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volume 34 issue 1 (march 2014) : 1-7,   Doi: 10.5958/j.0976-0547.34.1.001

TRAIT LINKED MICROSATELLITE MARKER BASED DIVERSITY ANALYSIS FOR YIELD ATTRIBUTING TRAITS IN SOME BENGAL LANDRACES OF RICE (ORYZA SATIVA L.)

T
Tirthankar Biswas*
S
Somnath Bhattacharyya
1Department of Genetics, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia – 741 252, India
Cite article:- Biswas* Tirthankar, Bhattacharyya Somnath (2025). TRAIT LINKED MICROSATELLITE MARKER BASED DIVERSITY ANALYSIS FOR YIELD ATTRIBUTING TRAITS IN SOME BENGAL LANDRACES OF RICE (ORYZA SATIVA L.). Agricultural Science Digest. 34(1): 1-7. doi: 10.5958/j.0976-0547.34.1.001.

ABSTRACT

Forty one diverse rice genotypes collected from West Bengal have been studied to assess genetic diversity using five SSR markers linked with QTL of yield attributing traits. Genotypes were grown at the Gayeshpur Regional Research Station (New Alluvial Zone), Bidhan Chandra Krishi Viswavidyalaya, West Bengal, India. Results shown that Polymorphic pattern were generated by all five SSR primers which altogether produced 14 reproducible alleles. Most of the markers generated two reproducible alleles whereas RM-3 and RM-16 generated three and four alleles respectively. The percentage of highest frequency alleles among the markers ranging from 70.73 % (RM-16) to 95.12 % (RM-5) where as PIC values varied from 0.1488 (RM-3) to 0.314 (RM-130). RM-16 generated maximum number of alleles although PIC value was maximum in case of RM-130. These two markers could be used for diversity analysis related to yield attributes in rice. The dendogram revealed 7 clusters at a cut-off similarity coefficient level of 0.64. At the similarity coefficient level of 0.35 and 0.62 Kumargore and Oradhan respectively were distinct where as rest of the genotypes grouped into 5 major clusters. On the basis of yield performance as well as presence of rare alleles of the used markers, Tulaipanji, Kumargore, Butadhan, Oradhan can be considered further as parental material for development of high yielding varieties of rice.

