Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia

The purpose of current study is to illustrate the utility of EST-derived SSR in characterizing wild populations of Macrobrachium rosenbergii in Malaysia‘s rivers. A novel set of EST-SSR was validated in a full panel of 120 samples from four wild populations through Polymerase Chain Reaction (PCR). S...

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Main Author:	Hedayati, Atin Khalaj
Format:	Thesis
Language:	English
Published:	2014
Subjects:	Macrobrachium rosenbergii - Peninsular Malaysia Shrimp culture Microsatellites (Genetics)
Online Access:	http://psasir.upm.edu.my/id/eprint/39821/7/FP%202014%2013%20IR%20A.pdf
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id	my-upm-ir.39821
record_format	uketd_dc
spelling	my-upm-ir.398212015-08-26T02:39:29Z Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia 2014-07 Hedayati, Atin Khalaj The purpose of current study is to illustrate the utility of EST-derived SSR in characterizing wild populations of Macrobrachium rosenbergii in Malaysia‘s rivers. A novel set of EST-SSR was validated in a full panel of 120 samples from four wild populations through Polymerase Chain Reaction (PCR). Seven EST-SSR loci were identified, characterized, and evaluated on 30 individuals each from the populations namely Sg. Tapah (Perak), Sg. Timun (Negeri Sembilan), Sg. Bernam (Selangor) and Sg. Johor (Johor). The average polymorphic informative content value (PIC) for these seven primers was found to be 0.5355 indicating considerable degree of polymorphism with number of alleles detected ranged from 5 to 17. The observed heterozygosity value count during multi-population analyses ranged from 0.3668 to 0.4554, whilst the expected ranged from 0.5192 to 0.5700. There was linkage disequilibrium (LD) observed between 2 pairs of EST-SSRs loci. All loci have deviation from the Hardy-Weinberg equilibrium (HWE) except EST-Mr-AS-31957, suggesting factors violating the neutral expectation such as selection and non random mating. The FIS index demonstrated indication of inbreeding among individuals of each population. There was evidence that all samples from four sampling sites assessed in this study are drawn from four clusters (k=4). Estimate of fixation index value in pairwise comparisons among the four localities revealed very low magnitude of differentiation (R ST ranged between 0.0000 to the highest of 0.17918). The findings of this study suggested that intra-specific diversity that occurs between studied populations were not extremely high, as very low variation was detected in pairwise comparisons and genetic structuring analyses. The ongoing gene flow either naturally or via translocations by humans are possible reasons for the low magnitude of genetic differentiation. The overall results suggest that all populations (Tapah, Timun, Bernam, and Johor) were composed of one large possible panmictic population for management purposes at present. Also the results indicated that these polymorphic EST-SSR derived from M. rosenbergii would be useful for population genetic structure analysis and genetic diversity assessment in prawn populations as part of management policies of natural resources to ensure sustainability of wild broodstock for future development of prawn culture industries. Macrobrachium rosenbergii - Peninsular Malaysia Shrimp culture Microsatellites (Genetics) 2014-07 Thesis http://psasir.upm.edu.my/id/eprint/39821/ http://psasir.upm.edu.my/id/eprint/39821/7/FP%202014%2013%20IR%20A.pdf application/pdf en public masters Universiti Putra Malaysia Macrobrachium rosenbergii - Peninsular Malaysia Shrimp culture Microsatellites (Genetics)
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
topic	Macrobrachium rosenbergii - Peninsular Malaysia Shrimp culture Microsatellites (Genetics)
spellingShingle	Macrobrachium rosenbergii - Peninsular Malaysia Shrimp culture Microsatellites (Genetics) Hedayati, Atin Khalaj Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
description	The purpose of current study is to illustrate the utility of EST-derived SSR in characterizing wild populations of Macrobrachium rosenbergii in Malaysia‘s rivers. A novel set of EST-SSR was validated in a full panel of 120 samples from four wild populations through Polymerase Chain Reaction (PCR). Seven EST-SSR loci were identified, characterized, and evaluated on 30 individuals each from the populations namely Sg. Tapah (Perak), Sg. Timun (Negeri Sembilan), Sg. Bernam (Selangor) and Sg. Johor (Johor). The average polymorphic informative content value (PIC) for these seven primers was found to be 0.5355 indicating considerable degree of polymorphism with number of alleles detected ranged from 5 to 17. The observed heterozygosity value count during multi-population analyses ranged from 0.3668 to 0.4554, whilst the expected ranged from 0.5192 to 0.5700. There was linkage disequilibrium (LD) observed between 2 pairs of EST-SSRs loci. All loci have deviation from the Hardy-Weinberg equilibrium (HWE) except EST-Mr-AS-31957, suggesting factors violating the neutral expectation such as selection and non random mating. The FIS index demonstrated indication of inbreeding among individuals of each population. There was evidence that all samples from four sampling sites assessed in this study are drawn from four clusters (k=4). Estimate of fixation index value in pairwise comparisons among the four localities revealed very low magnitude of differentiation (R ST ranged between 0.0000 to the highest of 0.17918). The findings of this study suggested that intra-specific diversity that occurs between studied populations were not extremely high, as very low variation was detected in pairwise comparisons and genetic structuring analyses. The ongoing gene flow either naturally or via translocations by humans are possible reasons for the low magnitude of genetic differentiation. The overall results suggest that all populations (Tapah, Timun, Bernam, and Johor) were composed of one large possible panmictic population for management purposes at present. Also the results indicated that these polymorphic EST-SSR derived from M. rosenbergii would be useful for population genetic structure analysis and genetic diversity assessment in prawn populations as part of management policies of natural resources to ensure sustainability of wild broodstock for future development of prawn culture industries.
format	Thesis
qualification_level	Master's degree
author	Hedayati, Atin Khalaj
author_facet	Hedayati, Atin Khalaj
author_sort	Hedayati, Atin Khalaj
title	Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
title_short	Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
title_full	Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
title_fullStr	Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
title_full_unstemmed	Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia
title_sort	population characterization of macrobrachium rosenbergii de man using est-ssr markers in western peninsular malaysia
granting_institution	Universiti Putra Malaysia
publishDate	2014
url	http://psasir.upm.edu.my/id/eprint/39821/7/FP%202014%2013%20IR%20A.pdf
_version_	1747811820326879232

Population characterization of Macrobrachium rosenbergii De Man using EST-SSR markers in western Peninsular Malaysia

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