Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.

A detailed study was carried out to discover single nucleotide polymorphisms (SNPs) from Neolamarckia cadamba partial XTH (~1283bp) and CesA (778bp) DNA sequences and further associates those SNPs with basic wood density. Primers were designed in flanking the partial XTH and CesA genes from 15 N. ca...

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Main Authors:	SY, Tiong, WS, Ho, SL, Pang, J, Ismail
Format:	Article
Language:	English
Published:	Asian Network for Scientific Information 2014
Subjects:	QD Chemistry SD Forestry
Online Access:	http://ir.unimas.my/7136/ http://ir.unimas.my/7136/ http://ir.unimas.my/7136/ http://ir.unimas.my/7136/1/Nucleotide%20Diversity%20and%20Association%20Genetics.pdf

id	unimas-7136
recordtype	eprints
spelling	unimas-71362015-09-14T02:11:38Z http://ir.unimas.my/7136/ Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba. SY, Tiong WS, Ho SL, Pang J, Ismail QD Chemistry SD Forestry A detailed study was carried out to discover single nucleotide polymorphisms (SNPs) from Neolamarckia cadamba partial XTH (~1283bp) and CesA (778bp) DNA sequences and further associates those SNPs with basic wood density. Primers were designed in flanking the partial XTH and CesA genes from 15 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 34 SNPs (2.65% occurrence) and 3 SNPs (0.39% occurrence) were found in 15 partial genomic DNA sequences of NcXTH1 and NcCesA1, respectively. All the SNPs were discovered in both exon and intron regions. NcXTH1 examined sites showed higher nucleotide diversities of π = 0.00402 and θw = 8.919 when compared to NcCesA1 (π = 0.00127; θw = 0.9226). The LD decayed slowly with distance of polymorphic sites in a linear pattern with the mean R2 value of 0.000687. Association genetics study showed that 2 SNPs from NcXTH1 genes were significantly associated with basic wood density (p<0.05) of N. cadamba. Once the gene-associated SNP markers in NcXTH1 genes are validated, it could be potentially used as a tool in Gene-Assisted Selection (GAS) of N. cadamba trees. This study has also demonstrated that the candidate-gene based association genetics is a powerful approach to dissect complex adaptive traits for organism lacking a genome sequence or reference genomic resources. Asian Network for Scientific Information 2014 Article PeerReviewed text en http://ir.unimas.my/7136/1/Nucleotide%20Diversity%20and%20Association%20Genetics.pdf SY, Tiong and WS, Ho and SL, Pang and J, Ismail (2014) Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba. Journal of Biological Sciences, 14 (4). pp. 267-275. ISSN 1727-3048 http://scialert.net/abstract/?doi=jbs.2014.267.275 DOI: 10.3923/jbs.2014.267.275
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Malaysia Sarawak
building	UNIMAS Institutional Repository
collection	Online Access
language	English
topic	QD Chemistry SD Forestry
spellingShingle	QD Chemistry SD Forestry SY, Tiong WS, Ho SL, Pang J, Ismail Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
description	A detailed study was carried out to discover single nucleotide polymorphisms (SNPs) from Neolamarckia cadamba partial XTH (~1283bp) and CesA (778bp) DNA sequences and further associates those SNPs with basic wood density. Primers were designed in flanking the partial XTH and CesA genes from 15 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 34 SNPs (2.65% occurrence) and 3 SNPs (0.39% occurrence) were found in 15 partial genomic DNA sequences of NcXTH1 and NcCesA1, respectively. All the SNPs were discovered in both exon and intron regions. NcXTH1 examined sites showed higher nucleotide diversities of π = 0.00402 and θw = 8.919 when compared to NcCesA1 (π = 0.00127; θw = 0.9226). The LD decayed slowly with distance of polymorphic sites in a linear pattern with the mean R2 value of 0.000687. Association genetics study showed that 2 SNPs from NcXTH1 genes were significantly associated with basic wood density (p<0.05) of N. cadamba. Once the gene-associated SNP markers in NcXTH1 genes are validated, it could be potentially used as a tool in Gene-Assisted Selection (GAS) of N. cadamba trees. This study has also demonstrated that the candidate-gene based association genetics is a powerful approach to dissect complex adaptive traits for organism lacking a genome sequence or reference genomic resources.
format	Article
author	SY, Tiong WS, Ho SL, Pang J, Ismail
author_facet	SY, Tiong WS, Ho SL, Pang J, Ismail
author_sort	SY, Tiong
title	Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
title_short	Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
title_full	Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
title_fullStr	Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
title_full_unstemmed	Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.
title_sort	nucleotide diversity and association genetics of xyloglucan endotransglycosylase/hydrolase (xth) and cellulose synthase (cesa) genes in neolamarckia cadamba.
publisher	Asian Network for Scientific Information
publishDate	2014
url	http://ir.unimas.my/7136/ http://ir.unimas.my/7136/ http://ir.unimas.my/7136/ http://ir.unimas.my/7136/1/Nucleotide%20Diversity%20and%20Association%20Genetics.pdf
first_indexed	2018-09-06T15:24:27Z
last_indexed	2018-09-06T15:24:27Z
_version_	1610872225112522752

Nucleotide diversity and association genetics of Xyloglucan Endotransglycosylase/hydrolase (XTH) and cellulose synthase (CesA) genes in Neolamarckia cadamba.

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