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Research Article

volume 44 issue 4 (april 2021) : 388-400,   Doi: 10.18805/LR-4119

Cross transferability of Chickpea genic SSR markers developed from Fusarium wilt resistance loci to orphan legumes

R
R. Raghu1
R
R.L. Ravikumar1,*
A
A.E. Sunil Subramanya1
1Department of Plant Biotechnology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra Campus, Bengaluru-560 065, Karnataka, India.

  • Submitted10-01-2019|

  • Accepted04-04-2019|

  • First Online 11-01-2020|

  • doi 10.18805/LR-4119

Cite article:- Raghu R., Ravikumar R.L., Subramanya Sunil A.E. (2019). Cross transferability of Chickpea genic SSR markers developed from Fusarium wilt resistance loci to orphan legumes . Legume Research. 44(4): 388-400. doi: 10.18805/LR-4119.

ABSTRACT

The availability of genomic resources in orphan legumes is limited for molecular research because of the high cost involved in development of SSR marker pool. In this study, 162 genic SSR markers derived from Fusarium wilt resistant genomic loci of chickpea were tested for cross-genera transferability across nine other legumes viz., cowpea, horse gram, black gram, pigeon pea, dolichos, rice bean, winged bean, soya bean and moth bean. Nineteen markers of chickpea amplified the genomic DNA of all other legumes indicating the sequence conserved across the genera. However, the markers exhibiting the cross-genera transferability is ranging from 24.40 to 32.14 %. The observed cross-genera transferability was highest in the cowpea (32.14 %), reflected in the closer relationship with chickpea followed by rice bean (31.55 %). The least transferability was reported in moth bean (24.40 %). These transferable genic SSR markers will serve as a valuable tool in genomic research of orphan legumes.

REFERENCES


  1. Aggarwal R.K., Hendre P.S., Varshney R.K., Bhat P.R., Krishnakumar V. and Singh L. (2007). Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics. 114(2): 359.

  2. Andersen J.R., and Lubberstedt T. (2003). Functional markers in plants. Trends in Plant Science. 8: 554–560.

  3. Cannon S.B., Sato S., Tabata S., Young N.D., and May G.D. (2011). Legumes as a model plant family. In: [Pratap A, Kumar J, (eds)]. Biology and Breeding of Food Legumes, Centre for Agriculture and Bioscience International, Oxfordshire, UK, 350p.

  4. Chaitieng B., Kaga A., Tomooka N., Isemura T., Kuroda Y. and Vaughan D.A. (2006). Development of a blackgram (Vigna mungo L. Hepper) linkage map and its comparison with an Azuki bean (Vigna angularis) Willd Ohwi and Ohashi linkage map. Theoretical and Applied Genetics. 113: 1261-1269

  5. Choudhary S., Sethy N.K., Shokeen B., and Bhatia S. (2009). Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics. 118: 591-608.

  6. Disasa T., Feyissa T. and Sertse D., (2016). Transferability of sorghum microsatellite markers to bamboo and detection of polymorphic markers. The Open Biotechnology Journal. 10: 223-233.

  7. Doyle J.J. and Doyle J.L. (1987). A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochemical bulletin. 19: 11-15.

  8. Erayman M., Ilhan E., Güzel Y. and Eren A.H. (2014). Transferability of SSR markers from distantly related legumes to Glycyrrhiza species. Turkish Journal of Agriculture and Forestry. 38(1): 32-38.

  9. Fan L., Zhang M.Y., Liu Q.Z., Li L.T., Song Y., Wang L.F., Zhang S.L. and Wu J. (2013). Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter. 31(6): 1271-1282.

  10. Gujaria N., Kumar A., Dauthal P., Dubey A., Hiremath P., Prakash A.B., Farmer A., Bhide M., et al. (2011). Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theoretical and Applied Genetics. 122(8): 1577-1589.

  11. Gupta P.K., Rustgi S., Sharma S., Singh R., Kumar N. and Balyan H.S. (2003). Transferable EST-SSRs markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics. 270: 315-323.

  12. Gupta and Prasad (2009). Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome. 52(9): 761-71.

  13. Gupta S.K. and Gopalakrishna T. (2010). Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome. 53(7): 508-523.

  14. He G., Woullard F.E., Marong I. and Guo B.Z. (2006). Transferability of soybean SSR markers in peanut (Arachis hypogaea L.). Peanut Science. 33(1): 22-28.

  15. Hou S., Sun Z., Li Y., Wang Y., Ling H., Xing G., Han Y. and Li H. (2017). Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae). Applications in Plant Sciences. 5(7): 1600137.

