title: Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas).
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Here, 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. wzhying@hotmail.com.
authors.forename: Zhangying
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. bpfang01@163.com.
authors.forename: Boping
authors.initials: B
authors.lastname: Fang
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. chenxinliang2010@163.com.
authors.forename: Xinliang
authors.initials: X
authors.lastname: Chen
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. lmhuan@163.com.
authors.forename: Minghuan
authors.initials: M
authors.lastname: Liao
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. victerchen@163.com.
authors.forename: Jingyi
authors.initials: J
authors.lastname: Chen
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. zhangxj289@163.com.
authors.forename: Xiongjian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. hlf157@163.com.
authors.forename: Lifei
authors.initials: L
authors.lastname: Huang
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. xiazi625@163.com.
authors.forename: Zhongxia
authors.initials: Z
authors.lastname: Luo
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. ivykassy@hotmail.com.
authors.forename: Zhufang
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. liyujun2005@hotmail.com.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Li
mesh_terms: D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D027723:Ipomoea batatas / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome