Advertisement

Physiology and Molecular Biology of Plants

, Volume 25, Issue 2, pp 407–419 | Cite as

Seedling stage salt stress response specific characterization of genetic polymorphism and validation of SSR markers in rice

  • Rima Kumari
  • Pankaj Kumar
  • V. K. SharmaEmail author
  • Harsh Kumar
Research Article
  • 108 Downloads

Abstract

Salt tolerance status at early seedling stage in 30 rice varieties including two tolerant (Pokkali and CSR-36) and two susceptible (IR-29 and IR-64) checks was assessed under different levels of salinity (0, 4, 8 and 16 dS m−1) created by salt mixture of NaCl, CaCl2, Na2SO4 in 7:2:1 ratio. Overall salinity tolerance indices clearly reflected that 17 varieties including the two tolerant checks were highly tolerant, seven varieties exhibited moderately tolerant, whereas six varieties including the two susceptible checks had highly susceptible response to salt stress. Molecular profiling of 13 tolerant and 5 susceptible rice varieties by using 24 SSR markers revealed 8.5 alleles per primer with altogether 114 shared and 91 unique allelic variants. Considering the allele number, polymorphism information content and polymorphism percent, SSR primers RM 302, RM 8094, RM 10665, RM 10694, RM 10748 and RM 10825 appeared to be highly polymorphic and comparatively more informative. Hierarchical classification and spatial distribution patterns based on amplification profiles dependent similarity indices unambiguously discriminated these 18 varieties in accordance with their salt tolerance response. Sequential exclusion of primers in further analysis led to validation of RM 140, RM 1287, RM 3412, RM 10745, RM 10764 and RM 10772 for their efficiency to distinguish salt tolerant varieties from susceptible ones. A specific combination of either four (RM 1287, RM 3412, RM 10764 and RM 10772) or even two markers (RM 1287 and RM 3412) also seemed to be equally effective in discrimination of entries according to their salt stress responsiveness. Principal coordinate analysis completely corroborated hierarchical classification of the varieties. Salt tolerance donors identified and SSR primers validated in the present study may be further utilized in the development of salt stress tolerant varieties of rice.

Keywords

Rice Salt tolerance Principal component analysis SSR markers Principal coordinate analysis 

Abbreviations

CTAB

Cetyl trimethyl ammonium bromide

CRD

Completely randomized design

PIC

Polymorphism information content

PP

Polymorphism percent

QTL

Quantitative trait locus

SSR

Simple sequence repeat

PCR

Polymerase chain reaction

Notes

Acknowledgements

Authors gratefully acknowledge the support of the Department of Plant Breeding and Genetics, Dr. Rajendra Prasad Central Agricultural University, Pusa (Samastipur), India for providing rice varieties utilized in the experiment and the Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa (Samastipur), India, for providing University Fellowship to the first author during the present investigation.