  16. Jafari N., Behroozi R., Bagheri A. and Moshtaghi N. (2013). Determination of genetic diversity of cultivated chickpea (Cicer arietinum L.) using Medicago truncatula EST-SSRs. Journal of Plant Molecular Breeding: 2: 1-6

  17. Jain M., Misra G., Patel R.K., Priya P., Jhanwar S., Khan A.W., Shah N., Singh V.K., Garg R. and Jeena G. (2013). A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant Journal. 74(5): 715-723.

  18. Jain M., Pole A.K., Singh V.K., Ravikumar R.L. and Garg R. (2015). Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars. Molecular Breeding. 35(10): 1-8.

  19. Jingade P., Bhosale L.V., Sanjayrao J.A., Rajanna R., Jain M. and Ravikumar R.L. (2014). Characterization of microsatellite markers, their transferability to orphan legumes and use in determination of genetic diversity among chickpea (Cicer arietinum L.) cultivars. Journal of Crop Science and Biotechnology. 17(3): 191-199.

  20. Kuleung C., Baenziger P.S. and Dweikat I. (2004). Transferability of SSR markers among wheat, rye, and triticale. Theoretical and Applied Genetics. 108(6): 1147-1150. 

  21. Miah G., Rafii M.Y., Ismail M.R., Puteh A.B., Rahim H.A., Islam K.N. and Latif M.A. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International Journal of Molecular Sciences. 14(11): 22499–22528. 

  22. Poncet V., Rondeau M., Tranchant C., Cayrel A., Hamon S., De Kochko A. and Hamon P. (2006). SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus. Molecular Genetics and Genomics. 276(5): 436-449.

  23. Peakall R., Gilmore S., Keys W., Morgante M. and Rafalski A. (1998). Cross-species amplification of soybean (Glycine max) simple sequence repeats (microsatellites) within the genus and other legume genera-implications for the transferability of microsatellites    in plants. Molecular Biology and Evolution. 15: 1275–1287. 

  24. Raghu R. and Ravikumar R.L. (2016) Development of novel microsatellite markers using genome sequence information in chickpea (Cicer arietinum L.). Mysore Journal of Agricultural Sciences. 50(2): 395-399.

  25. Ramu P., Deshpande S.P., Senthilvel S., Jayashree B., Billot C., Deu M., Anandareddy L. and Hash C.T. (2010). In silico mapping of important genes and markers available in the public domain for efficient sorghum breeding. Molecular Breeding. 26: 409–418.

  26. Satya P., Paswan P.K., Ghosh S., Majumdar S. and Ali N. (2016). Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species. 3 Biotech. 6(1): 65. 

  27. Squirrell J., Hollingsworth P.M, Woodhead M., Russell J., Lowe A.J., Gibby M. and Powell W. (2003). How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology. 12: 1339–1348.

  28. Thumilan B.M., Sajeevan R.S., Biradar J., Madhuri T., Nataraja K.N. and Sreeman S.M. (2016). Development and characterization of genic SSR markers from Indian mulberry transcriptome and their transferability to related species of Moraceae. PloS one. 11(9): e0162909.

  29. Thiel T., Michalek W., Varshney R.K. and Graner A. (2003). Exploiting EST databases for the development and characterization of genederived SSR markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics. 106: 411–422.

  30. Varshney R.K., Song C., Saxena R.K., Azam S., Yu S., Sharpe A.G., Cannon S., Baek J., et al., (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology. 31: 240-246.

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

  32. Varshney R.K. (2010). Gene-based marker systems in plants: high throughput approaches for discovery and genotyping. In: Molecular Techniques in Crop Improvement. [Jain S M, Brar D S (eds)] Springer, The Netherlands, 119–142p.

  33. Varshney R.K., Hiremath P.J., Lekha P., Kashiwagi J., Balaji J., Deokar A.A., Vadez V., Xiao Y., et al. (2009). A comprehensive resource of drought-and salinity responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics. 10: 523

  34. Yan Z., Wu F., Luo K., Zhao Y., Yan Q., Zhang Y., Wang Y. and Zhang J. (2017). Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research. Scientific Reports. 7(1):17959.

