Evaluation of changes in the expression profile of candidate genes in apple rootstockss with a different degree of frost tolerance .
Sylwia Keller-Przybyłkowicz
sylwia.keller@inhort.plZakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice (Poland)
http://orcid.org/0000-0002-3473-9706
Mariusz Lewandowski
Zakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice (Poland)
http://orcid.org/0000-0002-4852-5514
Abstract
The aim of presented study was to identify putative candidate genes associated with apple rootstock winter hardiness. The assessment of changes in expression profile of isolated differentially expressed genes, was performed using two subsequent experiments: RNAseq (based on New Generation Sequencing, NGS) and qRT-PCR (Real Time transcript amplification). In terms of traits of interests two apple rootstocks P 66 (frost tolerant) and M.9 (frost sensitive) were evaluated. As a result of the RNA sequence readings (de novo sequencing, Illumina Solid system), approximately 167 million reads of unique sequences were identified. Finally, fifteen functionally annotated expressed tags, representing different expression profile, were chosen. Selected putative genes coding: structural and integral proteins of cell membranes and cellular vacuoles, transcription factors, proteins regulating intercellular and intracellular transport, C-O and C-N bonds hydrolyzes, and proteins binding macro- and microelements.
In order to verify the type of regulation of the transcriptome sequences obtained in NGS technology, qRT-PCR tests were carried out for the same samples layout. Three of studied sequences, represented identical type of regulation in both RNA-seq and qRT-PCR experiments. The selected genes seems to represent potential candidate sequences (functional molecular markers), enabling the early selection of frost-tolerant apple rootstocks.
Supporting Agencies
Keywords:
expression profile, gene annotation, Malus domestica Borkh., new generation sequencing (NGS), quantitative transcript level (qRT-PCR)References
Artlip, T. S., Callahan, A.M., Bassett, C.L., Wisniewski, M.E. (1997). Seasonal expression of a dehydrin in sibling deciduous and evergree genotypes of peach (Prunus persica [L.] Batsch). Plant Molecular Biology, 33: 61‒70.
Google Scholar
Aygun, A. (2005). The late spring frost hardiness of some apple varieties at various stage of flower buds. Tarim Bilimeri Degrisi, 11 (3): 283‒285.
Google Scholar
Bai Y, Dougherty, L., Xu, K. (2014). Towards an improved apple reference transcriptome using RNA-seq. Mol. Genet Genomics, 289: 427‒438.
Google Scholar
Callesen, O. (1996). Testing 20 apple rootstocks. VI Inter.Symposium on Integrated Canopy, Rootstock, Environmental Physiol.in Orchard Systems. Acta Hort., 451: 137‒146.
Google Scholar
Chinnusamy, V., Zhu, J., Zhu, J. K. (2006). Gene regulation during cold acclimation in plants. Physiol. Plant., 126: 52‒61. DOI: 10.1111/j.1399‒3054.2006.00596.
Google Scholar
Du, X., Xiao, Q., Zhao, R., Wu, F., Xu, Q., Chong, K., Meng, Z. (2008). TrMADS3, a New Mad-box gene, from a perennial species Taihangiarupestris is upregulated by cold and experiences seasonal fluctuation in expression level. Dev. Genes Evol., 218: 281‒292.
Google Scholar
Edwards, D., Batley, J. (2010). Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal, 8 (10): 2‒9.
Google Scholar
Feng M-X., Zhao, Q., Zhao L-L., Qiao, Y., Xie X-B., Li H-F., Yao Y-X., You C-X., Hao Y-J. (2012). The cold-induced basis helix-loop-helix transcrition factor gene MdCIbHLH1 encodes ans ICE-like protein in apple. Plant Biology, 12: 22.
Google Scholar
Gilmour, S. J., Zarka, D.G., Stockinger, E. J., Salazar, M. P., Houghton J. M., Thomashow, M. F. (1998). Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold induced COR gene expression. The Plant Journal, 16: 433‒442. DOI: 10.1046/j.1365‒313x.1998.00310.
Google Scholar
Girardi, C. L., Rombaldi, C. V., Cero, J. D., Nobile, P. M., Laurens, F., Bouzayen, M., Quecini, V. (2013). Genome-wide analysis of the AP2/ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis. Scientia Horticulturae, 151: 112‒121.
