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Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)

Neolamarckia cadamba or locally known as kelampayan, is one of the valuable timber tree species. In forest industry, genetic improvement programs based on Single Nucleotide Polymorphisms (SNPs) at the molecular level has become an important tool in the selection of germplasm with desired traits. In...

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Main Author: Choo, Hui Yik
Format: Final Year Project Report
Language:English
English
Published: Universiti Malaysia Sarawak, (UNIMAS) 2011
Subjects:
QK Botany
SD Forestry
Online Access:http://ir.unimas.my/id/eprint/5344/1/SEQUENCE%20POLYMORPHISM%20OF%20HEAT%20SHOCK%20PROTEIN%2070%20%28HSP70%29%20GENE%20%2824pgs%29.pdf
http://ir.unimas.my/id/eprint/5344/8/Sequence%20polymorphism%20of%20heat%20shock%20protein%2070%20%28HSP70%29%20gene%20in%20kelampayan%20%28Neolamarckia%20cadamba%29%20%28fulltext%29.pdf
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spelling my.unimas.ir.53442023-02-02T09:59:53Z http://ir.unimas.my/id/eprint/5344/ Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba) Choo, Hui Yik QK Botany SD Forestry Neolamarckia cadamba or locally known as kelampayan, is one of the valuable timber tree species. In forest industry, genetic improvement programs based on Single Nucleotide Polymorphisms (SNPs) at the molecular level has become an important tool in the selection of germplasm with desired traits. In this study, DNA sequence of Hsp70 which is gene responsible for heat stress was amplified by polymerase chain reaction (PCR) technique with the specific designed primers based on the cDNA sequence of Hsp70 in N. cadamba. The 527 bp Hsp70 amplicons were subjected to BLASTn analysis to perform the sequence homology search through all known template sequence available in the NCBI. Each sequence was then aligned using CLC Free Workbench 4 software for manual detection of SNPs. A total of ninety SNPs were detected only in the exons of the Hsp70 gene with 12 non-synonymous mutations and 78 synonymous mutations. The sequence of the twelve Hsp70 DNA samples was then subjected to in silico restriction analysis. The exclusiveness of the restriction enzymes BssS1, BstBI, HpyCH4IV, SacI, BsrGI, and Bfa1 obtained for the SNPs at nucleotide 113, 124, 217, 293, 341, and 463 respectively could be useful for genetic markers development. Universiti Malaysia Sarawak, (UNIMAS) 2011 Final Year Project Report NonPeerReviewed text en http://ir.unimas.my/id/eprint/5344/1/SEQUENCE%20POLYMORPHISM%20OF%20HEAT%20SHOCK%20PROTEIN%2070%20%28HSP70%29%20GENE%20%2824pgs%29.pdf text en http://ir.unimas.my/id/eprint/5344/8/Sequence%20polymorphism%20of%20heat%20shock%20protein%2070%20%28HSP70%29%20gene%20in%20kelampayan%20%28Neolamarckia%20cadamba%29%20%28fulltext%29.pdf Choo, Hui Yik (2011) Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba). [Final Year Project Report] (Unpublished)
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
English
topic QK Botany
SD Forestry
spellingShingle QK Botany
SD Forestry
Choo, Hui Yik
Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
description Neolamarckia cadamba or locally known as kelampayan, is one of the valuable timber tree species. In forest industry, genetic improvement programs based on Single Nucleotide Polymorphisms (SNPs) at the molecular level has become an important tool in the selection of germplasm with desired traits. In this study, DNA sequence of Hsp70 which is gene responsible for heat stress was amplified by polymerase chain reaction (PCR) technique with the specific designed primers based on the cDNA sequence of Hsp70 in N. cadamba. The 527 bp Hsp70 amplicons were subjected to BLASTn analysis to perform the sequence homology search through all known template sequence available in the NCBI. Each sequence was then aligned using CLC Free Workbench 4 software for manual detection of SNPs. A total of ninety SNPs were detected only in the exons of the Hsp70 gene with 12 non-synonymous mutations and 78 synonymous mutations. The sequence of the twelve Hsp70 DNA samples was then subjected to in silico restriction analysis. The exclusiveness of the restriction enzymes BssS1, BstBI, HpyCH4IV, SacI, BsrGI, and Bfa1 obtained for the SNPs at nucleotide 113, 124, 217, 293, 341, and 463 respectively could be useful for genetic markers development.
format Final Year Project Report
author Choo, Hui Yik
author_facet Choo, Hui Yik
author_sort Choo, Hui Yik
title Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
title_short Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
title_full Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
title_fullStr Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
title_full_unstemmed Sequence polymorphism of heat shock protein 70 (HSP70) gene in kelampayan (Neolamarckia cadamba)
title_sort sequence polymorphism of heat shock protein 70 (hsp70) gene in kelampayan (neolamarckia cadamba)
publisher Universiti Malaysia Sarawak, (UNIMAS)
publishDate 2011
url http://ir.unimas.my/id/eprint/5344/1/SEQUENCE%20POLYMORPHISM%20OF%20HEAT%20SHOCK%20PROTEIN%2070%20%28HSP70%29%20GENE%20%2824pgs%29.pdf
http://ir.unimas.my/id/eprint/5344/8/Sequence%20polymorphism%20of%20heat%20shock%20protein%2070%20%28HSP70%29%20gene%20in%20kelampayan%20%28Neolamarckia%20cadamba%29%20%28fulltext%29.pdf
http://ir.unimas.my/id/eprint/5344/
_version_ 1758582465971093504
score 13.251813

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