Staff View: Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome

Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome

Neolamarckia cadamba (or locally known as kelampayan) is an important fast growing plantation tree species that confers various advantages for timber industry as a strategy for reducing the logging pressure on natural forests for wood production to an acceptable level. Hence, attempts were made to d...

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Main Authors:	S.L., Lai,, P.S.,, Ho, W.S., Pang
Format:	Article
Language:	English
Published:	Asian Network for Scientific Information 2013
Subjects:	Q Science (General) QK Botany SB Plant culture SD Forestry
Online Access:	http://ir.unimas.my/id/eprint/7145/1/Pang.pdf http://ir.unimas.my/id/eprint/7145/ http://www.scialert.net/fulltext/?doi=biotech.2013.225.235&org=11
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spelling	my.unimas.ir.71452021-06-30T16:40:44Z http://ir.unimas.my/id/eprint/7145/ Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome S.L., Lai, P.S.,, Ho W.S., Pang Q Science (General) QK Botany SB Plant culture SD Forestry Neolamarckia cadamba (or locally known as kelampayan) is an important fast growing plantation tree species that confers various advantages for timber industry as a strategy for reducing the logging pressure on natural forests for wood production to an acceptable level. Hence, attempts were made to develop a set of EST-SSR markers for kelampayan trees based on the EST sequences of kelampayan (NcdbEST) and further assessed the polymorphisms and transferability of the markers to other species. In this study, 155 (2.34%) out of 6,622 EST sequences which contain 232 SSRs were mined from NcdbEST. Of these, 97 ESTs were assigned with putative functions and gene ontology terms. Eighteen EST-SSR markers were developed according to the criteria, and further characterized and validated by using 50 individuals of kelampayan from two selected mother trees. The markers exhibited a considerable high level of polymorphism in kelampayan trees with an average of 4.17 and 4.11 alleles per locus, and PIC values of 0.465 and 0.537, respectively for mother trees T1 and T2. Parentage assignment analysis suggests a high probability for kelampayan trees to be predominantly outcrossed. The transferability rate was ranging from 16.7-94.4% among the five cross-genera species of kelampayan. The present study is the first report of the development of EST-SSR markers in kelampayan. These markers will be valuable genomic resources that could pave the way for exploiting the genotype data for comparative genome mapping, association genetics, population genetics studies and molecular breeding of kelampayan and other indigenous tropical tree species in future. Asian Network for Scientific Information 2013 Article PeerReviewed text en http://ir.unimas.my/id/eprint/7145/1/Pang.pdf S.L., Lai, and P.S.,, Ho and W.S., Pang (2013) Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome. Biotechnology, 12 (6). pp. 225-235. ISSN 1682-296X http://www.scialert.net/fulltext/?doi=biotech.2013.225.235&org=11 DOI: 10.3923/biotech.2013.225.235
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	Q Science (General) QK Botany SB Plant culture SD Forestry
spellingShingle	Q Science (General) QK Botany SB Plant culture SD Forestry S.L., Lai, P.S.,, Ho W.S., Pang Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
description	Neolamarckia cadamba (or locally known as kelampayan) is an important fast growing plantation tree species that confers various advantages for timber industry as a strategy for reducing the logging pressure on natural forests for wood production to an acceptable level. Hence, attempts were made to develop a set of EST-SSR markers for kelampayan trees based on the EST sequences of kelampayan (NcdbEST) and further assessed the polymorphisms and transferability of the markers to other species. In this study, 155 (2.34%) out of 6,622 EST sequences which contain 232 SSRs were mined from NcdbEST. Of these, 97 ESTs were assigned with putative functions and gene ontology terms. Eighteen EST-SSR markers were developed according to the criteria, and further characterized and validated by using 50 individuals of kelampayan from two selected mother trees. The markers exhibited a considerable high level of polymorphism in kelampayan trees with an average of 4.17 and 4.11 alleles per locus, and PIC values of 0.465 and 0.537, respectively for mother trees T1 and T2. Parentage assignment analysis suggests a high probability for kelampayan trees to be predominantly outcrossed. The transferability rate was ranging from 16.7-94.4% among the five cross-genera species of kelampayan. The present study is the first report of the development of EST-SSR markers in kelampayan. These markers will be valuable genomic resources that could pave the way for exploiting the genotype data for comparative genome mapping, association genetics, population genetics studies and molecular breeding of kelampayan and other indigenous tropical tree species in future.
format	Article
author	S.L., Lai, P.S.,, Ho W.S., Pang
author_facet	S.L., Lai, P.S.,, Ho W.S., Pang
author_sort	S.L., Lai,
title	Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
title_short	Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
title_full	Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
title_fullStr	Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
title_full_unstemmed	Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome
title_sort	development, characterization and cross-species transferability of expressed sequence tag-simple sequence repeat (est-ssr) markers derived from kelampayan tree transcriptome
publisher	Asian Network for Scientific Information
publishDate	2013
url	http://ir.unimas.my/id/eprint/7145/1/Pang.pdf http://ir.unimas.my/id/eprint/7145/ http://www.scialert.net/fulltext/?doi=biotech.2013.225.235&org=11
_version_	1705060429685850112
score	13.211869

Development, Characterization and Cross-species Transferability of Expressed Sequence Tag-simple Sequence Repeat (EST-SSR) Markers Derived from Kelampayan Tree Transcriptome

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