Polymorphic SSR marker identification for water use efficiency in groundnut (Arachis hypogea L.) parental lines

DOI: 10.18805/LR-3980    | Article Id: LR-3980 | Page : 303-311
Citation :- Polymorphic SSR marker identification for water use efficiency in groundnut (Arachis hypogea L.) parental lines.Legume Research-An International Journal.2020.(43):303-311
C. Nandini, D.L. Savithramma, Pushpa Doddaraju and Pavan kumar nandini.vinutha@gmail.com
Address : Department of Genetics and Plant breeding, University of Agricultural Sciences, G.K.V.K, Bengaluru-560 065, Karnataka, India.
Submitted Date : 30-12-2017
Accepted Date : 2-04-2018

Abstract

Groundnut is world important oilseed crop; productivity is low in the semi-arid regions due to frequent occurrence of drought. Identification of genotypes that have a greater ability to use limited available water is important to enhance productivity of the crop. Water Use Efficiency (WUE) is one such important trait, which increases yield under drought situation. Low level of DNA polymorphism has been detected in most of the laboratories due to allotetraploid nature. In the present study two parental lines of Recombinant Inbred line population NRCG12568 and NRCG12326 diverse for WUE related trait, such as Carbon Isotopic Discrimination (D13C), Specific Leaf Area (SLA) and SPAD chlorophyll meter reading were studied for polymorphism using 350 simple sequence repeat (SSR) markers. Out of these, only 119 (34%) markers showed polymorphism in NRCG12568 and NRCG12326. Detection of polymorphism opens up the possibility of use of these markers for QTL map development for D13C in groundnut.

Keywords

Carbon Isotopic Discrimination (D13C) DNA polymorphism Recombinant Inbred line population (RIL).

