wang et al, 2015). In addition, overexpression of Maize Lc gene in transgenic sweetpotato induced the activation of the lignin biosynthetic pathway in the developing roots, leading to pencil-type root differentiation (Wang H. et al, 2016).…”

Recent Progress in Molecular Studies on Storage Root Formation in Sweetpotato (<i>Ipomoea batatas</i>)

“…The data also indicated that the expressions of several regulatory genes involved in meristematic tissue identity and maintenance are elaborately controlled during the storage root initiation process. Wang et al (2015) also analyzed the transcriptional profiles of sweetpotato roots in seven distinct developmental stages using a microarray containing 39,724 genes, and found 5,368 genes showing significant changes in gene expression during storage root development. The results suggested that starch biosynthesis is up-regulated and lignin biosynthesis is down-regulated during storage root development, along with changes in other biological processes, as summarized in Table 1.…”

“…These gene expression studies also reported the changes in expression of several regulatory genes during the formation of storage roots. McGregor (2006) and Wang et al (2015) reported the differential expression of auxin-responsible genes in fibrous and storage roots. Also, McGregor (2006) and Firon et al (2013) reported the differential expression of ethylene-responsive factors.…”

“…These results imply the involvement of auxin and ethylene in the formation of storage roots. Preferential expression of the homologues of the Arabidopsis SHORT-ROOT gene in fibrous roots was described by Tao et al (2012), Firon et al (2013), and Wang et al (2015). As the SHORT-ROOT protein of Arabidopsis is involved in the radial patterning of roots (Helariutta et al 2000), this gene is possibly involved in the determination of root architecture during the initial stage of adventitious root development.…”

“…As the SHORT-ROOT protein of Arabidopsis is involved in the radial patterning of roots (Helariutta et al 2000), this gene is possibly involved in the determination of root architecture during the initial stage of adventitious root development. McGregor (2006) and Wang et al (2015) reported differential expression of MADS-box family proteins, while Firon et al (2013) and Wang et al (2015) reported upregulation of class I knotted1-like homeobox (KNOXI) genes in the storage roots. The involvement of these genes in the formation of storage roots was also suggested in the molecular biological studies described below.…”