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Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba

Association genetics study is a powerful approach to detect the potential genetic variants (i.e., SNPs) underlying the common and complex adaptive traits. Once the quantitative trait nucleotides are identified, such powerful approach provides significant advantages to the forest industry. Hence, att...

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Main Authors: Ho, Wei Seng, Tchin, Boon Ling, Pang, S.L, Ismail, Jusoh
Format: Article
Language:English
Published: Science Alert 2012
Subjects:
QH Natural history
Online Access:http://ir.unimas.my/id/eprint/30925/1/Association%20Genetics.pdf
http://ir.unimas.my/id/eprint/30925/
https://scialert.net/abstract/?doi=biotech.2012.307.317
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spelling my.unimas.ir.309252022-01-24T02:00:50Z http://ir.unimas.my/id/eprint/30925/ Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba Ho, Wei Seng Tchin, Boon Ling Pang, S.L Ismail, Jusoh QH Natural history Association genetics study is a powerful approach to detect the potential genetic variants (i.e., SNPs) underlying the common and complex adaptive traits. Once the quantitative trait nucleotides are identified, such powerful approach provides significant advantages to the forest industry. Hence, attempts were made to discover SNPs from Neolamarckia cadamba partial C4H (3,538 bp) and CAD (2,354 bp) DNA sequences and further associate those SNPs with basic wood density. Overlapping primers were designed in flanking the partial C4H and CAD DNA from 12 N. cadamba trees. The amplified DNA fragments were sequenced and the basic wood density measurements were determined for each tree. The sequence variation analyses revealed that there were 60 and 32 SNPs detected in the partial C4H and CAD DNA sequences, respectively. Those SNPs were distributed throughout the exon, intron, 5’-UTR and 3’-UTR regions. The total nucleotide diversities were π = 0.00302 and θW = 0.00412. The synonymous mutations (π = 0.00983; θW = 0.01210) were more common than nonsynonymous mutations (π = 0.00045; θw = 0.00089) for both C4H and CAD genes. LD declined linearly over short distance at the loci examined. Association genetics study also revealed that 4 and 6 SNPs from C4H and CAD genes, respectively were in significant associations with basic wood density of N. cadamba (p<0.05). The genetic variation identified by the SNP markers, once validated, will facilitate the selection of N. cadamba parental lines or seedlings with optimal quality through Gene-assisted Selection (GAS) approach. Science Alert 2012 Article PeerReviewed text en http://ir.unimas.my/id/eprint/30925/1/Association%20Genetics.pdf Ho, Wei Seng and Tchin, Boon Ling and Pang, S.L and Ismail, Jusoh (2012) Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba. Biotechnology, 11 (6). pp. 307-317. ISSN 1682-296X https://scialert.net/abstract/?doi=biotech.2012.307.317 DOI: 10.3923/biotech.2012.307.317
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
topic QH Natural history
spellingShingle QH Natural history
Ho, Wei Seng
Tchin, Boon Ling
Pang, S.L
Ismail, Jusoh
Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
description Association genetics study is a powerful approach to detect the potential genetic variants (i.e., SNPs) underlying the common and complex adaptive traits. Once the quantitative trait nucleotides are identified, such powerful approach provides significant advantages to the forest industry. Hence, attempts were made to discover SNPs from Neolamarckia cadamba partial C4H (3,538 bp) and CAD (2,354 bp) DNA sequences and further associate those SNPs with basic wood density. Overlapping primers were designed in flanking the partial C4H and CAD DNA from 12 N. cadamba trees. The amplified DNA fragments were sequenced and the basic wood density measurements were determined for each tree. The sequence variation analyses revealed that there were 60 and 32 SNPs detected in the partial C4H and CAD DNA sequences, respectively. Those SNPs were distributed throughout the exon, intron, 5’-UTR and 3’-UTR regions. The total nucleotide diversities were π = 0.00302 and θW = 0.00412. The synonymous mutations (π = 0.00983; θW = 0.01210) were more common than nonsynonymous mutations (π = 0.00045; θw = 0.00089) for both C4H and CAD genes. LD declined linearly over short distance at the loci examined. Association genetics study also revealed that 4 and 6 SNPs from C4H and CAD genes, respectively were in significant associations with basic wood density of N. cadamba (p<0.05). The genetic variation identified by the SNP markers, once validated, will facilitate the selection of N. cadamba parental lines or seedlings with optimal quality through Gene-assisted Selection (GAS) approach.
format Article
author Ho, Wei Seng
Tchin, Boon Ling
Pang, S.L
Ismail, Jusoh
author_facet Ho, Wei Seng
Tchin, Boon Ling
Pang, S.L
Ismail, Jusoh
author_sort Ho, Wei Seng
title Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
title_short Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
title_full Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
title_fullStr Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
title_full_unstemmed Association Genetics of the Cinnamyl Alcohol Dehydrogenase (CAD) and Cinnamate 4-hydroxylase (C4H) Genes with Basic Wood Density in Neolamarckia cadamba
title_sort association genetics of the cinnamyl alcohol dehydrogenase (cad) and cinnamate 4-hydroxylase (c4h) genes with basic wood density in neolamarckia cadamba
publisher Science Alert
publishDate 2012
url http://ir.unimas.my/id/eprint/30925/1/Association%20Genetics.pdf
http://ir.unimas.my/id/eprint/30925/
https://scialert.net/abstract/?doi=biotech.2012.307.317
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score 13.211869

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