Genome-Wide Identification, Characterization and Expression Profiling of the CONSTANS -like Genes in Potato ( Solanum tuberosum L.)

: CONSTANS -like ( COL ) genes play important regulatory roles in flowering, tuber formation and the development of the potato ( Solanum tuberosum L.). However, the COL gene family in S. tuberosum has not been systematically identified, restricting our knowledge of the function of these genes in S. tuberosum . In our study, we identified 14 COL genes, which were unequally distributed among eight chromosomes. These genes were classified into three groups based on differences in gene structure characteristics. The COL proteins of S. tuberosum and Solanum lycopersicum were closely related and showed high levels of similarity in a phylogenetic tree. Gene and protein structure analysis revealed similarities in the exon–intron structure and length, as well as the motif structure of COL proteins in the same subgroup. We identified 17 orthologous COL gene pairs between S . tuberosum and S. lycopersicum . Selection pressure analysis showed that the evolution rate of COL homologs is controlled by purification selection in Arabidopsis , S . tuberosum and S. lycopersicum . StCOL genes showed different tissue-specific expression patterns. StCOL5 and StCOL8 were highly expressed specifically in the leaves of plantlets. StCOL6 , StCOL10 and StCOL14 were highly expressed in flowers. Tissue-specific expression characteristics suggest a functional differentiation of StCOL genes during evolution. Cis-element analysis revealed that the StCOL promoters contain several regulatory elements for hormone, light and stress signals. Our results provide a theoretical basis for the understanding of the in-depth mechanism of COL genes in regulating the flowering time and tuber development in S. tuberosum .

[1]  F. Romero-Campero,et al.  CONSTANS alters the circadian clock in Arabidopsis thaliana , 2023, bioRxiv.

[2]  Z. Ye,et al.  The tomato CONSTANS-LIKE protein SlCOL1 regulates fruit yield by repressing SFT gene expression , 2022, BMC Plant Biology.

[3]  G. Bryan,et al.  Genome evolution and diversity of wild and cultivated potatoes , 2022, Nature.

[4]  Arif Hasan Khan Robin,et al.  Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses , 2021, BMC Genomics.

[5]  Dawei Li,et al.  Genome design of hybrid potato , 2021, Cell.

[6]  Ming Li,et al.  A CONSTANS-LIKE gene of Nelumbo nucifera could promote potato tuberization , 2021, Planta.

[7]  Hao Chen,et al.  Brassica napus COL transcription factor BnCOL2 negatively affects the tolerance of transgenic Arabidopsis to drought stress , 2020 .

[8]  C. Bachem,et al.  Haplotype-resolved genome analyses of a heterozygous diploid potato , 2020, Nature Genetics.

[9]  Jiming Jiang,et al.  Construction of a chromosome-scale long-read reference genome assembly for potato , 2020, GigaScience.

[10]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[11]  Qi Sun,et al.  Identification of reliable reference genes for qRT-PCR in the ephemeral plant Arabidopsis pumila based on full-length transcriptome data , 2019, Scientific Reports.

[12]  E. Heuvelink,et al.  Coincidence of potato CONSTANS (StCOL1) expression and light cannot explain night‐break repression of tuberization , 2018, Physiologia plantarum.

[13]  Silvio C. E. Tosatto,et al.  The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..

[14]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[15]  Juan C. Sánchez-DelBarrio,et al.  DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. , 2017, Molecular biology and evolution.

[16]  Jessika Adrian,et al.  The Transcription Factor COL12 Is a Substrate of the COP1/SPA E3 Ligase and Regulates Flowering Time and Plant Architecture1 , 2017, Plant Physiology.

[17]  Ning Zhang,et al.  Selection and validation of reference genes for RT-qPCR analysis in potato under abiotic stress , 2017, Plant Methods.

[18]  Shanshan Zhu,et al.  OsCOL16, encoding a CONSTANS-like protein, represses flowering by up-regulating Ghd7 expression in rice. , 2017, Plant science : an international journal of experimental plant biology.

[19]  Xianzhong Huang,et al.  Generation, Annotation, and Analysis of a Large-Scale Expressed Sequence Tag Library from Arabidopsis pumila to Explore Salt-Responsive Genes , 2017, Front. Plant Sci..

[20]  W. Liu,et al.  CONSTANS-Like 9 (OsCOL9) Interacts with Receptor for Activated C-Kinase 1(OsRACK1) to Regulate Blast Resistance through Salicylic Acid and Ethylene Signaling Pathways , 2016, PloS one.

[21]  L. Xiong,et al.  Ghd2, a CONSTANS-like gene, confers drought sensitivity through regulation of senescence in rice , 2016, Journal of experimental botany.

[22]  Shanshan Zhu,et al.  A CONSTANS-like transcriptional activator, OsCOL13, functions as a negative regulator of flowering downstream of OsphyB and upstream of Ehd1 in rice , 2016, Plant Molecular Biology.

[23]  J. Franco-Zorrilla,et al.  Potato StCONSTANS-like1 Suppresses Storage Organ Formation by Directly Activating the FT-like StSP5G Repressor , 2016, Current Biology.

[24]  Shanshan Zhu,et al.  OsCOL10, a CONSTANS-Like Gene, Functions as a Flowering Time Repressor Downstream of Ghd7 in Rice. , 2016, Plant & cell physiology.

[25]  Xiaoming Song,et al.  Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom , 2015, Scientific Reports.