References

  1. Abbas MK, Ali AS, Hasan HH, Ghal RH (2013) Salt tolerance study of six cultivars of rice (Oryza sativa L.) during germination and early seedling growth. J Agric Sci 5:250–259Google Scholar
  2. Agnihotri RK, Palni LMS, Pandey DK (2006) Screening of landraces of rice under cultivation in kumaun himalaya for salinity stress during germination and early seedling growth. Indian J Plant Physiol 11:266–272Google Scholar
  3. Ali MS, Karim MA, Hamid A (1996) Effect of sodium chloride on seed germination, growth and photosynthesis of rice. In: Abstracts: 2nd international crop science congress., p 55. New DelhiGoogle Scholar
  4. Ali MN, Yeasmin L, Gantait S, Goswami R, Chakraborty S (2014) Screening of rice landraces for salinity tolerance at seedling stage through morphological and molecular markers. Physiol Mol Biol Pla 20:411–423CrossRefGoogle Scholar
  5. Aliyu R, Adamu AK, Muazu S, Alonge SO, Gregorio GB (2011) Tagging and validation of SSR markers to salinity tolerance QTLs in rice. Int Proc Chem Biol Environ Eng 1:328–332Google Scholar
  6. Aliyu RE, Adamu AK, Muazu S, Alonge S, Gregorio GB (2013) Validation of rice markers tagged to salinity stress. Afr J Biotechnol 12:3239–3243Google Scholar
  7. Anderson JA, Chhurchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181CrossRefGoogle Scholar
  8. Bajracharya J, Steele KA, Jarvis DI, Sthapit BR, Witcombe JR (2006) Rice landraces diversity in Nepal: variability of agro- morphological traits and SSR markers in landraces from a high-altitude site. Field Crops Res 95:327–335CrossRefGoogle Scholar
  9. Bhowmik SK, Titov S, Islam MM, Siddika A, Sultana S, Haque MDS (2009) Phenotypic and genotypic screening of rice genotype at seedling stage for salt tolerance. Afr J Biotechnol 8:6490–6494Google Scholar
  10. Bhumbla DR, Singh NT (1965) Effect of salt on seed germination. Curr Sci 31:96–97Google Scholar
  11. Borba TCO, Mendes CA, Guimaraes EP, Brunes TO, Fonseca JR, Brondani RV, Brondani C (2009) Genetic variability of Brazilian rice landraces determined by SSR markers. Pesqui Agropecu Bras 44:706–712CrossRefGoogle Scholar
  12. Brondani C, Rangel PHN, Borba TCO, Brondani RPV (2003) Transferability of microsatellite and sequence tagged site markers in Oryza species. Hereditas 138:187–192CrossRefGoogle Scholar
  13. Brondani C, Caldeira KS, Borba TCO, Rangel PN, Morais OP, Castro EM, Rangel PHN, Mendonca JA, Brondani RV (2006) Genetic variability analysis of elite upland rice genotypes with SSR markers. Crop Breed Appl Biotechnol 6:9–17CrossRefGoogle Scholar
  14. Chattopadhyay K, Nath D, Mohanta RL, Bhattacharyya S, Marndi BC, Nayak AK, Singh DP, Sarkar RK, Singh ON (2014) Diversity and validation of microsatellite markers in Saltol QTL region in contrasting rice genotypes for salt tolerance at the early vegetative stage. Aust J Crop Sci 8:356–362Google Scholar
  15. Davla D, Sasidharan N, Macwana S, Chakraborty S, Trivedi R, Ravikiran R, Shsh G (2013) Molecular characterization of rice (Oryza sativa L) genotypes for salt tolerance using microsatellite markers. Bioscan 8:499–502Google Scholar
  16. De Leon TB, Linscombe S, Subudhi PK (2017) Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace `Pokkali. PLoS ONE 12:e0175361.  https://doi.org/10.1371/journal.pone.0175361 CrossRefGoogle Scholar
  17. Dhar P, Ashrafuzzaman M, Begum SN, Islam MM, Chowdhury MMH (2012) Identification of salt tolerant rice genotypes and their genetic diversity analysis using SSR markers. Int J Biosci 2:40–50Google Scholar
  18. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26(3):297–302CrossRefGoogle Scholar
  19. Doyle JJ, Doyle JN (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  20. Ebana K, Kojima Y, Fukuoka S, Nagamine T, Kawase M (2008) Development of mini core collection of Japanese rice landrace. Breed Sci 58:281–291CrossRefGoogle Scholar
  21. Ganie SA, Borgohain MJ, Kritika K, Talukdar A, Pani DR, Mondal TK (2016) Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes. Physiol Mol Biol Plants 22:107–114CrossRefGoogle Scholar
  22. Ganie SA, Karmakar J, Roychowdhury R, Mondal TK, Dey N (2014) Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome. Plant Syst Evol 300:1741–1747.  https://doi.org/10.1007/s00606-014-0999 CrossRefGoogle Scholar
  23. Garris AJ, Tai TH, Coburn SK, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638CrossRefGoogle Scholar
