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Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing

  • 1.

    Bandyopadhyay, T., Muthamilarasan, M. & Prasad, M. Millets for next generation climate-smart agriculture. Front. Plant Sci. 8, 1266 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 2.

    Vetriventhan, M. et al. Genetic and genomic resources, and breeding for accelerating improvement of small millets: Current status and future interventions. Nucleus 63, 1–23 (2020).

    Article 

    Google Scholar 

  • 3.

    Jones, J. Grain-based foods and health. Cereal Foods World 51, 108 (2006).

    ADS 

    Google Scholar 

  • 4.

    Lata, C., Gupta, S. & Prasad, M. Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses. Crit. Rev. Biotechnol. 33, 328–343 (2013).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    Upadhyaya, H. D., Vetriventhan, M., Dwivedi, S. L., Pattanashetti, S. K. & Singh, S. K. Genetic and Genomic Resources for Grain Cereals Improvement 321–343 (Elsevier, 2016).

    Book 

    Google Scholar 

  • 6.

    Hamid, R., Siahpoosh, M., Mamaghani, R. & Siahpoosh, A. Evaluation the genetic diversity of 10 milk thistle (Silybum marianum L.) ecotypes using morphological, phenological and phytochemical traits (2014).

  • 7.

    Zarei, A., Zamani, Z. & Sarkhosh, A. Biodiversity, germplasm resources and breeding methods. In The Pomegranate: Botany, Production and Uses 94 (2020).

  • 8.

    Sandhu, N. et al. Marker assisted breeding to develop multiple stress tolerant varieties for flood and drought prone areas. Rice 12, 1–16 (2019).

    Article 

    Google Scholar 

  • 9.

    Boopathi, N. M. Genetic Mapping and Marker Assisted Selection 107–178 (Springer, 2020).

    Book 

    Google Scholar 

  • 10.

    Rathod, V. et al. Peanut (Arachis hypogaea) transcriptome revealed the molecular interactions of the defense mechanism in response to early leaf spot fungi (Cercospora arachidicola). Plant Gene 23, 100243 (2020).

    CAS 
    Article 

    Google Scholar 

  • 11.

    Biswas, M. K. et al. Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Sci. Rep. 10, 1–13 (2020).

    Article 
    CAS 

    Google Scholar 

  • 12.

    Nadeem, M. A. et al. DNA molecular markers in plant breeding: Current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnol. Equip. 32, 261–285 (2018).

    CAS 
    Article 

    Google Scholar 

  • 13.

    Rathod, V. et al. Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis. 3 Biotech 10, 1–15 (2020).

    Article 

    Google Scholar 

  • 14.

    Cho, Y. G. et al. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 713–722 (2000).

    CAS 
    Article 

    Google Scholar 

  • 15.

    Zhang, M., Mao, W., Zhang, G. & Wu, F. Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS ONE 9, e94881 (2014).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 16.

    Taheri, S. et al. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci. Rep. 9, 1–14 (2019).

    Google Scholar 

  • 17.

    Hamid, R., Marashi, H., Tomar, R. S., Malekzadeh Shafaroudi, S. & Sabara, P. H. Transcriptome analysis identified aberrant gene expression in pollen developmental pathways leading to CGMS in cotton (Gossypium hirsutum L.). PLoS ONE 14, e0218381 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Ge, Y. et al. Transcriptome sequencing of different avocado ecotypes: De novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. Forests 10, 411 (2019).

    Article 

    Google Scholar 

  • 19.

    Mathi Thumilan, B. et al. Development and characterization of genic SSR markers from Indian mulberry transcriptome and their transferability to related species of Moraceae. PLoS ONE 11, e0162909 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Chen, H. et al. Development and validation of EST-SSR markers from the transcriptome of adzuki bean (Vigna angularis). PLoS ONE 10, e0131939 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 21.

    Sabu, K., Shehenaz, M. & Amrutha, J. Transcriptome mining for Est-Indels and development of EST-SSR markers in turmeric (Curcuma longa L.). Int. J. Agric., Environ. Biotechnol. 11, 487–491 (2018).

    Google Scholar 

  • 22.

    Tao, S.-Q., Cao, B., Tian, C.-M. & Liang, Y.-M. Development and characterization of novel genic-SSR markers in apple-Juniper rust pathogen Gymnosporangium yamadae (Pucciniales: Pucciniaceae) using next-generation sequencing. Int. J. Mol. Sci. 19, 1178 (2018).

    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 23.

    Hamid, R. et al. Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton (Gossypium hirsutum L.). Gene 660, 80–91 (2018).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Gupta, P. K. et al. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol. Genet. Genom. 270, 315–323 (2003).

    CAS 
    Article 

    Google Scholar 

  • 25.

