International Journal of Genetics and Genomics

| Peer-Reviewed |

Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh

Received: 16 December 2018    Accepted: 28 December 2018    Published: 28 January 2019
Views:       Downloads:

Share This Article

Abstract

Bangladesh had harbored numerous submergence tolerant rice local cultivars or landraces (popularly known as Joli Aman). As the local cultivars endure intervallic flash-flooding year after year, it is presumed that genes/Quantitative Trait Loci (QTLs) that give resilience are probably going to be available in these genotypes. In submergence screening, the performance of three tested accessions (Lakhi, Atshotti and Damsi) demonstrated them to be as tolerant as the check FR13A. Other germplasm accessions (DSL-78-8, Laldepa, Putidepa, Laxmi digha) performed great recuperation capacity after de-submergence. Damsi, Rajasail, Haloi, Lal Digha, Manik Digha, Bhawalia, DSL-78-8, Putidepa, Atshotti and Jalda IRRI don't have the SUB1 QTL and furthermore not like the BR5, a submergence susceptible check variety. Bajal, Horkoach, Pathornuti, Laxmi Digha, Horinga Digha, Bhawalia Digha and BR5 was not amplified by Gns2 conferring SUB1 QTL (submergence tolerance specific QTL). Significantly, the local cultivars i.e. DSL-78-8, Putidepa and Sadadanga boro were identified as having better submergence tolerance however having no resistant alleles of GnS2 and Sub1C173, indel markers specific to SUB1 QTL. The result of molecular screening revealed new submergence tolerant rice cultivars which do not possess SUB1 QTL. To discover new submergence tolerant QTLs other than SUB1 through QTL mapping, newly identified submergence tolerant germplasm can be utilized.

DOI 10.11648/j.ijgg.20180604.12
Published in International Journal of Genetics and Genomics (Volume 6, Issue 4, December 2018)
Page(s) 44-51
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Submergence, Molecular Screening, Accessions, Landraces, SUB1 QTL, Indel Markers