Google Scholar
Everaert C, Luypaert M, Maag, J. L. V., Cheng, Quek Xiu, Marcel, E. (2017). Benchmarking of RNA-sequencing analysis workflows using wholetranscriptomeRT-qPCR expression. Nature: 7. 1559. DOI: 10.1038/s41598‒017‒01617‒3
Google Scholar
Imelfort, M., Edwards, D. (2009). De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics, 10 (6): 609‒618.
Google Scholar
Kalberer, S., Wisniewski, M., Arora, R. (2006). Deaclimation and reaclimation of cold-hardy plants: Current understanding and emerging concepts. Plant Scince, 171: 3‒16.
Google Scholar
Kumar, S., Blaxter, M. L. (2010). Comparing de novo assemblers for 454 transcriptome data. BMC Genomics, 11: 571.
Google Scholar
Luby, J. J. (1991). Breeding cold-hardy fruit crops in Minnesota. HortSci., 26: 507‒512.
Google Scholar
Medina, J., Bargues, M., Terol, J., Perez-Alonso, M., Salinas, J. (1999). The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol., 119: 463‒469.
Google Scholar
Medina, J., Catalá, R., Salinas, J. (2011). The CBFs: Three Arabidopsis transcription factors to cold acclimate. Plant Science, 180: 3‒11.
Google Scholar
Orvar Bjorn, L., Sangwan, V., Omann, F., Dhirdsa, R. S. (2000). Early steps in cold sensing by plant cells: the role of actin, cytosceleton and membrane fluidity. The Plant Journal, 23 (6): 785‒794.
Google Scholar
Quamme, H.A. (1990). Cold hardiness of apple rootstocks. Com.Fruit Tree, 23: 11‒16.
Google Scholar
Takata, N., Kasuga, J., Takezawa, D., Arakawa, K., Fujikawa, S. (2007). Gene expression associated with increased supercooling capability in xylem parenhyma cells of larch (Larix kaempferi). Journal of Experimental Botany, 58 (13). 3731‒3742.
Google Scholar
Thomashow, M. F. (1998). Role of Cold-Responsive genes in plant freezing tolerance. Plant Physiol., 118: 1‒7. DOI.org/10.1104/pp.118.1.1.
Google Scholar
Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S. K., Troggio, M., Pruss, D., Salvi, S., Pindo, M., Baldi, P., Castelletti, S., Cavaiuolo, M., Coppola, G., Costa, F., Cova, V., Dal Ri, A., Goremykin, V., Komjanc, M., Longhi, S., Magnago, P., Malacarne, G., Malnoy, M., Micheletti, D., Moretto, M., Perazzolli, M., Si-Ammour, A., Vezzulli, S., Zini, E., Eldredge, G., Fitzgerald, L. M., Gutin, N., Lanchbury, J., Macalma, T., Mitchell, J. T., Reid, J., Wardell, B., Kodira, C., Chen, Z., Desany, B., Niazi, F., Palmer, M., Koepke, T., Jiwan, D., Schaeffer, S., Krishnan, V., Wu, C., Chu, V.T., King, S.T., Vick, J., Tao, Q., Mraz, A., Stormo, A., Stormo, K., Bogden, R., Ederle, D., Stella, A., Vecchietti, A., Kater, M.M., Masiero, S., Lasserre, P., Lespinasse, Y., Allan, A.C., Bus, V., Chagné, D., Crowhurst, R.N., Gleave, A.P., Lavezzo, E., Fawcett, J.A., Proost, S., Rouzé, P., Sterck, L., Toppo, S., Lazzari, B., Hellens, R.P., Durel, C.E., Gutin, A., Bumgarner, R.E., Gardiner, S.E., Skolnick, M., Egholm, M., Van de Peer, Y., Salamini, F., Viola, R. (2010). The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics, 42 (10): 833‒841.
Google Scholar
Wisniewski, M., Basset, C., Gusta, V. L. (2003). An overview of cold hardiness in woody plants: Seeing the forest through the trees. HortScience, 38 (5): 952‒959.
Google Scholar
Wisniewski, M., Bassett C, Norelli, J., Artlip, T. (2007). Using biotechnology to improve resistance to environmental stress in fruit crops: The importance of understanding physiology. Acta Hort., 738: 145‒156.
Google Scholar
Wiśniewski, M., Bassett, C., Norelli, J., Macarisisn, D., Artlip, T., Gasic, K., Korban, S. (2008). Expressed sequence tag analysis of the response of apple (Malus x domestica ‘Royal Gala’) to low temperature and water deficit. Phisiologia Plantarum, 133: 298‒317.