  24. Giarrocco LE, Marassi MA, Salerno GL (2005) Assessment of the genetic diversity in Argentine rice cultivars with SSR markers. Crop Sci 4:853–858Google Scholar
  25. Gomez KA, Gomez AA (1984) Statistical procedure for agricultural research, 2nd edn. Wiley, New YorkGoogle Scholar
  26. Gopalan C, Rama Sastri BV, Balasubramanian SC (1980) Nutritive value of Indian foods. National Institute of Nutrition (NIN), Indian Council of Medical Research, IndiaGoogle Scholar
  27. Gregorio GB, Senadhira D, Mendoza RD (1997) Screening rice for salinity tolerance. IRRI discussion paper series no. 22. International Rice Research Institute, Manila, pp 1–30Google Scholar
  28. Hariadi YC, Nurhayati AY, Soeparjono S, Arif I (2015) Screening six varieties of rice (Oryza sativa) for salinity tolerance. Procedia Environ Sci 28:78–87CrossRefGoogle Scholar
  29. Herrera TH, Duque DP, Almeida IP, Nunez GT, Pieters AJ, Martinez CP, Tohme JM (2008) Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Electron J Biotechnol 11.  https://doi.org/10.2225/vol11-issue5-fulltext-6
  30. Islam MR, Singh RK, Salam MA, Hassan L, Gregorio GB (2008) Molecular diversity of stress tolerant rice genotypes using SSR markers. Sabrao J Breed Genet 40:127–139Google Scholar
  31. Islam ASMF, Ali MR, Gregorio GB, Islam MR (2012) Genetic diversity analysis of stress tolerant rice (Oryza sativa L.). Afr J Biotechnol 11:15123–15129Google Scholar
  32. Islam SN, Islam MM, Ullah MA, Alam MS (2015) Molecular characterization of selected landraces of rice for salt tolerance using SSR markers. Int J Inno Sci Res 17:206–218Google Scholar
  33. Jamil M, Lee D, Jung KY, Ashraf M, Lee SC, Rha ES (2006) Effect of salt stress on germination and early seedling growth of four vegetables species. J Cent Eur Agric 7:273–282Google Scholar
  34. Joshi RK, Behera L (2006) Identification and differentiation of indogenous non-basmati aromatic rice genotypes of India using microsatellite markers. Afric J Biotechnol 6:48–354Google Scholar
  35. Kanawapee N, Sanitchon J, Srihaban P, Theerakulpisut P (2011) Genetic diversity analysis of rice cultivars differing in salinity tolerance based on RAPD and SSR markers. Electron J Biotechnol 14:1–15Google Scholar
  36. Kranto S, Chankaew S, Monkham T, Theerakulpisut P, Sanitchon J (2016) Evaluation for salt tolerance in rice using multiple screening methods. J Agric Sci Technol 18:1921–1931Google Scholar
  37. Kumar P, Kumari R, Sharma VK (2018) Choice of microsatellite markers for isolation of fertility restorers of wild abortive (WA) type cytoplasmic male sterility in rice. Indian J Genet Plant Breed 78:202–210CrossRefGoogle Scholar
  38. Kumari R, Sharma VK, Kumar H (2015) Seed culture of rice cultivars under salt stress. Int J Pure Appl Biosci 3:191–202Google Scholar
  39. Kumari R, Kumar P, Sharma VK, Kumar H (2016a) Molecular characterization for salinity tolerance in rice using microsatellite markers. Int J Agric Environ Biotechnol 9:163–174CrossRefGoogle Scholar
  40. Kumari R, Kumar P, Sharma VK, Kumar H (2016b) In vitro seed germination and seedling growth for salt tolerance in rice cultivars. J Cell Tissue Res 16:5901–5910Google Scholar
  41. Kumari S, Kumar P, Sharma VK (2018a) Identification of microsatellite markers for genetic differentiation and authentication of promising aerobic rice genotypes. J Pharmacogn Phytochem 7:2772–2776Google Scholar
  42. Kumari R, Kumar P, Sharma VK, Kumar H (2018b) Evaluation of salinity tolerance of rice varieties through in vitro seed germination and seedling growth. Int J Curr Microbiol Appl Sci 7(special:issue):2648–2659Google Scholar
  43. Lang NT, Li ZK, Bui CB (2001) Microsatellite markers linked to salt tolerance in rice. Omonrice 9:9–21Google Scholar
  44. Lapitan VC, Brar DS, Abe T, Redona ED (2007) Assessment of genetic diversity of Philippine rice cultivars carrying good quality traits using SSR markers. Breed Sci 57:263–270CrossRefGoogle Scholar
  45. Mass EV, Hoffman GJ (1977) Crop salt tolerance current assessment. J Irrig Drain Div ASCE 103:115–134Google Scholar
  46. Meghana HS, Hittalmani S, Gandhi RV, Meera N (2015) Phenotypic screening for salt tolerance at germination and seedling stage and SSR marker validation in rice (Oryza sativa L.). Mysore J Agric Sci 49:686–692Google Scholar
  47. Mohammadi-Nejad G, Arzani A, Rezai AM, Singh RK, Gregorio GB (2008) Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the Saltol QTL. Afr J Biotechnol 7:730–736Google Scholar