  35. Zhang M., Mao W., Zhang G. and Wu F. (2014). Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One. 9(4): e94881.
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    Research Article

    volume 44 issue 4 (april 2021) : 388-400,   Doi: 10.18805/LR-4119

    Cross transferability of Chickpea genic SSR markers developed from Fusarium wilt resistance loci to orphan legumes

    R
    R. Raghu1
    R
    R.L. Ravikumar1,*
    A
    A.E. Sunil Subramanya1
    1Department of Plant Biotechnology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra Campus, Bengaluru-560 065, Karnataka, India.

    • Submitted10-01-2019|

    • Accepted04-04-2019|

    • First Online 11-01-2020|

    • doi 10.18805/LR-4119

    Cite article:- Raghu R., Ravikumar R.L., Subramanya Sunil A.E. (2019). Cross transferability of Chickpea genic SSR markers developed from Fusarium wilt resistance loci to orphan legumes . Legume Research. 44(4): 388-400. doi: 10.18805/LR-4119.

    ABSTRACT

    The availability of genomic resources in orphan legumes is limited for molecular research because of the high cost involved in development of SSR marker pool. In this study, 162 genic SSR markers derived from Fusarium wilt resistant genomic loci of chickpea were tested for cross-genera transferability across nine other legumes viz., cowpea, horse gram, black gram, pigeon pea, dolichos, rice bean, winged bean, soya bean and moth bean. Nineteen markers of chickpea amplified the genomic DNA of all other legumes indicating the sequence conserved across the genera. However, the markers exhibiting the cross-genera transferability is ranging from 24.40 to 32.14 %. The observed cross-genera transferability was highest in the cowpea (32.14 %), reflected in the closer relationship with chickpea followed by rice bean (31.55 %). The least transferability was reported in moth bean (24.40 %). These transferable genic SSR markers will serve as a valuable tool in genomic research of orphan legumes.

    REFERENCES


    1. Aggarwal R.K., Hendre P.S., Varshney R.K., Bhat P.R., Krishnakumar V. and Singh L. (2007). Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics. 114(2): 359.

    2. Andersen J.R., and Lubberstedt T. (2003). Functional markers in plants. Trends in Plant Science. 8: 554–560.

    3. Cannon S.B., Sato S., Tabata S., Young N.D., and May G.D. (2011). Legumes as a model plant family. In: [Pratap A, Kumar J, (eds)]. Biology and Breeding of Food Legumes, Centre for Agriculture and Bioscience International, Oxfordshire, UK, 350p.

    4. Chaitieng B., Kaga A., Tomooka N., Isemura T., Kuroda Y. and Vaughan D.A. (2006). Development of a blackgram (Vigna mungo L. Hepper) linkage map and its comparison with an Azuki bean (Vigna angularis) Willd Ohwi and Ohashi linkage map. Theoretical and Applied Genetics. 113: 1261-1269

    5. Choudhary S., Sethy N.K., Shokeen B., and Bhatia S. (2009). Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics. 118: 591-608.

    6. Disasa T., Feyissa T. and Sertse D., (2016). Transferability of sorghum microsatellite markers to bamboo and detection of polymorphic markers. The Open Biotechnology Journal. 10: 223-233.

    7. Doyle J.J. and Doyle J.L. (1987). A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochemical bulletin. 19: 11-15.

    8. Erayman M., Ilhan E., Güzel Y. and Eren A.H. (2014). Transferability of SSR markers from distantly related legumes to Glycyrrhiza species. Turkish Journal of Agriculture and Forestry. 38(1): 32-38.

    9. Fan L., Zhang M.Y., Liu Q.Z., Li L.T., Song Y., Wang L.F., Zhang S.L. and Wu J. (2013). Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter. 31(6): 1271-1282.

    10. Gujaria N., Kumar A., Dauthal P., Dubey A., Hiremath P., Prakash A.B., Farmer A., Bhide M., et al. (2011). Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theoretical and Applied Genetics. 122(8): 1577-1589.

    11. Gupta P.K., Rustgi S., Sharma S., Singh R., Kumar N. and Balyan H.S. (2003). Transferable EST-SSRs markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics. 270: 315-323.

    12. Gupta and Prasad (2009). Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome. 52(9): 761-71.

    13. Gupta S.K. and Gopalakrishna T. (2010). Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome. 53(7): 508-523.

    14. He G., Woullard F.E., Marong I. and Guo B.Z. (2006). Transferability of soybean SSR markers in peanut (Arachis hypogaea L.). Peanut Science. 33(1): 22-28.

    15. Hou S., Sun Z., Li Y., Wang Y., Ling H., Xing G., Han Y. and Li H. (2017). Transcriptomic analysis, genic SSR development, and genetic diversity of proso millet (Panicum miliaceum; Poaceae). Applications in Plant Sciences. 5(7): 1600137.

