Genomewide analysis of TCP transcription factor gene family in Malus domestica

Teosinte branched1/cycloidea/proliferating cell factor1 (TCP) proteins are a large family of transcriptional regulators in angiosperms. They are involved in various biological processes, including development and plant metabolism pathways. In this study, a total of 52 TCP genes were identified in apple (Malus domestica) genome. Bioinformatic methods were employed to predicate and analyse their relevant gene classification, gene structure, chromosome location, sequence alignment and conserved domains of MdTCP proteins. Expression analysis from microarray data showed that the expression levels of 28 and 51 MdTCP genes changed during the ripening and rootstock–scion interaction processes, respectively. The expression patterns of 12 selected MdTCP genes were analysed in different tissues and in response to abiotic stresses. All of the selected genes were detected in at least one of the tissues tested, and most of them were modulated by adverse treatments indicating that the MdTCPs were involved in various developmental and physiological processes. To the best of our knowledge, this is the first study of a genomewide analysis of apple TCP gene family. These results provide valuable information for studies on functions of the TCP transcription factor genes in apple.

[1]  Steven B Cannon,et al.  The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana , 2004, BMC Plant Biology.

[2]  Jennifer Hayes Clark,et al.  Control of Organ Asymmetry in Flowers of Antirrhinum , 1999, Cell.

[3]  J. Meng,et al.  [MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data]. , 2003, Yi chuan = Hereditas.

[4]  S. Kosugi,et al.  PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. , 1997, The Plant cell.

[5]  S. Tabata,et al.  RNA Interference of the Arabidopsis Putative Transcription Factor TCP16 Gene Results in Abortion of Early Pollen Development , 2006, Plant Molecular Biology.

[6]  Chongrong Sun,et al.  Control of petal shape and floral zygomorphy in Lotus japonicus. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[7]  E. Coen,et al.  The TCP domain: a motif found in proteins regulating plant growth and development. , 1999, The Plant journal : for cell and molecular biology.

[8]  Jun Yang,et al.  Genetic control of floral zygomorphy in pea (Pisum sativum L.) , 2008, Proceedings of the National Academy of Sciences.

[9]  David W Mount,et al.  Using the Basic Local Alignment Search Tool (BLAST). , 2007, CSH protocols.

[10]  Peer Bork,et al.  SMART 7: recent updates to the protein domain annotation resource , 2011, Nucleic Acids Res..

[11]  A. Nag,et al.  miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis , 2009, Proceedings of the National Academy of Sciences.

[12]  Makoto Matsuoka,et al.  The OsTB1 gene negatively regulates lateral branching in rice. , 2003, The Plant journal : for cell and molecular biology.

[13]  R. Olmstead,et al.  Evolution of the TCP gene family in Asteridae: cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. , 2003, Molecular biology and evolution.

[14]  K. Hiratsu,et al.  Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. , 2003, The Plant journal : for cell and molecular biology.

[15]  Richard C. Moore,et al.  The early stages of duplicate gene evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[16]  C. You,et al.  Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis. , 2011, Journal of plant physiology.

[17]  Javier F. Palatnik,et al.  Control of leaf morphogenesis by microRNAs , 2003, Nature.

[18]  J. Doebley,et al.  The evolution of apical dominance in maize , 1997, Nature.

[19]  C. Mariani,et al.  Heat shock transcriptional factors in Malus domestica: identification, classification and expression analysis , 2012, BMC Genomics.

[20]  Pilar Cubas,et al.  Arabidopsis BRANCHED1 Acts as an Integrator of Branching Signals within Axillary Buds[W] , 2007, The Plant Cell Online.

[21]  Hai Huang,et al.  TCP transcription factors interact with AS2 in the repression of class-I KNOX genes in Arabidopsis thaliana. , 2012, The Plant journal : for cell and molecular biology.

[22]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[23]  Matthew W. Hahn,et al.  The evolution of transcriptional regulation in eukaryotes. , 2003, Molecular biology and evolution.

[24]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[25]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[26]  R. Punnett,et al.  The journal of genetics , 1910, Zeitschrift für Induktive Abstammungs- und Vererbungslehre.

[27]  A. Millar,et al.  TCP Transcription Factors Link the Regulation of Genes Encoding Mitochondrial Proteins with the Circadian Clock in Arabidopsis thaliana[W][OA] , 2010, Plant Cell.

[28]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[29]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.

[30]  Guodong Yang,et al.  Genome-wide analysis of the RING finger gene family in apple , 2011, Molecular Genetics and Genomics.

[31]  Peter Doerner,et al.  Arabidopsis TCP20 links regulation of growth and cell division control pathways. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  F. Ma,et al.  Genome-wide identification and expression profiling of dehydrin gene family in Malus domestica , 2012, Molecular Biology Reports.

[33]  M. Brameier.  Genome-wide comparative analysis of microRNAs in three non-human primates , 2010, BMC Research Notes.

[34]  A. Jauneau,et al.  In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development[C][W] , 2008, Plant Physiology.

[35]  Pilar Cubas,et al.  TCP genes: a family snapshot ten years later. , 2010, Trends in plant science.

[36]  Ping Wang,et al.  Genome-wide analysis and expression profiling of the DREB transcription factor gene family in Malus under abiotic stress , 2012, Molecular Genetics and Genomics.

[37]  Stijn Dhondt,et al.  Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically1[C][W] , 2012, Plant Physiology.

[38]  A. Dong,et al.  The Arabidopsis transcription factor AtTCP15 regulates endoreduplication by modulating expression of key cell-cycle genes. , 2012, Molecular plant.

[39]  Martin Kieffer,et al.  TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis , 2011, The Plant journal : for cell and molecular biology.

[40]  Ping Zheng,et al.  The Genome Database for Rosaceae (GDR): year 10 update , 2013, Nucleic Acids Res..

[41]  Roger E Bumgarner,et al.  The genome of the domesticated apple (Malus × domestica Borkh.) , 2010, Nature Genetics.