    Tulsani, N. J. et al. Transcriptome landscaping for gene mining and SSR marker development in coriander (Coriandrum sativum L.). Genomics 112, 1545–1553 (2020).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 26.

    Karcι, H., Paizila, A., Topçu, H., Ilikçioğlu, E. & Kafkas, S. Transcriptome sequencing and development of novel genic SSR markers from Pistacia vera L. Front. Genet. 11, 1021 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 27.

    Pedrini, S. & Dixon, K. W. International principles and standards for native seeds in ecological restoration. Restor. Ecol. 28, S286–S303 (2020).

    Google Scholar 

  • 28.

    Hamid, R., Jacob, F., Marashi, H., Rathod, V. & Tomar, R. S. Uncloaking lncRNA-meditated gene expression as a potential regulator of CMS in cotton (Gossypium hirsutum L.). Genomics 112, 3354–3364 (2020).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 29.

    Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 30.

    Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 31.

    Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 32.

    Bosamia, T. C., Mishra, G. P., Thankappan, R. & Dobaria, J. R. Novel and stress relevant EST derived SSR markers developed and validated in peanut. PLoS ONE 10, e0129127 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Parekh, M. J. et al. Development and validation of novel fiber relevant dbEST–SSR markers and their utility in revealing genetic diversity in diploid cotton (Gossypium herbaceum and G. arboreum). Ind. Crops Prod. 83, 620–629 (2016).

    CAS 
    Article 

    Google Scholar 

  • 34.

    Kristamtini, K., Taryono, T., Basunanda, P. & Murti, R. H. High resolution microsatellite marker analysis of some rice landraces using metaphor agarose gel electrophoresis. Indones. J. Biotechnol. 20, 54–61 (2016).

    Article 

    Google Scholar 

  • 35.

    Asif, M., Mirza, J. & Zafar, Y. High resolution metaphor agarose gel electrophoresis for genotyping with microsatellite markers. Pak. J. Agric. Sci. 45, 75–79 (2008).

    Google Scholar 

  • 36.

    Sánchez-Pérez, R., Ballester, J., Dicenta, F., Arús, P. & Martínez-Gómez, P. Comparison of SSR polymorphisms using automated capillary sequencers, and polyacrylamide and agarose gel electrophoresis: Implications for the assessment of genetic diversity and relatedness in almond. Sci. Hortic. 108, 310–316 (2006).

    Article 
    CAS 

    Google Scholar 

  • 37.

    Weir, B. S. Genetic Data Analysis Methods for Discrete Population Genetic Data (Sinauer Associates, Inc. Publishers, 1990).

    Google Scholar 

  • 38.

    Rohlf, F. NTSYS-pc. Numerical Taxonomy and Multivariate Analysis: Version 2.02 (Exeter Software, 1998).

    Google Scholar 

  • 39.

    R Core Team. R: A Language and Environment for Statistical Computing (R Core Team, 2013).

    Google Scholar 

  • 40.

    Meyer, S., Held, L. & Höhle, M. hhh4: Endemic-epidemic modeling of areal count time series. J. Stat. Softw. 1, 1–55 (2016).

    Google Scholar 

  • 41.

    Wickham, H. Elegant graphics for data analysis. Media 35, 10–1007 (2009).

    MATH 

    Google Scholar 

  • 42.

    Sonah, H., Deshmukh, R., Sharma, A., Singh, V. & Gupta, D. Genome-wide distribution and organization of microsatellites in plants: An insight. PLoS ONE 6, e21298 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 43.

    Li, Y. et al. Benefiting others and self: Production of vitamins in plants. J. Integr. Plant Biol. 63, 210–227 (2021).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 44.

    Saleh, A. S. M. et al. Millet grains: nutritional quality, processing, and potential health benefits. Compr. Rev. Food Sci. Food Saf. 12(3), 281–295 (2013).

    CAS 
    Article 

    Google Scholar 

  • 45.

    Devi, P. B., Vijayabharathi, R., Sathyabama, S., Malleshi, N. G. & Priyadarisini, V. B. Health benefits of finger millet (Eleusine coracana L.) polyphenols and dietary fiber: A review. J. Food Sci. Technol. 51, 1021–1040 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 46.

    De, L. Edible seeds and nuts in human diet for immunity development. Int. J. Recent Sci. Res. 6, 38877–38881 (2020).

    Google Scholar 

  • 47.

    Ramashia, S. E., Anyasi, T. A., Gwata, E. T., Meddows-Taylor, S. & Jideani, A. I. O. Processing, nutritional composition and health benefits of finger millet in sub-Saharan Africa. Food Sci. Technol. 39, 253–266 (2019).

    Article 

    Google Scholar 

  • 48.

    Singh, R. K. & Prasad, M. The Foxtail Millet Genome 63–75 (Springer, 2017).

    Book 

    Google Scholar 

  • 49.