[26]  Borivoj Vojtesek,et al.  Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets , 2015, Bioinform..

[27]  Siyuan Zhu,et al.  Identification of a CONSTANS homologous gene with distinct diurnal expression patterns in varied photoperiods in ramie (Boehmeria nivea L. Gaud). , 2015, Gene.

[28]  C. Kim,et al.  The CONSTANS-like 4 transcription factor, AtCOL4, positively regulates abiotic stress tolerance through an abscisic acid-dependent manner in Arabidopsis. , 2015, Journal of integrative plant biology.

[29]  Bo Hu,et al.  GSDS 2.0: an upgraded gene feature visualization server , 2014, Bioinform..

[30]  M. Muthamilarasan,et al.  Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[31]  R. Macknight,et al.  Isolation and functional analysis of CONSTANS-LIKE genes suggests that a central role for CONSTANS in flowering time control is not evolutionarily conserved in Medicago truncatula , 2014, Front. Plant Sci..

[32]  J. Botto,et al.  The BBX family of plant transcription factors. , 2014, Trends in plant science.

[33]  B. Liu,et al.  CONSTANS-LIKE 7 regulates branching and shade avoidance response in Arabidopsis , 2013, Journal of experimental botany.

[34]  Sakarindr Bhumiratana,et al.  Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model , 2012, BMC Systems Biology.

[35]  P. Suárez-López,et al.  Potato CONSTANS is involved in photoperiodic tuberization in a graft-transmissible manner. , 2012, The Plant journal : for cell and molecular biology.

[36]  Jian-ye Chen,et al.  Molecular characterization and expression profiles of MaCOL1, a CONSTANS-like gene in banana fruit. , 2012, Gene.

[37]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[38]  J. Abelenda,et al.  Control of flowering and storage organ formation in potato by FLOWERING LOCUS T , 2011, Nature.

[39]  E. Kramer,et al.  In the Light of Evolution: A Reevaluation of Conservation in the CO–FT Regulon and Its Role in Photoperiodic Regulation of Flowering Time , 2011, Front. Plant Sci..

[40]  F. Valverde.  CONSTANS and the evolutionary origin of photoperiodic timing of flowering. , 2011, Journal of experimental botany.

[41]  R. Amasino.  Seasonal and developmental timing of flowering. , 2010, The Plant journal : for cell and molecular biology.

[42]  R. Green,et al.  Over-expression of CONSTANS-LIKE 5 can induce flowering in short-day grown Arabidopsis , 2009, Planta.

[43]  S. Jackson.  Plant responses to photoperiod. , 2009, The New phytologist.

[44]  Dmitri A. Nusinow,et al.  FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis , 2007, Science.

[45]  D. Weigel,et al.  Move on up, it's time for change--mobile signals controlling photoperiod-dependent flowering. , 2007, Genes & development.

[46]  Fabio Fornara,et al.  FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis , 2007, Science.

[47]  Stefan Jansson,et al.  CO/FT Regulatory Module Controls Timing of Flowering and Seasonal Growth Cessation in Trees , 2006, Science.

[48]  S. Prat,et al.  Seasonal control of tuberization in potato: conserved elements with the flowering response. , 2006, Annual review of plant biology.

[49]  Magnus Holm,et al.  Arabidopsis CONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth[W] , 2005, The Plant Cell Online.

[50]  Zeng-Yu Wang,et al.  Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. , 2005, The Plant journal : for cell and molecular biology.

[51]  K. Goto,et al.  TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. , 2005, Plant & cell physiology.

[52]  Shelley Hepworth,et al.  CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis , 2004, Development.

[53]  G. Coupland,et al.  The Molecular Basis of Diversity in the Photoperiodic Flowering Responses of Arabidopsis and Rice , 2004, Plant Physiology.

[54]  G. Coupland,et al.  The Evolution of CONSTANS-Like Gene Families in Barley, Rice, and Arabidopsis1 , 2003, Plant Physiology.

[55]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[56]  S. Prat,et al.  Control of photoperiod-regulated tuberization in potato by the Arabidopsis flowering-time gene CONSTANS , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Takashi Araki,et al.  Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. , 2002, Plant & cell physiology.

[58]  M. Yano,et al.  Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. , 2002, Genes & development.

[59]  G. Coupland,et al.  Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. , 2002, The Plant journal : for cell and molecular biology.

[60]  Hitoshi Onouchi,et al.  CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis , 2001, Nature.

[61]  L. Etkin,et al.  Two B or not two B? Overview of the rapidly expanding B-box family of proteins. , 2001, Differentiation; research in biological diversity.

[62]  M. Yano,et al.  Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS , 2000, Plant Cell.

[63]  U. Lagercrantz,et al.  Rapid evolution of the family of CONSTANS LIKE genes in plants. , 2000, Molecular biology and evolution.

[64]  B. Thomas,et al.  Regulation of transcript levels of a potato gibberellin 20-oxidase gene by light and phytochrome B. , 2000, Plant physiology.

[65]  K. Borden.  RING domains: master builders of molecular scaffolds? , 2000, Journal of molecular biology.

[66]  L. E. Gregory.  SOME FACTORS FOR TUBERIZATION IN THE POTATO PLANT , 1956 .

[67]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .

[68]  Yuexue Liu,et al.  Genome-Wide Identification, Characterization, and Expression Profile Analysis of CONSTANS-like Genes in Woodland Strawberry (Fragaria vesca) , 2022, Frontiers in Plant Science.