References
[1] Pusadee, T., Jamjod, S., Chiang, Y. C., Rerkasem, B., Schaal, B. A. (2009). Genetic structure and isolation by distance in 482 a landrace of Thai rice. Proc Nat Acad Sci 106:13880-13885.
[2] Yang, J., Kloepper, J. W., Ryu, C. M. (2009). Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14:1–4
[3] Zhao, D. Y., Ma, T., Zeng, J., Yan, W. M., Wang, J. Q., Huang, R., Wang, M. (2011). Effects of lake water chemistry on bacterioplankton community structures of three lakes. Afr. J. Microbiol. Res., 5: 4820-4831.
[4] Hanamaratti, N., Prashanthi, S., Salimath, P. M., Hanchinal, R. R., Mohankumar, H. D., Parameshwarappa, K. G., Raikar, S. D. (2008). Traditional land races of rice in Karnataka: Reservoirs of valuable traits. Current Science. 94. 242-247.
[5] Lisa, A. L., Sabrina, L., Rahman, M., Saima S., Iwasaki, T., Hasan, A. K. M., Kosuge, K., Fukami, Y. & Seraj, Z. (2011). Physiology and gene expression of the rice landrace Horkuch under salt stress. Functional Plant Biology. 38. 282-292. 10.1071/FP10198.
[6] Matin, S., Ashrafuzzaman, M., Islam, M., Sikdar, S., Zobayer, N. (2012). Molecular marker based (SSR) genetic diversity analysis in deep water rice germplasms of Bangladesh. International Journal of Biosciences. 2. 64-72.
[7] Xu, K., Xu, X., Ronald P. C., Mackill D. J., (2000). A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet, 263(4): 681–689
[8] Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang, R. R., Heuer, S., Ismail A. M., Bailey S. J., Ronald, P. C., Mackill D. J., (2006). Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature, 442: 705–708.
[9] [9] Singh, N., Dang, T. T. M., Vergara, G. V., Pandey, D. M., Sanchez, D., Neeraja, C. N., Septiningsih, E. M., Mendioro, M., Tecson, M. E. M., Ismail, A. M., Mackill, D. J., Heuer, S. (2010). Molecular marker survey and expression analyses of the rice submergence tolerance gene SUB1A. Theor Appl Genet, 121(8): 1441–1453.
[10] Fukao, T., Bailey, S. J. (2008). Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc Natl Acad Sci U S A.
[11] Fukao, T. Xu, K., Ronald, P. C., Bailey, S. J. (2006). A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell, 18:2021-2034.
[12] Jung, K. H., Cao, P., Seo, Y. S., Dardick, C., Ronald, P. C. (2010). The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family. Trends Plant Sci. 15:595–599. doi: 10.1016/j.tplants.2010.08.004.
[13] Xu, K., Mackill, D. J. (1996). A major locus for submergence tolerance mapped on rice chromosome 9. Molecular Breeding. 2:219–224.
[14] Nandi, S., Subudhi, P. K., Senadhira, D., Manigbas, N. L., Sen-Mandi, S., Huang, N. (1997). Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Molecular and General Genetics. 255:1–8
[15] Toojinda, T., Siangliw, M., Tragroonrung, S., Vanavichit, A. (2003). Molecular genetics of submergence tolerance in rice: QTL analysis of key traits. Annals of Botany. 91:243–253.
[16] Neeraja, C., Maghirang-Rodriguez, R., Pamplona, A., Heuer, S., Collard, B., Septiningsih, E. (2007). A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoretical and Applied Genetics. 115:767–776.
[17] Sarkar, R. K., Reddy, J. N., Sharma, S. G., Ismail, A. M. (2006). Physiological basis of submergence tolerance in rice and implications for crop improvement. Current Science. 91:899–906.
[18] Septiningsih, E. M., Pamplona, A. M., Sanchez, D. L., Neeraja, C. N., Vergara, G. V., Heuer, S., Ismail A. M., and Mackill. D. J. (2009). Development of submergence tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot. 103: 151-160.
[19] Septiningsih, E. M., Collard, B. C. Y., Heuer, S., Bailey-Serres, J., Ismail, A. M., and Mackill, D. J. (2013). Applying genomics tools for breeding submergence tolerance in rice. In: R. K. Varshney and R. Tuberosa (eds). Translational genomics for crop breeding: Volume 2 - Improvement for abiotic stress, quality and yield improvement. Wiley-Blackwell, USA, pp. 9-30.
[20] Septiningsih, E. M., Hidayatun, N., Sanchez, D. L., Nugraha, Y., Carandang, J., Pamplona, A. M., Collard, B. C. Y., Ismail A. M., and Mackill. D. J. (2014). Accelerating the development of new submergence tolerant rice varieties: the case of Ciherang-Sub1 and PSB Rc18-Sub1. Euphytica. [DOI: 10.1007/s10681-014-1287-x]
[21] Iftekharuddaula, K. M., Newaz, M. A., Salam, M. A., Ahmed, H. U., Mahbub, M. A. A., Septiningsih, E. M., Collard, B. C. Y., Sanchez, D. L., Pamplona, A. M. and Mackill, D. J. (2011). Rapid and High-Precision Marker Assisted Backcrossing to Introgress the SUB1 QTL into BR11, the Rainfed Lowland Rice Mega Variety of Bangladesh. Euphytica, 178, 83-97. http://dx.doi.org/10.1007/s10681-010-0272-2
[22] Das, S., Misra, R. C., and Patnaik, M. C. (2009). G × E interaction of mid-late rice genotypes in LR and AMMI model and evaluation of adaptability and yield stability. Environ. and Ecol. 27:529-535.
[23] Setter, T & Ellis, M & V Laureles, E & S Ella, E & Senadhira, D & B Mishra, S & Sarkarung, S & Datta, Swapan. (1997). Physiology and Genetics of Submergence Tolerance in Rice. Ann. Bot. 79. 10.1093/oxfordjournals.aob.a010308.
[24] Mohanty, H. K., Mallik, S., and Grover, A. (2000) Prospects of improving flooding tolerance in lowland rice varieties by conventional breeding and genetic engineering. Current Science. 78: 132-137.
[25] Yesmin, N., Elias, S. M., Rahman, M. S., Haque, T., Hasan, A. K. M. M., Seraj, Z. I. (2014). Unique genotypic differences discovered among indigenous Bangladeshi rice landracesInt. J. Genomics. p. 210328, 10.1155/2014/210328
[26] Chakravarthi, B. K., Naravaneni, R. (2006). SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativa. L). African J Biotech 5: 684-688.
[27] Allen, G., Flores, M., Krasnyanski, S., Kumar, S., Thompson, W. (2006). A modified protocol for rapid DNA isolation from plant tissue using cetyltrimethylammonium bromide. Nature protocols. 1. 2320-5. 10.1038/nprot.2006.384.
Author Information
  • Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh

  • Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh

  • Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Director (Research) Office, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Director (Administration and Common Services) Office, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Department of Breeding and Varieties, Sugar Research Australia (SRA), Gordonvale, Australia

Cite This Article
  • APA Style

    Al Amin, Khandakar Md Iftekharuddaula, Animesh Sarker, Ashraf Hossain Talukder, Sharmishtha Ghoshal, et al. (2019). Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh. International Journal of Genetics and Genomics, 6(4), 44-51. https://doi.org/10.11648/j.ijgg.20180604.12

    Copy | Download

    ACS Style

    Al Amin; Khandakar Md Iftekharuddaula; Animesh Sarker; Ashraf Hossain Talukder; Sharmishtha Ghoshal, et al. Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh. Int. J. Genet. Genomics 2019, 6(4), 44-51. doi: 10.11648/j.ijgg.20180604.12

    Copy | Download

    AMA Style

    Al Amin, Khandakar Md Iftekharuddaula, Animesh Sarker, Ashraf Hossain Talukder, Sharmishtha Ghoshal, et al. Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh. Int J Genet Genomics. 2019;6(4):44-51. doi: 10.11648/j.ijgg.20180604.12