    Huang, X. et al. De novo transcriptome analysis and molecular marker development of two Hemarthria species. Front. Plant Sci. 7, 496 (2016).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Zhao, H. et al. High-throughput sequencing analysis reveals effects of short-term low-temperature storage on miRNA-mediated flavonoid accumulation in postharvest toon buds. Plant Gene 26, 100291 (2021).

    CAS 
    Article 

    Google Scholar 

  • 51.

    Zheng, X. et al. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae). BMC Genom. 14, 490 (2013).

    CAS 
    Article 

    Google Scholar 

  • 52.

    Wei, W. et al. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genom. 12, 451 (2011).

    CAS 
    Article 

    Google Scholar 

  • 53.

    Zhang, W. et al. Characterization of flower-bud transcriptome and development of genic SSR markers in Asian lotus (Nelumbo nucifera Gaertn.). PLoS ONE 9, e112223 (2014).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 54.

    Varshney, R. et al. Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor. Appl. Genet. 113, 239 (2006).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 55.

    Peng, J. & Lapitan, N. L. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct. Integr. Genom. 5, 80–96 (2005).

    CAS 
    Article 

    Google Scholar 

  • 56.

    Raju, N. L. et al. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol. 10, 45 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 57.

    Yang, Z., Peng, Z. & Yang, H. Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.). Genet. Mol. Res. 15, 15017509 (2016).

    Google Scholar 

  • 58.

    Zhai, L. et al. Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Mol. Breed. 33, 611–624 (2014).

    CAS 
    Article 

    Google Scholar 

  • 59.

    Tiwari, N., Tiwari, S. & Tripathi, N. Genetic characterization of Indian little millet (Panicum sumatrense) genotypes using random amplified polymorphic DNA markers. Agric. Nat. Resour. 52, 347–353 (2018).

    Google Scholar 

  • 60.

    Johnson, M., Deshpande, S., Vetriventhan, M., Upadhyaya, H. D. & Wallace, J. G. Genome-wide population structure analyses of three minor millets: Kodo millet, little millet, and proso millet. Plant Genome 12, 190021 (2019).

    CAS 
    Article 

    Google Scholar 

  • 61.

    Ali, A. et al. Development of EST-SSRs and assessment of genetic diversity in little millet (Panicum sumatrense) germplasm. Korean J. Plant Resour. 30, 287–297 (2017).

    Google Scholar 

  • 62.

    Das, R. R., Pradhan, S. & Parida, A. De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense. Sci. Rep. 10, 1–14 (2020).

    Article 
    CAS 

    Google Scholar 

  • 63.

    Vendramin, E. et al. A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species. Mol. Ecol. Notes 7, 307–310 (2007).

    CAS 
    Article 

    Google Scholar 

  • 64.

    Varshney, R. K., Graner, A. & Sorrells, M. E. Genic microsatellite markers in plants: Features and applications. Trends Biotechnol. 23, 48–55 (2005).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 65.

    Vieira, M. L. C., Santini, L., Diniz, A. L. & Munhoz, C. D. F. Microsatellite markers: What they mean and why they are so useful. Genet. Mol. Biol. 39, 312–328 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 66.

    Senthilvel, S. et al. Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol. 8, 1–9 (2008).

    Article 
    CAS 

    Google Scholar 

  • 67.

    Sonah, H. et al. Genome-wide distribution and organization of microsatellites in plants: An insight into marker development in Brachypodium. PLoS ONE 6, e21298 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 68.

    Temnykh, S. et al. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genom. Res. 11, 1441–1452 (2001).

    CAS 
    Article 

    Google Scholar 

  • 69.

    Xu, R., Wang, Z., Su, Y. & Wang, T. Characterization and development of microsatellite markers in Pseudotaxus chienii (Taxaceae) based on transcriptome sequencing. Front. Genet. 11, 1249 (2020).

    Google Scholar 

  • 70.

    Hina, F., Yisilam, G., Wang, S., Li, P. & Fu, C. D. novo transcriptome assembly, gene annotation and SSR marker development in the moon seed genus Menispermum (Menispermaceae). Front. Genet. 11, 380 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    You, Y. et al. Leaf transcriptome analysis and development of EST-SSR markers in arrowhead (Sagittaria trifolia L. var. Sinensis). Trop. Plant Biol. 13, 1–12 (2020).

    Article 
    CAS 

    Google Scholar 

  • 72.

    Colinas, M. & Fitzpatrick, T. B. Natures balancing act: Examining biosynthesis de novo, recycling and processing damaged vitamin B metabolites. Curr. Opin. Plant Biol. 25, 98–106 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 73.

    Strobbe, S. & Van Der Straeten, D. Toward eradication of B-vitamin deficiencies: Considerations for crop biofortification. Front. Plant Sci. 9, 443 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

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