  48. Molla KA, Debnath AB, Ganie SA, Mondal TK (2015) Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.). BMC Plant Biol 15:122.  https://doi.org/10.1186/s12870-015-0498-1 CrossRefGoogle Scholar
  49. Pervaiz ZH, Rabbani MA, Pearce SR, Malik SA (2009) Determination of genetic variability of Asian rice (Oryza sativa L.) varieties using microsatellite markers. Afr J Biotechnol 8:5641–5651CrossRefGoogle Scholar
  50. Pervaiz ZH, Rabbani MA, Khaliq I, Pearce SR, Malik SA (2010) Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces. Electron J Biotechnol 13.  https://doi.org/10.2225/vol13-issue3-fulltext-5
  51. Priyadarshini M, Kumar P, Sharma VK (2018) Molecular differentiation and classification in relation to fragrance of landraces and improved varieties of aromatic rice using microsatellite markers. Int J Chem Stud 6:3014–3021Google Scholar
  52. Qin Z, Wang Y, Wang Q, Li A, Hou F, Zhang L (2015) Evolution analysis of simple sequence repeats in plant genome. PLoS ONE 10(12):e0144108.  https://doi.org/10.1371/journalpone0144108 CrossRefGoogle Scholar
  53. Rabbani MA, Masood MS, Shinwari ZK, Shinozaki KY (2010) Genetic analysis of basmati and non-basmati Pakistani rice (Oryza sativa L.) cultivars using microsatellite markers. Pak J Bot 42:2551–2564Google Scholar
  54. Rashid MM, Imran S, Islam MA, Hassan L (2018) Genetic diversity analysis of rice landraces (Oryza sativa L.) for salt tolerance using SSR markers in Bangladesh. Fundam Appl Agric 3:460–466CrossRefGoogle Scholar
  55. Reddy PJ, Vaidyanath K (1982) Note on the salt tolerance of some rice varieties of Andra Pradesh during germination and early seedling growth. Indian J Agric Sci 52:72–474Google Scholar
  56. Reddy SKN, Reddy BM, Ankaiah R (1994) Effect of initial germination levels on vigour, growth and yield in rice. Seed Res 22:22–25Google Scholar
  57. Rohlf FJ (1997) NTSYS-pc numerical taxonomy and multivariate analysis system, version 2.00. Exeter Software, New YorkGoogle Scholar
  58. Sajib AM, Hossain MM, Mosnaz ATMZ, Hossain H, Islam MM, Ali MS et al (2012) SSR-marker based molecular characterization and genetic diversity analysis of aromatic landraces of rice (Oryza sativa L.). J Biosci Biotechnol 2:107–116Google Scholar
  59. Senadhira D (1987) Salinity as a concept to increasing rice production in Asia. In: Proeedings of. Regional Workshop in Maintenance of Life Support Species in Asia Pacific Region. NBPGR, New Delhi, IndiaGoogle Scholar
  60. Shakil SK, Sultana S, Hasan MM, Hossain MM, Ali MS, Prodhan SH (2013) SSR marker based genetic diversity analysis of modern rice varieties and coastal landraces in Bangladesh. Indian J Biotechnol 14:33–41Google Scholar
  61. Shannon MC, Rhoades JD, Draper JH, Scardaci SC, Spyres MD (1998) Assessment of salt tolerance in rice cultivars in response to salinity problems in California. Crop Sci 38:394–398CrossRefGoogle Scholar
  62. Singh RK, Gregorio GB, Jain RK (2007) QTL mapping for salinity tolerance in rice. Physiol Mol Biol Plants 13:87–99Google Scholar
  63. Singh AK, Kumar R, Singh A, Bansal S, Singh D, Tomar A (2011) Studies on genetic variability in rice using molecular markers. Vegetos 24:123–131Google Scholar
  64. Sudharani M, Reddy PR, Reddy GH (2013) Identification of genetic diversity in rice (Oryza sativa L.) genotypes using microsatellite markers for salinity tolerance. Int J Sci Innov Discov 3:22–30Google Scholar
  65. Thomson MJ, De Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:128–160.  https://doi.org/10.1007/s12284-010-9053-8 CrossRefGoogle Scholar
  66. Vasuki A, Geetha S (2016) Validation of ‘Saltol’ QTL under sodicity. Electron J Plant Breed 7:838–841CrossRefGoogle Scholar
  67. Wong SC, Yiu PH, Bong STW, Lee HH, Neoh PNP, Rajan A (2009) Analysis of Sarawak Bario rice diversity using microsatellite markers. Am J Agric Biol Sci 4:298–304CrossRefGoogle Scholar
  68. Yeo AR, Flowers TJ (1986) The physiology of salinity tolerance in rice (Oryza sativa) and a pyramiding approach to breeding varieties for saline soils. Aust J Plant Physiol 13:75–91Google Scholar

Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2018

Authors and Affiliations

  • Rima Kumari
    • 1
  • Pankaj Kumar
    • 1
  • V. K. Sharma
    • 1
    Email author
  • Harsh Kumar
    • 1
  1. 1.Department of Agricultural Biotechnology and Molecular BiologyDr. Rajendra Prasad Central Agricultural UniversityPusa (Samastipur)India

Personalised recommendations