Abstract
Availability of transcriptome datasets for use in accelerated molecular-based breeding in Musa species is limited. Illumina Hiseq technology was employed to determine differential gene expression between the contrasting cultivars for three different stresses (Eumusae leaf spot –Mycosphaerella eumusae, root lesion nematode – Pratylenchus coffeae and moisture deficit stress) under challenged and unchallenged conditions. An average of 34.72 million of reads was assembled into ~47629 contigs, and ~5,466 simple sequence repeats (SSR) from each library were identified. GO annotation and KEGG pathway analysis were carried for all the transcripts and the SSR, SNPs were also detected. Based on this information, a MusatransSSRDB has been developed. Currently, the database consists of 32,800 SSRs with the unique information like putative function of the SSR-containing genes and their metabolic pathway and expression profiling under various stress conditions. This database provides information on in silico polymorphic SSRs (2830 SSRs) between the contrasting cultivars for each stress and within stress. Information on in silico polymorphic SSRs specific to differentially expressed genes under challenged condition for each stress can also be accessed. This database facilitates the retrieval of results by navigating the tabs for cultivars, stress and polymorphism. This database was developed using HTML, Java and PHP; datasets are stored in MySQL database and accessible in the public domain (http://bioinfnrcb.byethost7.com/nrcbbio/). This unique information facilitates the banana breeder to select the SSR primers based on specific objectives. MusatransSSRDB along with other genomics databases will facilitate the genetic dissection and breeding for complex traits in banana. Thus, this database is a step forward in economizing cost, time, manpower and other resources.
Similar content being viewed by others
Abbreviations
- BLAST:
-
Basic Local Alignment Search Tool
- GO:
-
gene ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- SCTs:
-
SSR-containing transcripts
- SSR:
-
simple sequence repeats
References
Atkinson NJ and Urwin PE 2012 The interaction of plant biotic and abiotic stresses: from genes to the field. J. Exp. Bot. 63 3523–3543
Backiyarani S, Uma S, Saraswathi MS and Chandrasekar A 2014 Transcriptome Analysis of Musa and its applications in banana improvement; in Sustainable Horticultural Systems (eds) Nandwani D (Springer, Cham) pp 275–299
Backiyarani S, Uma S, Saraswathi MS, Saravanakumar AS and Chandrasekar A 2015 Transcriptome analysis of banana (Musa balbisiana) based on next generation sequencing technology. Turk. J. Agric. Forest 39 705–717
Backiyarani S, Uma S, Varatharj P and Saraswathi MS 2012 Mining of EST-SSR markers of Musa and their transferability studies among the members of order the Zingiberales. Appl. Biochem. Biotechnol. 169 228–238
Dela Cruz FS, Jr., Gueco LS, Damasco OP, Huelgas VC, dela Cueva FM, Dizon TO, Sison MLJ, Banasihan IG, Sinohin VO and Molina AB Jr 2008 Farmers’ handbook on introduced and local banana cultivars in the Philippines. (Bioversity Int) p 67
Doddamani D, Katta MA, Khan AW, Agarwal G, Shah TM and Varshney RK 2014 CicArMiSatDB: the chickpea microsatellite database. BMC Bioinformatics 15 212
Gadaleta A, Giancaspro A, Giove SL, Zacheo S, Mangini G, Simeone R, Signorile A and Blanco A 2009 Genetic and physical mapping of new EST-derived SSRs on A and B genome chromosomes of wheat. Theor. Appl. Genet. 118 1015–1025
Heslop-Harrison JS and Schwarzacher T 2007 Domestication, genomics and the future for banana. Ann. Bot. 100 1073–1084
Kadkhodaei S, Khayyam Nekouei M, Shahnazari M, Etminani H, Imani A, Ghaderi Zefrehei M, Elahy M and Arbakariya BA 2011 Molecular tagging of agronomic traits using simple sequence repeats: Informative markers for almond (Prunusdulcis) molecular breeding. Aust. J. Crop. Sci. 5 1199–1209
Kaliyappan R, Viswanathan S, Suthanthiram B, Subbaraya U, MarimuthuSomasundram S and Muthu M 2016 Evolutionary expansion of WRKY gene family in banana and its expression profile during the infection of root lesion nematode, Pratylenchuscoffeae. PLoS ONE 11 e0162013
Li C, Shao J, Wang Y, Li W, Guo D, Yan B, Xia Y and Peng M 2013 Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. Cubense. BMC Genomics 14 851
Loh JP, Kiew K, Set O, Gan LH and Gan YY 2000 Amplified fragment length polymorphism fingerprinting of 16 banana cultivars (Musa cvs.). Mol. Phylogenet. Evol. 17 360–366
MathiThumilan B, Sajeevan RS, Biradar J, Madhuri T, Nataraja K and Sreeman SM 2016 Development and characterization of genic SSR MARKERS from Indian mulberry transcriptome and their transferability to related species of Moraceae. PLoS ONE 11 e0162909
Menon R, Cherian A, Suma A, Maicykutty Mathew P, Nair S and Aipe KC 2011 Developing resistant banana and plantain cultivars through conventional breeding techniques. Acta Hort. 897 207–213
Muthusamy M, Uma S, Backiyarani S, Saraswathi MS and Chandrasekar A 2016 Transcriptomic changes of drought-tolerant and sensitive banana cultivars exposed to drought stress. Front. Plant Sci. 7 1609
Passos MA, de Cruz VO, Emediato FL, de Teixeira CC, Azevedo VC, Brasileiro AC, Amorim EP, Ferreira CF, et al. 2013 Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. BMC Genomics 14 78
Ravi I, Uma S, Vaganan MM and Mustaffa MM 2013 Phenotyping bananas for drought resistance. Front. Physiol. 4 9
Saha S, Karaca M, Jenkins J N, Zipf AE, Reddy O U K and Kantety RV 2003 Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130 355–364
Tabbasam N, Zafa Y and Mehboob-ur-Rahman 2014 Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium. Plant. Syst. Evol. 300 559–575
Thiel T, Michalek W, Varshney RK and Graner A 2003 Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106 411–422
Uma S, Backiyarani S, Saravanakumar AS, Chandrasekar A, Thangavelu R and Saraswathi MS 2016 Identification of Mycosphaerella eumusae responsive unique genes/transcripts from a resistant banana cultivar. Acta Hortic. 1114 https://doi.org/10.17660/actahortic.2016.1114.16
Acknowledgements
This study was supported by Indian Council of Agricultural Research (ICAR), India, under the project NPTC–Functional Genomics. We express our sincere gratitude to Director, ICAR–National Research Centre for Banana, India, for the facilities provided to develop this database.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by BJ Rao.
Corresponding editor: BJ Rao
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Backiyarani, S., Chandrasekar, A., Uma, S. et al. MusatransSSRDB (a transcriptome derived SSR database) – An advanced tool for banana improvement. J Biosci 44, 4 (2019). https://doi.org/10.1007/s12038-018-9819-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s12038-018-9819-5