Google Scholar
Wisniewski, M., Norelli, J., Bassett, C., Artlip, T., Macarisin, D. (2011). Ectopic expression of novel peach (Prunus persica) CBF transcription factor in apple (Malus x domestica) results in short–day induced dormancy and increased cold hardiness. Planta, 233 (5): 971‒983.
Google Scholar
Xu. (2010). The Apple genome: A delicious promise. New York Fruit Quarterly, 18 (4): 11‒14
Google Scholar
Zeng, Ying, Yang, Tao (2002): RNA isolation from highly viscous samples rich in polyphenols and polysaccharides. Plant Molecular Biology Reporter, 20, 417‒417
Google Scholar
Zhao, T., Liang, D., Wang, P., Liu, J., Ma F. (2012). Genome –wide analysis and expression profiling of the DREB transctiption factor gene family in Malus under abiotic stress. Mol. Genet. Genomics, 287: 423‒436.
Google Scholar
Authors
Sylwia Keller-Przybyłkowiczsylwia.keller@inhort.pl
Zakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice Poland
http://orcid.org/0000-0002-3473-9706
Authors
Mariusz LewandowskiZakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice Poland
http://orcid.org/0000-0002-4852-5514
Statistics
Abstract views: 350PDF downloads: 203 PDF downloads: 56
License
Copyright (c) 2020 Sylwia Keller-Przybyłkowicz
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Upon submitting the article, the Authors grant the Publisher a non-exclusive and free license to use the article for an indefinite period of time throughout the world in the following fields of use:
- Production and reproduction of copies of the article using a specific technique, including printing and digital technology.
- Placing on the market, lending or renting the original or copies of the article.
- Public performance, exhibition, display, reproduction, broadcasting and re-broadcasting, as well as making the article publicly available in such a way that everyone can access it at a place and time of their choice.
- Including the article in a collective work.
- Uploading an article in electronic form to electronic platforms or otherwise introducing an article in electronic form to the Internet or other network.
- Dissemination of the article in electronic form on the Internet or other network, in collective work as well as independently.
- Making the article available in an electronic version in such a way that everyone can access it at a place and time of their choice, in particular via the Internet.
Authors by sending a request for publication:
- They consent to the publication of the article in the journal,
- They agree to give the publication a DOI (Digital Object Identifier),
- They undertake to comply with the publishing house's code of ethics in accordance with the guidelines of the Committee on Publication Ethics (COPE), (http://ihar.edu.pl/biblioteka_i_wydawnictwa.php),
- They consent to the articles being made available in electronic form under the CC BY-SA 4.0 license, in open access,
- They agree to send article metadata to commercial and non-commercial journal indexing databases.
Most read articles by the same author(s)
- Mariusz Lewandowski, Sylwia Keller-Przybyłkowicz, Breeding value of selected apple cultivars (Malus domestica) for the resistance to apple scab and powdery mildew , Bulletin of Plant Breeding and Acclimatization Institute: No. 291 (2020): Special issue
- Sylwia Keller-Przybyłkowicz, Agnieszka Masny, Bogusława Idczak, Krystyna Strączyńska, Abdelrahmen Mostafa Abdelwahab Mohamed, Preparation of the mapping population derived from the cross of ‘Elsanta’and ‘Senga Sengana’ sutble for analysis of QTL regions linked to selected Fragaria traits. , Bulletin of Plant Breeding and Acclimatization Institute: No. 291 (2020): Special issue
- Mariusz Lewandowski, Sylwia Keller-Przybyłkowicz, Małgorzata Korbin, Edward Żurawicz, Genetic and molecular analysis of selected apple genotypes (Malus domestica) for shortening of the juvenile period and quality improvement of the fruits , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
- Małgorzata Korbin, Sylwia Keller-Przybyłkowicz, Agnieszka Masny, Bogusława Idczak, Krystyna Strączyńska, Research on saturation of the genetic map of ‘Elsanta Senga’ × ‘Sengana’ for locating genes linked to important traits of strawberry (Fragaria × ananassa) , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
- Sylwia Keller-Przybyłkowicz, Mariusz Lewandowski, Małgorzata Korbin, Identification of the genome regions correlated with cold hardiness of apple rootstocks by transcriptomic analysis of differentially expressed candidate genes , Bulletin of Plant Breeding and Acclimatization Institute: No. 286 (2019): Special issue
