title: Transcriptome response of cassava leaves under natural shade.
abstract: Cassava is an important staple crop in tropical and sub-tropical areas. As a common farming practice, cassava is usually cultivated intercropping with other crops and subjected to various degrees of shading, which causes reduced productivity. Herein, a comparative transcriptomic analysis was performed on a series of developmental cassava leaves under both full sunlight and natural shade conditions. Gene expression profiles of these two conditions exhibited similar developmental transitions, e.g. genes related to cell wall and basic cellular metabolism were highly expressed in immature leaves, genes involved in lipid metabolism and tetrapyrrole synthesis were highly expressed during the transition stages, and genes related to photosynthesis and carbohydrates metabolism were highly expressed in mature leaves. Compared with the control, shade significantly induced the expression of genes involved in light reaction of photosynthesis, light signaling and DNA synthesis/chromatin structure; however, the genes related to anthocyanins biosynthesis, heat shock, calvin cycle, glycolysis, TCA cycle, mitochondrial electron transport, and starch and sucrose metabolisms were dramatically depressed. Moreover, the shade also influenced the expression of hormone-related genes and transcriptional factors. The findings would improve our understanding of molecular mechanisms of shade response, and shed light on pathways associated with shade-avoidance syndrome for cassava improvement.
authors.affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan 571101, China.
authors.forename: Zehong
authors.initials: Z
authors.lastname: Ding
authors.affiliation: Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, USA.|Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: CAS-Key laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Fangfang
authors.initials: F
authors.lastname: Liu
authors.affiliation: Computational Biology Service Unit, Life Sciences Core Laboratories Center, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
authors.affiliation: CAS-Key laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China.
authors.forename: Xinguang
authors.initials: X
authors.lastname: Zhu
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa 50011, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.affiliation: Computational Biology Service Unit, Life Sciences Core Laboratories Center, Cornell University, Ithaca, New York 14850, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Sun
authors.affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan 571101, China.
authors.forename: Wenquan
authors.initials: W
authors.lastname: Wang
authors.affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan 571101, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Peng
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Brutnell
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomic Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
authors.forename: Pinghua
authors.initials: P
authors.lastname: Li
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D002365:Manihot / Q000235:genetics / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome / Q000502:physiology*