References

  1. Anjali, B., Krishna, T.G., Bhatia, C.R., (1997), RAPD analysis of induce mutants of groundnut (Arachis hypogea L.).J. Genet. 76: 201-208.
  2. Cabuslay, G.S., Ito O., Alejar A.A., (2002). Physiological evaluation of rice (Oryza sativa) to water deficit. Plant Sci. 163: 815-827.
  3. Cuc, L.M., Mace, E.S., Crouch, J.H., Quang, V.U., Long, T.D., Varshney, R.K., (2008). Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogea L.). BMC Plant Biol. 8: 55-66.
  4. Draufurd, P.Q., Wheeler, T.R., Williams, J.H., (1999). Effect of temperature and water deficit on water use efficiency, carbon isotope discrimination and specific leaf area in peanut. Crop Sci. 39: 136-142.
  5. Ferguson, M.E., Burow, M.F, Schulze, S.R., Bramel, P.J., Paterson, A.H., Kresovich, S., Mitchell, S., (2004). Microsatellite identification and characterization in peanut (Arachis hypogea L.). Theor. Appl. Genet., 108: 1064-1070
  6. Gautami, B.K, Ravi, M.L. Narasu, D.A. Hoisington, Varshney, R.K, (2009). Novel set of groundnut SSR Markers for germplasm analysis and interspecific transferability. Int.J. Integrative Biol., 7(2), 100-106.
  7. Gimenes, M.A., Hoshino, A.V.G. Barbosa, D.A. Palmieri, Lopes, (2007). Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogea L.). BMC Plant Biol., 7: 9.
  8. Guohao, H., Meng, R., Newman, M., Gao, G., Pitman, R. and Prakash, C.S., (2003). Microsatellites as DNA markers in cultivafte peanut (Arachis hypogaea L.). BMC Pl Biol; 3 (3): 1-6.
  9. Guo, B., Chen, X., Hong, Y., Liang, X., Phat, D, Brenneman. T., Holbrook, C., Culbreath, A., (2009). Analysis of gene Expression profiles in leaf tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery. Inter J of Plant Genomics. http://dx.doi.org/10.1155/2009/715605.
  10. Gupta, P.K. and Varshney, R.K., (2000). The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica, 113: 163–185.
  11. Halward, T., Stalker, H.T., Larue, E.A., Kochert, G., (1992). Use of single primer DNA amplifications in genetic studies of peanut (Arachis hypogea L.). Plant Mol. Biol., 18: 315-325.
  12. Halward, T., Stalker, H,T., Larue, E.A., Kochert, G., (1991). Genetic variation detectable with molecular markers among unadapted germplasm resources of peanut (Arachis hypogaea L.) and related wild species. Genome. 34: 1013-1020
  13. He, G., Meng, R., Newman, M., Gao, G., Pittman, R.N, Prakash, C.S., (2003). Microsatellite as DNA Marker in cultivated Peanut (Arachis hypogea L.). BMC Plant Biol., 3: 3.
  14. Hopkins, M.S., Casa, A.M., Wang, T., Mitchell, S.E., Aean, R.E., Kochert, G.D, Kresovich, S., (1999). Discovery and characterization of polymorphic simple sequence repeats (SSR’s) in peanut. Crop Sci., 39: 1243-1247.
  15. Kolody, G.N., (1984). An improved method for increasing the resolution and sensitivity of silver staining of nucleic acid bands in polyacrylamide gels. Ann. Biochem, 138: 66-67.
  16. Latha, P., Reddy, P.V., (2007), Water use efficiency and its rearion to specific leaf area, carbon isotope discrimination and total soluble proteins under mid-season moisture stress conditions in groundnut (Arachis hypogea L.) genotypes. J. oilseeds. Res., 24: 77-80.
  17. Luo, M., Dang, P., Guo, B.Z., He G., Holbrook, C.C., Bausher, M.G., Lee, R.D. (2005), Generation of expressed sequence tags (EST’s) for gene discovery and marker development in cultivated peanut. Crop Sci., 45: 346-353. 
  18. Lu, M. C., Emma, S., Mace, Jonathan, H.C., Vu, D. Q., Tran, D. L. and Varshney, R. K. (2008). Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biology., 8:55
  19. Nelson, M.N., Phan, S.R., Ellwood, M., Moolhuijzen P.J., Williams A., O’lone C.E, Nyarko J. F., et al . The first gene-based map of lupinus angustifolius l.-location of domestication genes and conserved synteny with medicago truncatula. Theor. Appl. Genet.,113:225-238.
  20. Palmieri, D.A., Hoshino A.A., Bravo J.P., Lopes C.R. and Gimenes M.A., (2002). Isolation and characterization of microsatellite loci from the forage species Arachispintoi (Genus Arachis). Mol. ecol. Notes 255: 1-553.
  21. Proite, K., Leal, B.S.C., Bertioli, D.J., Moretzsohn, M.C., Silva, D.F.R., Martins, N.F., Guimaraes, P.M., 2007, ESTS from a wild arachis species for gene discovery and marker development. BMC plant Biol., 7: 7.
  22. Rakoczy-Trojanowska, M. and Bolibok, H., (2004). Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants. Cell Mol Biol Lett, 9(2):221-38.
  23. Rowland, D., Blankenship, P., Puppala, N., Beasley, J., Burow, M., Gorbet, D., Jordan, D., Melouk, H., Simpson, C., and Bostick, J. (2004).Variation in water-use efficiency of peanut varieties across peanut production regions. Proceedings for the 4th International Crop Science Congress, Brisbane, Australia, 26 September–1 October.
  24. Sagai- maroof, M.A., Soliman, R.A., Jorgensen, Allard, R.W., (1984). Ribosomal DNA spacer- length polymorphism in barley: mendelian inheritance, chromosomal location and population dynamics. Proceedings of National Academy Of Sciences, U.S.A., 81: 8014-8018.
  25. Smartt J, (2012) The Groundnut Crop: A Scientific Basis For Improvement. Springer Science & Business Media,
  26. Varshney, R.K., Bertioli, D.J., Moretzsohn, M.C., Vadez, V., Krishnamurthy, L., Aruna, R., Nigam, S.N., Moss, B.J., Seetha, K., Ravi, K., He, G., Knapp, S. J., Hoisington, D.A., (2009). The first SSR based genetic linkage map for cultivated groundnut (Arachis Hypogea L.). Theor. appl. genet., 118:729-739.
  27. Varshney, R.K., Mahendar, T., Aruna, R., Igam, S.N., Neelima, K., Vadez, V., Hoisington, D.A., (2009). High level of natural variation in a groundnut (Arachis Hypogea L.) germplasm collection assayed by selected informative SSR markers. Plant Breed. 128(5), 486-494. 
  28. Varshney, R.K., Mahendar, T., Aruna, R., Nigam, S.N., Neelima, K., Vadez, V., Hoisington, D.A., (2009). High level of natural variation in a groundnut (Arachis Hypogea L.) germplasm collection assayed by selected informative ssr markers. Plant Breed. 128(5), 486-494. 
  29. Wang, C.T. Yang X.D, D.X. Chen, S.L. Yu, G.Z. Liu, Y.Y. Tang, J.Z. Xu, (2007). Isolation of simple sequence repeats from groundnut. Electronic J. Biotech., 10(3), 473-480. 

Global Footprints