    Copy | Download

  • @article{10.11648/j.ijgg.20180604.12,
      author = {Al Amin and Khandakar Md Iftekharuddaula and Animesh Sarker and Ashraf Hossain Talukder and Sharmishtha Ghoshal and A. K. M. Shalahuddin and Tamal Lata Aditya and Md Ansar Ali and Bertrand Collard},
      title = {Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh},
      journal = {International Journal of Genetics and Genomics},
      volume = {6},
      number = {4},
      pages = {44-51},
      doi = {10.11648/j.ijgg.20180604.12},
      url = {https://doi.org/10.11648/j.ijgg.20180604.12},
      eprint = {https://download.sciencepg.com/pdf/10.11648.j.ijgg.20180604.12},
      abstract = {Bangladesh had harbored numerous submergence tolerant rice local cultivars or landraces (popularly known as Joli Aman). As the local cultivars endure intervallic flash-flooding year after year, it is presumed that genes/Quantitative Trait Loci (QTLs) that give resilience are probably going to be available in these genotypes. In submergence screening, the performance of three tested accessions (Lakhi, Atshotti and Damsi) demonstrated them to be as tolerant as the check FR13A. Other germplasm accessions (DSL-78-8, Laldepa, Putidepa, Laxmi digha) performed great recuperation capacity after de-submergence. Damsi, Rajasail, Haloi, Lal Digha, Manik Digha, Bhawalia, DSL-78-8, Putidepa, Atshotti and Jalda IRRI don't have the SUB1 QTL and furthermore not like the BR5, a submergence susceptible check variety. Bajal, Horkoach, Pathornuti, Laxmi Digha, Horinga Digha, Bhawalia Digha and BR5 was not amplified by Gns2 conferring SUB1 QTL (submergence tolerance specific QTL). Significantly, the local cultivars i.e. DSL-78-8, Putidepa and Sadadanga boro were identified as having better submergence tolerance however having no resistant alleles of GnS2 and Sub1C173, indel markers specific to SUB1 QTL. The result of molecular screening revealed new submergence tolerant rice cultivars which do not possess SUB1 QTL. To discover new submergence tolerant QTLs other than SUB1 through QTL mapping, newly identified submergence tolerant germplasm can be utilized.},
     year = {2019}
    }
    

    Copy | Download

  • TY  - JOUR
    T1  - Identification of Novel Submergence Tolerant Local Rice Cultivars of Bangladesh
    AU  - Al Amin
    AU  - Khandakar Md Iftekharuddaula
    AU  - Animesh Sarker
    AU  - Ashraf Hossain Talukder
    AU  - Sharmishtha Ghoshal
    AU  - A. K. M. Shalahuddin
    AU  - Tamal Lata Aditya
    AU  - Md Ansar Ali
    AU  - Bertrand Collard
    Y1  - 2019/01/28
    PY  - 2019
    N1  - https://doi.org/10.11648/j.ijgg.20180604.12
    DO  - 10.11648/j.ijgg.20180604.12
    T2  - International Journal of Genetics and Genomics
    JF  - International Journal of Genetics and Genomics
    JO  - International Journal of Genetics and Genomics
    SP  - 44
    EP  - 51
    PB  - Science Publishing Group
    SN  - 2376-7359
    UR  - https://doi.org/10.11648/j.ijgg.20180604.12
    AB  - Bangladesh had harbored numerous submergence tolerant rice local cultivars or landraces (popularly known as Joli Aman). As the local cultivars endure intervallic flash-flooding year after year, it is presumed that genes/Quantitative Trait Loci (QTLs) that give resilience are probably going to be available in these genotypes. In submergence screening, the performance of three tested accessions (Lakhi, Atshotti and Damsi) demonstrated them to be as tolerant as the check FR13A. Other germplasm accessions (DSL-78-8, Laldepa, Putidepa, Laxmi digha) performed great recuperation capacity after de-submergence. Damsi, Rajasail, Haloi, Lal Digha, Manik Digha, Bhawalia, DSL-78-8, Putidepa, Atshotti and Jalda IRRI don't have the SUB1 QTL and furthermore not like the BR5, a submergence susceptible check variety. Bajal, Horkoach, Pathornuti, Laxmi Digha, Horinga Digha, Bhawalia Digha and BR5 was not amplified by Gns2 conferring SUB1 QTL (submergence tolerance specific QTL). Significantly, the local cultivars i.e. DSL-78-8, Putidepa and Sadadanga boro were identified as having better submergence tolerance however having no resistant alleles of GnS2 and Sub1C173, indel markers specific to SUB1 QTL. The result of molecular screening revealed new submergence tolerant rice cultivars which do not possess SUB1 QTL. To discover new submergence tolerant QTLs other than SUB1 through QTL mapping, newly identified submergence tolerant germplasm can be utilized.
    VL  - 6
    IS  - 4
    ER  - 

    Copy | Download

  • Sections