IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) IN THE TRANSCRIPTOME OF SUGARCANE VARIETY Co 86032 EXPOSED TO OXIDATIVE STRESS
219 / 103
Authors
-
S Gayathri
ICAR- Sugarcane Breeding Institute
-
M Arockiyajainmary
ICAR- Sugarcane Breeding Institute
-
R Shalini
ICAR- Sugarcane Breeding Institute
-
M Ram Vannish
ICAR- Sugarcane Breeding Institute
-
A Selvi
ICAR- Sugarcane Breeding Institute
-
Ramaswamy A Manimekalai
ICAR- Sugarcane Breeding Institute
Abstract
Sugarcane is an economically substantial crop used for sugar and latest for ethanol production. NGS technologies have started to resolve the complex nature of sugarcane genome and leads to the large-scale discovery of high through put markers like single nucleotide polymorphisms (SNPs). Transcriptome sequencing is preferred over genome sequencing as it finds the SNP on the genes. In this study, transcriptome sequencing of the sugarcane variety Co 86032 under oxidative stress was performed to identity SNPs related to differentially expressed genes. Nearly, 55.4 million high quality clean reads were generated out of 57.6 million unfiltered raw reads. The de novo assembly of the clean reads using Trinity resulted in an average of 61,671 transcripts. Functional annotation of these transcripts with Uniprot database showed that 71% of transcripts had significant match with Viridiplantae protein database. Around 87,834 single nucleotide variants were identified in the differentially expressed (535 up-regulated and 593 down-regulated) transcripts. Thirteen SNPs were predicted in up regulated transcripts from control and 21 SNPs from upregulated transcripts from stressed samples with reference to pooled transcripts. From the down regulated transcripts between control and stressed sample, we identified 80 SNPs and 92 SNPs respectively. The data in this study forms an important resource for future sugarcane improvement programs.
References
Anders, S., and Huber, W. Differential expression analysis for sequence count data. Genome Biology 11 (2010) R106, doi:10.1186/gb-2010-11-10-r106.
Cardoso-Silva, C.B., Costa, E.A., Mancini, M.C., Balsalobre, T.W.A., Canesin, L.E.C., Pinto, L.R., et al. (2014). De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties. PLOS ONE 9, e88462. doi: 10.1371/journal.pone.0088462.
D’Hont A, Grivet L, Feldmann P, Glaszmann J.C, Rao S, and Berding N (1996). Characterization of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol. Genet. Genomics 250, 405-413.
D’Hont, A. and Glaszman, J. C. Sugarcane genome analysis with molecular markers, a first decade of research. Proceedings of the International Society for Sugar Cane Technology, vol. 24, pp. 556-559, 2001.
D’Hont, A. Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenetic and genome research 109, 27–33 (2005).
De Azevedo Neto, A.D.; Prisco, J.T.; Enéas-Filho, J.; Rolim Medeiros, J.V.; GomesFilho, E. Hydrogen peroxide pre-treatment induces salt-stress acclimation in maize plants. J. Plant Physiol.2005, 162, 1114-1122.
Fukushima A, Kusano M. A network perspective on nitrogen metabolism
from model to crop plants using integrated 'omics' approaches. Journal of experimental botany. 2014; 65(19):5619–30. doi: 10.1093/jxb/eru322 PMID: 25129130.
Gadjev I, Stone J.M, Gechev T.S. Programmed Cell Death in Plants: New Insights into Redox Regulation and the Role of Hydrogen Peroxide. In International Review of Cell and Molecular Biology; Kwang, W.J., Ed.; Academic Press: Waltham, MA, USA, 2008; Volume 270, pp. 87-144.
Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature methods. 2011; 8(6):469–77. doi: 10.1038/nmeth.1613 PMID: 21623353.
Garsmeur, O.,Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K.S., et al. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications. 9: 2638. doi: 10.1038/s41467-018-05051-5.
Gongora-Castillo E, Buell CR. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Natural product reports. 2013; 30(4):490–500. doi: 10.1039/c3np20099j PMID: 23377493.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology. 2011; 29(7):644–52. doi: 10.1038/nbt.1883 PMID: 21572440; PubMed Central PMCID: PMC3571712.
Halliwell, B. Reactive species and antioxidants. Redox biology is a fundamental theme of aerobic life. Plant Physiol. 2006, 141, 312-322.
Hoang Nam V, Furtado Agnelo, Mason Patrick J, Marquardt AnnelieA, Kasirajan Lakshmi, Thirugnanasambandam Prathima P et al. (2017) A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics. 18:395. doi: 10.1186/s12864-017-3757-8.
