Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach
American Journal of Plant Biology
Volume 3, Issue 4, December 2018, Pages: 33-40
Received: Feb. 23, 2019; Accepted: Mar. 28, 2019; Published: May 6, 2019
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Authors
Al Amin, Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
KM Iftekharuddaula, Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
Animesh Sarker, Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
Md. Abdul Kader, Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
Ashraf Hossain Talukder, Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
Tamal Lata Aditya, Research Department, Bangladesh Rice Research Institute, Gazipur, Bangladesh
Md. Ansar Ali, Administration and Common Services Department, Bangladesh Rice Research Institute, Gazipur, Bangladesh
Md. Shahjahan Kabir, General Office, Bangladesh Rice Research Institute, Gazipur, Bangladesh
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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.
Keywords
Deep Water Rice, Molecular Screening, SNORKEL1, SNORKEL2, In-silico Study
To cite this article
Al Amin, KM Iftekharuddaula, Animesh Sarker, Md. Abdul Kader, Ashraf Hossain Talukder, Tamal Lata Aditya, Md. Ansar Ali, Md. Shahjahan Kabir, Exploration of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach, American Journal of Plant Biology. Vol. 3, No. 4, 2018, pp. 33-40. doi: 10.11648/j.ajpb.20180304.11
Copyright
Copyright © 2018 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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