    16. Jafari N., Behroozi R., Bagheri A. and Moshtaghi N. (2013). Determination of genetic diversity of cultivated chickpea (Cicer arietinum L.) using Medicago truncatula EST-SSRs. Journal of Plant Molecular Breeding: 2: 1-6

    17. Jain M., Misra G., Patel R.K., Priya P., Jhanwar S., Khan A.W., Shah N., Singh V.K., Garg R. and Jeena G. (2013). A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant Journal. 74(5): 715-723.

    18. Jain M., Pole A.K., Singh V.K., Ravikumar R.L. and Garg R. (2015). Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars. Molecular Breeding. 35(10): 1-8.

    19. Jingade P., Bhosale L.V., Sanjayrao J.A., Rajanna R., Jain M. and Ravikumar R.L. (2014). Characterization of microsatellite markers, their transferability to orphan legumes and use in determination of genetic diversity among chickpea (Cicer arietinum L.) cultivars. Journal of Crop Science and Biotechnology. 17(3): 191-199.

    20. Kuleung C., Baenziger P.S. and Dweikat I. (2004). Transferability of SSR markers among wheat, rye, and triticale. Theoretical and Applied Genetics. 108(6): 1147-1150. 

    21. Miah G., Rafii M.Y., Ismail M.R., Puteh A.B., Rahim H.A., Islam K.N. and Latif M.A. (2013). A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. International Journal of Molecular Sciences. 14(11): 22499–22528. 

    22. Poncet V., Rondeau M., Tranchant C., Cayrel A., Hamon S., De Kochko A. and Hamon P. (2006). SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus. Molecular Genetics and Genomics. 276(5): 436-449.

    23. Peakall R., Gilmore S., Keys W., Morgante M. and Rafalski A. (1998). Cross-species amplification of soybean (Glycine max) simple sequence repeats (microsatellites) within the genus and other legume genera-implications for the transferability of microsatellites    in plants. Molecular Biology and Evolution. 15: 1275–1287. 

    24. Raghu R. and Ravikumar R.L. (2016) Development of novel microsatellite markers using genome sequence information in chickpea (Cicer arietinum L.). Mysore Journal of Agricultural Sciences. 50(2): 395-399.

    25. Ramu P., Deshpande S.P., Senthilvel S., Jayashree B., Billot C., Deu M., Anandareddy L. and Hash C.T. (2010). In silico mapping of important genes and markers available in the public domain for efficient sorghum breeding. Molecular Breeding. 26: 409–418.

    26. Satya P., Paswan P.K., Ghosh S., Majumdar S. and Ali N. (2016). Confamiliar transferability of simple sequence repeat (SSR) markers from cotton (Gossypium hirsutum L.) and jute (Corchorus olitorius L.) to twenty two Malvaceous species. 3 Biotech. 6(1): 65. 

    27. Squirrell J., Hollingsworth P.M, Woodhead M., Russell J., Lowe A.J., Gibby M. and Powell W. (2003). How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology. 12: 1339–1348.

    28. Thumilan B.M., Sajeevan R.S., Biradar J., Madhuri T., Nataraja K.N. and Sreeman S.M. (2016). Development and characterization of genic SSR markers from Indian mulberry transcriptome and their transferability to related species of Moraceae. PloS one. 11(9): e0162909.

    29. Thiel T., Michalek W., Varshney R.K. and Graner A. (2003). Exploiting EST databases for the development and characterization of genederived SSR markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics. 106: 411–422.

    30. Varshney R.K., Song C., Saxena R.K., Azam S., Yu S., Sharpe A.G., Cannon S., Baek J., et al., (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology. 31: 240-246.

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

    32. Varshney R.K. (2010). Gene-based marker systems in plants: high throughput approaches for discovery and genotyping. In: Molecular Techniques in Crop Improvement. [Jain S M, Brar D S (eds)] Springer, The Netherlands, 119–142p.

    33. Varshney R.K., Hiremath P.J., Lekha P., Kashiwagi J., Balaji J., Deokar A.A., Vadez V., Xiao Y., et al. (2009). A comprehensive resource of drought-and salinity responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics. 10: 523

    34. Yan Z., Wu F., Luo K., Zhao Y., Yan Q., Zhang Y., Wang Y. and Zhang J. (2017). Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research. Scientific Reports. 7(1):17959.

    35. Zhang M., Mao W., Zhang G. and Wu F. (2014). Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One. 9(4): e94881.
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