REFERENCES

  1. Akagi, H.; Inagaki, Y.A. and Fujimura, T. (1997). Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet., 94: 61-67.
  2. Ashikari, M.; Sakakibara, H.; Lin, S.Y.; Yamamoto, T.; Takashi, T. and Nishimura, A. (2005). Cytokinin oxidase regulates rice grain production. Science, 309: 741–745.
  3. Bautista, S.N.; Vaughan, D.; Jayasuriya, A.H.M.; Liyanage, A.S.U.; Kaga, A. and Tomooka, N. (2006). Genetic diversity in AA and CC genome Oryza species in southern South Asia. Genet. Res. Crop Evol., 53: 631–640.
  4. Causse, M.; Fulton, T.M.; Cho, Y.G.; Ahn, S.N.; Chunwongse, K.; Wu, J.; Xiao, Z.; Yu, P.C.; Ronald, S.B.;Harington, G.; Second, S.R. and McCouch, S.D. (1994). Saturated molecular map of the rice genome based on an inter specific backcross population. Genetics, 138: 1251–1274.
  5. Chakravarthy, K.B. and Rambabu, N. (2006). SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa L.). African J. Biotechnol., 5: 684–688.
  6. Chattopadhyay, K.; Bhattacharyya, S.; Mandal, N. and Sarkar, H. K. (2008). PCR-based characterization of mungbean (Vigna radiata) genotypes from Indian subcontinent at intra-and-inter-specific level. J. Plant Biochem. Biotech., 17: 141–148.
  7. Cho, Y.G.; Ishii, T.; Temnykh, S.; Chen, X.; Lipovich, L.; Park, W.D.; Ayres, N.; Cartinhour, S. and McCouch, S.R. (2000). Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet., 100: 713-722.
  8. DeWoody, J.A.; Honeycutt, R.L. and Skow, L.C. (1995). Microsatellite markers in white-tailed deer. J. Hered., 86: 317–319.
  9. Harrington, S. (2000). “A survey of genetic diversity of eight AA genome species of Oryza using microsatellite markers.” MS Thesis, Cornell University, Ithaca, NY.
  10. Kobayashi, S.; Fukuta, Y.; Morita, S.; Sato, T.; Osaki, M. and Khush, G.S. (2003). Quantitative trait loci affecting flag leaf development in rice (Oryza sativa L.). Breed. Sci., 53: 255-262.
  11. McCouch, S.R.; Temnykh, S.; Lukashova, A.; Coburn, J.; Declerck, G. and Cartinhour, S. (2001). Microsatellite markers in rice: Abundance, diversity and applications. In: Rice Genetics IV. IRRI, Manila, Philippines: 117–135.
  12. Ravi, M.; Geethanjali, S.; Sameeyafarheen, F. and Maheswaran, M. (2003). Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) using RAPD and SSR markers. Euphytica., 133: 243–252.
  13. Rohlf, F.J. (2000). NTSYS-pc: Numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Publications, New York, USA.
  14. Septiningsih, E.M.; Prasetiyono, J.; Lubis, E.; Tai, T.H.; Tjubaryat, T.; Moeljopawiro, S. and McCouch, S.R. (2003). Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor. Appl. Genet., 107: 1419–1432.
  15. Song, X. J.; Huang, W.; Shi, M.; Zhu, M. Z. and Lin, H. X. (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet., 39: 623–630.
  16. Temnykh, S.; Park, W.D.; Ayres, N.; Cartinhour, S.; Hauck, N. and Lipovtiesich, L. (2000). Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Applied Genet., 100: 697–2.
  17. Yan, J.Q., Zhu, J.; He, C.X.; Benmousa, M. and Wu, P. (1999). Molecular marker-assisted dissection of genotype × environment interaction for plant type traits in rice (Oryza sativa L.). Crop Sci., 39: 538–544.
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    volume 34 issue 1 (march 2014) : 1-7,   Doi: 10.5958/j.0976-0547.34.1.001

    TRAIT LINKED MICROSATELLITE MARKER BASED DIVERSITY ANALYSIS FOR YIELD ATTRIBUTING TRAITS IN SOME BENGAL LANDRACES OF RICE (ORYZA SATIVA L.)

    T
    Tirthankar Biswas*
    S
    Somnath Bhattacharyya
    1Department of Genetics, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia – 741 252, India
    Cite article:- Biswas* Tirthankar, Bhattacharyya Somnath (2025). TRAIT LINKED MICROSATELLITE MARKER BASED DIVERSITY ANALYSIS FOR YIELD ATTRIBUTING TRAITS IN SOME BENGAL LANDRACES OF RICE (ORYZA SATIVA L.). Agricultural Science Digest. 34(1): 1-7. doi: 10.5958/j.0976-0547.34.1.001.

    ABSTRACT

    Forty one diverse rice genotypes collected from West Bengal have been studied to assess genetic diversity using five SSR markers linked with QTL of yield attributing traits. Genotypes were grown at the Gayeshpur Regional Research Station (New Alluvial Zone), Bidhan Chandra Krishi Viswavidyalaya, West Bengal, India. Results shown that Polymorphic pattern were generated by all five SSR primers which altogether produced 14 reproducible alleles. Most of the markers generated two reproducible alleles whereas RM-3 and RM-16 generated three and four alleles respectively. The percentage of highest frequency alleles among the markers ranging from 70.73 % (RM-16) to 95.12 % (RM-5) where as PIC values varied from 0.1488 (RM-3) to 0.314 (RM-130). RM-16 generated maximum number of alleles although PIC value was maximum in case of RM-130. These two markers could be used for diversity analysis related to yield attributes in rice. The dendogram revealed 7 clusters at a cut-off similarity coefficient level of 0.64. At the similarity coefficient level of 0.35 and 0.62 Kumargore and Oradhan respectively were distinct where as rest of the genotypes grouped into 5 major clusters. On the basis of yield performance as well as presence of rare alleles of the used markers, Tulaipanji, Kumargore, Butadhan, Oradhan can be considered further as parental material for development of high yielding varieties of rice.