Ishibashi Y, Yamaguchi H, Yuasa T, Iwaya-Inoue M, Arima S, Zheng S.H. Hydrogen peroxide spraying alleviates drought stress in soybean plants. J. Plant Pysiol. 2011, 168, 1562-1567.
Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., & Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111.
Kumar N, Ebel R.C, Roberts P.D. Antioxidant metabolism of grapefruit infected with Xanthomonas axonopodis pv. Citri. Environ. Exp. Bot. 2011, 71, 41-49.
Langmead, B. and Salzberg, S. L. Fast gapped-read alignment tool . Nat Meth, Vol. 9, No. 4. (4 April 2012), pp. 357-359, doi:10.1038/nmeth.1923.
Li H A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. Epub 2011 Sep 8. [PMID: 21903627].
Liu F, Huang N, Wang L, Ling H,Sun T, Ahmad W, Muhammad K,Guo J, Xu L, Gao S, Que Y and Su Y(2018) A Novel L-ascorbate Peroxidase 6 Gene, ScAPX6, Plays an Important Role in the Regulation of Response to Biotic and Abiotic Stresses in Sugarcane.Front. Plant Sci.8:2262.doi: 10.3389/fpls.2017.02262.
Mittler R, Vanderauwera S, Gollery M, Van Breusegem F. Reactive oxygen gene net†work of plants. TRENDS Plant Sci. 2004;9(10):490-498. DOI: 10.1016/j.tplants. 2004.08.009
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M.; KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).
Muhammad Azhar Nadeem, Muhammad Amjad Nawaz, Muhammad QasimShahid, YıldızDoğan, Gonul Comertpay et al. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomicselection and genome editing, Biotechnology & Biotechnological Equipment, 32:2, 261-285. doi: 10.1080/13102818.2017.1400401.
Mukherjee, S.K. 1950. Search for wild relatives of sugarcane in India. International Sugar Journal 52: 261–262.
Peng L.T, Jiang Y.M, Yang S.Z, Pan S.Y. Accelerated senescence of fresh-cut chinese water chestnut tissues in relation to hydrogen peroxide accumulation. J. Plant Phsiol. Mol. Biol. 2005, 31, 527-532.
Riaño-Pachón, D. M., and Mattiello, L. (2017). Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 2; referees: 2 approved] F1000Research, 6:861. doi: 10.12688/f1000research.11859.2.
Savage N. Fuel options: the ideal biofuel. Nature. 2011; 474: S9-11.
Souza G. M., Berges H., Bocs S., Casu R., D’Hont A., Ferreira J. E., et al. (2011). The sugarcane genome challenge: strategies for sequencing a highly complex genome. Trop. Plant Biol. 4 145-156.
Sreenivasan T. V., Ahloowalia B. S., Heinz D. J. Cytogenetics. In: Heinz D. J. (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 211-253; 1987.
Vargas L, Santa Brı´gida AB, Mota Filho JP, de Carvalho TG, Rojas CA, et al. (2014) Drought Tolerance Conferred to Sugarcane by Association with Gluconacetobacter diazotrophicus: A Transcriptomic View of Hormone Pathways. PLoS ONE 9(12): e114744. doi:10.1371/journal.pone.0114744.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics. 2009; 10(1):57-63. doi: 10.1038/nrg2484 PMID: 19015660; PubMed Central PMCID: PMC2949280.
XuS, WangJ, ShangH, HuangY, YaoW, ChenB, and ZangM. (2018). Transcriptomic characterizationand potential marker development of contrasting sugarcane cultivars. Nature 8:1683. doi: :10.1038/s41598-018-19832-x.
Yun KY, Park M, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic V, Bruskiewich R, de los Reyes B. Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant. Biol. 2010, 10, 1-29.
Zeng Q, Ling Q, Fan L, Li Y, Hu F, Chen J, et al. (2015) Transcriptome Profiling of Sugarcane Roots in Response to Low Potassium Stress. PLoS ONE 10(5): e0126306. https://doi.org/10.1371/journal.pone.0126306
ZhangJ, ZhangX, TangH, ZhangQ, HuaX, MaX, et al. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.Nature Genetics. doi: 10.1038/s41588-018-0237-2.
Zhang XL, Jia XF, Yu B, Gao Y, Bai JG. Exogenous hydrogen peroxide influences antioxidant enzyme activity and lipid peroxidation in cucumber leaves at low light. Sci. Hortic. 2011, 129, 656-662.
Downloads
Submitted
Published
Issue
Section
License
It is mandatory on the part of the corresponding author to furnish the article declaration form at the time of submission of the manuscript or after acceptance.
Authors who publish with JSR agree to the following terms:
- Authors retain copyright and grant JSR right of first publication with the work simultaneously licensed under Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
Society for Sugarcane Research and Development