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Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach

Received: 23 February 2019     Accepted: 28 March 2019     Published: 6 May 2019
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Abstract

The molecular screening of deep water rice landraces showed that out of 21 landraces, 15 landraces possess the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes conferring stem elongation of paddy plant survive in increased water level of deep water ecosystem. Both genes/Quantitative trait loci (QTLs) were subjected to study through in-silico approaches. The fasta sequences, secondary structure and 3D structure of those proteins were identified and verified using bioinformatics tools. The physico-chemical properties and functions were also predicted. The in-silico study of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL have also revealed the capacity and way of survival of deep water rice germplasm noticeably. This study illustrates the many deep water rice varieties having SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL and others do not possess the these QTLs though they are cultivated in deep water ecosystem. The molecular screening and in-silico study output of deep water rice landraces can be applied for establishing morphological correlation that 15 landraces are more elongating type than others and more adapted in natural deep water condition.

Published in American Journal of Plant Biology (Volume 3, Issue 4)
DOI 10.11648/j.ajpb.20180304.11
Page(s) 33-40
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), 2019. Published by Science Publishing Group

Keywords

Deep Water Rice, Molecular Screening, SNORKEL1, SNORKEL2, In-silico Study

References
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Cite This Article
  • APA Style

    Al Amin, KM Iftekharuddaula, Animesh Sarker, Md. Abdul Kader, Ashraf Hossain Talukder, et al. (2019). Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach. American Journal of Plant Biology, 3(4), 33-40. https://doi.org/10.11648/j.ajpb.20180304.11

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    ACS Style

    Al Amin; KM Iftekharuddaula; Animesh Sarker; Md. Abdul Kader; Ashraf Hossain Talukder, et al. Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach. Am. J. Plant Biol. 2019, 3(4), 33-40. doi: 10.11648/j.ajpb.20180304.11

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    AMA Style

    Al Amin, KM Iftekharuddaula, Animesh Sarker, Md. Abdul Kader, Ashraf Hossain Talukder, et al. Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach. Am J Plant Biol. 2019;3(4):33-40. doi: 10.11648/j.ajpb.20180304.11

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  • @article{10.11648/j.ajpb.20180304.11,
      author = {Al Amin and KM Iftekharuddaula and Animesh Sarker and Md. Abdul Kader and Ashraf Hossain Talukder and Tamal Lata Aditya and Md. Ansar Ali and Md. Shahjahan Kabir},
      title = {Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach},
      journal = {American Journal of Plant Biology},
      volume = {3},
      number = {4},
      pages = {33-40},
      doi = {10.11648/j.ajpb.20180304.11},
      url = {https://doi.org/10.11648/j.ajpb.20180304.11},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajpb.20180304.11},
      abstract = {The molecular screening of deep water rice landraces showed that out of 21 landraces, 15 landraces possess the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes conferring stem elongation of paddy plant survive in increased water level of deep water ecosystem. Both genes/Quantitative trait loci (QTLs) were subjected to study through in-silico approaches. The fasta sequences, secondary structure and 3D structure of those proteins were identified and verified using bioinformatics tools. The physico-chemical properties and functions were also predicted. The in-silico study of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL have also revealed the capacity and way of survival of deep water rice germplasm noticeably. This study illustrates the many deep water rice varieties having SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL and others do not possess the these QTLs though they are cultivated in deep water ecosystem. The molecular screening and in-silico study output of deep water rice landraces can be applied for establishing morphological correlation that 15 landraces are more elongating type than others and more adapted in natural deep water condition.},
     year = {2019}
    }
    

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  • TY  - JOUR
    T1  - Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach
    AU  - Al Amin
    AU  - KM Iftekharuddaula
    AU  - Animesh Sarker
    AU  - Md. Abdul Kader
    AU  - Ashraf Hossain Talukder
    AU  - Tamal Lata Aditya
    AU  - Md. Ansar Ali
    AU  - Md. Shahjahan Kabir
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    DO  - 10.11648/j.ajpb.20180304.11
    T2  - American Journal of Plant Biology
    JF  - American Journal of Plant Biology
    JO  - American Journal of Plant Biology
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    EP  - 40
    PB  - Science Publishing Group
    SN  - 2578-8337
    UR  - https://doi.org/10.11648/j.ajpb.20180304.11
    AB  - The molecular screening of deep water rice landraces showed that out of 21 landraces, 15 landraces possess the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes conferring stem elongation of paddy plant survive in increased water level of deep water ecosystem. Both genes/Quantitative trait loci (QTLs) were subjected to study through in-silico approaches. The fasta sequences, secondary structure and 3D structure of those proteins were identified and verified using bioinformatics tools. The physico-chemical properties and functions were also predicted. The in-silico study of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL have also revealed the capacity and way of survival of deep water rice germplasm noticeably. This study illustrates the many deep water rice varieties having SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL and others do not possess the these QTLs though they are cultivated in deep water ecosystem. The molecular screening and in-silico study output of deep water rice landraces can be applied for establishing morphological correlation that 15 landraces are more elongating type than others and more adapted in natural deep water condition.
    VL  - 3
    IS  - 4
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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

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

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

  • Research Department, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • Administration and Common Services Department, Bangladesh Rice Research Institute, Gazipur, Bangladesh

  • General Office, Bangladesh Rice Research Institute, Gazipur, Bangladesh

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