    REFERENCES

    1. Akagi, H.; Inagaki, Y.A. and Fujimura, T. (1997). Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet., 94: 61-67.
    2. Ashikari, M.; Sakakibara, H.; Lin, S.Y.; Yamamoto, T.; Takashi, T. and Nishimura, A. (2005). Cytokinin oxidase regulates rice grain production. Science, 309: 741–745.
    3. Bautista, S.N.; Vaughan, D.; Jayasuriya, A.H.M.; Liyanage, A.S.U.; Kaga, A. and Tomooka, N. (2006). Genetic diversity in AA and CC genome Oryza species in southern South Asia. Genet. Res. Crop Evol., 53: 631–640.
    4. Causse, M.; Fulton, T.M.; Cho, Y.G.; Ahn, S.N.; Chunwongse, K.; Wu, J.; Xiao, Z.; Yu, P.C.; Ronald, S.B.;Harington, G.; Second, S.R. and McCouch, S.D. (1994). Saturated molecular map of the rice genome based on an inter specific backcross population. Genetics, 138: 1251–1274.
    5. Chakravarthy, K.B. and Rambabu, N. (2006). SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa L.). African J. Biotechnol., 5: 684–688.
    6. Chattopadhyay, K.; Bhattacharyya, S.; Mandal, N. and Sarkar, H. K. (2008). PCR-based characterization of mungbean (Vigna radiata) genotypes from Indian subcontinent at intra-and-inter-specific level. J. Plant Biochem. Biotech., 17: 141–148.
    7. Cho, Y.G.; Ishii, T.; Temnykh, S.; Chen, X.; Lipovich, L.; Park, W.D.; Ayres, N.; Cartinhour, S. and McCouch, S.R. (2000). Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet., 100: 713-722.
    8. DeWoody, J.A.; Honeycutt, R.L. and Skow, L.C. (1995). Microsatellite markers in white-tailed deer. J. Hered., 86: 317–319.
    9. Harrington, S. (2000). “A survey of genetic diversity of eight AA genome species of Oryza using microsatellite markers.” MS Thesis, Cornell University, Ithaca, NY.
    10. Kobayashi, S.; Fukuta, Y.; Morita, S.; Sato, T.; Osaki, M. and Khush, G.S. (2003). Quantitative trait loci affecting flag leaf development in rice (Oryza sativa L.). Breed. Sci., 53: 255-262.
    11. McCouch, S.R.; Temnykh, S.; Lukashova, A.; Coburn, J.; Declerck, G. and Cartinhour, S. (2001). Microsatellite markers in rice: Abundance, diversity and applications. In: Rice Genetics IV. IRRI, Manila, Philippines: 117–135.
    12. Ravi, M.; Geethanjali, S.; Sameeyafarheen, F. and Maheswaran, M. (2003). Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) using RAPD and SSR markers. Euphytica., 133: 243–252.
    13. Rohlf, F.J. (2000). NTSYS-pc: Numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Publications, New York, USA.
    14. Septiningsih, E.M.; Prasetiyono, J.; Lubis, E.; Tai, T.H.; Tjubaryat, T.; Moeljopawiro, S. and McCouch, S.R. (2003). Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor. Appl. Genet., 107: 1419–1432.
    15. Song, X. J.; Huang, W.; Shi, M.; Zhu, M. Z. and Lin, H. X. (2007). A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet., 39: 623–630.
    16. Temnykh, S.; Park, W.D.; Ayres, N.; Cartinhour, S.; Hauck, N. and Lipovtiesich, L. (2000). Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Applied Genet., 100: 697–2.
    17. Yan, J.Q., Zhu, J.; He, C.X.; Benmousa, M. and Wu, P. (1999). Molecular marker-assisted dissection of genotype × environment interaction for plant type traits in rice (Oryza sativa L.). Crop Sci., 39: 538–544.
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