Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids

Grouper (Genus: Epinephe/us) represent one of the high value fisheries resource in Malaysia and several inter-specific hybrids have been developed by the fish breeders. DNA based markers are ideal elucidation of the fundamental associated with inheritance and linkage in determinate hybrids. First ge...

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Main Author:	Ahmad Zaidi Tani
Format:	Thesis
Language:	English English
Published:	2015
Subjects:	QL614-639.8 Fishes
Online Access:	https://eprints.ums.edu.my/id/eprint/38575/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38575/2/FULLTEXT.pdf
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spelling	my-ums-ep.385752024-04-29T02:39:46Z Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids 2015 Ahmad Zaidi Tani QL614-639.8 Fishes Grouper (Genus: Epinephe/us) represent one of the high value fisheries resource in Malaysia and several inter-specific hybrids have been developed by the fish breeders. DNA based markers are ideal elucidation of the fundamental associated with inheritance and linkage in determinate hybrids. First generation markers (Microsatellite, RAPD, ISSR etc.) have limitations when applied to characterize intraspecific hybrids. This study set forth to overcome this limitation by developing the second generation of non-coding non informative anonymous nuclear markers (ncni-ANM) for subsequent genetic characterization of Fl grouper hybrids. Smallinsert genomic DNA library of Epinephelus lanceolatus (EL) and Epinephelus fuscoguttatus (EF) were constructed via a shotgun approach following which they were annotated, subjected to a similarity searches using the blastn algorithms and deposited at the GenBank. Annotated genomic sequences of E lanceolatus and E fuscoguttatuswere than used for designation of anonymous nuclear markers (ANM) and further categorized into being non-coding non-informative ANM (ncni-ANM), non-coding informative ANM (nci-ANM) or coding informative ANM (ci-ANM). Intraspecific DNA fingerprinting analysis was carried out using five E lanceo/atus and 12 E fuscoguttatus broodstock, scored as binary matrix and calculated for genetic distance (GD), genetic similarity (GS) and cophenetic correlation index (CCC) via Jaccard's and Dice's coefficient. An unweighted pair-group method with arithmetic mean (UPGMA) phenogram was constructed based on the GD and CCC values to verify the genetic relationship among the grouper broodstock operational taxonomic units (OTUs). Subsequently, thirty two half-sib Fl hybrids obtained by crossing of female E fuscoguttatus and male E /anceo/atus (EFEL) brooders were characterized using 34 male E. lanceolatus and 32 E. fuscoguttatus ncni-ANM in order to evaluate Mendelian segregation pattern based on genetic inheritance and segregation distortion analyses. A library of 127 genomic sequences was developed of which seven E. lanceolatus and 16 E. fuscoguttatus sequences could be mapped back to the Dicentrarchus labrax genome. Locus specific markers were developed using 60 E. lanceolatus and 67 E. fuscoguttatus genomic sequences. A total of 46 £ lanceolatus ANM were designed containing 34 ncni-ANM, 4 nci-ANM and 8 ci-ANM. While as in total of 42 E. fuscoguttatus ANM were designed containing 32 ncni-ANM, 3 nci-ANM and 7 ci-ANM. Polymerase chain reaction (PCR) amplification patterns of ncni-ANM in both £ lanceolatus and £ fuscoguttatus broodstocks revealed 11 £ lanceolatus and 10 E. fuscoguttatus ncni-ANM were reproducible. Among these 13 E. lanceolatus and E. fuscoguttatus ncni-ANM loci ranged in size from 153 to 177 bp and 157 to 624 bp respectively revealing variation across all OTUs through visualization of agarose gel electrophoresis patterns and binary matrix scoring. Clustering comparison based on CCC goodness-of-fit showed both species samples were best presented using Jaccard's coefficient. The phenogram constructed for the five E /anceolatus OTUs showed two clusters with polyphyletic groups. The first cluster (Cl) consisted of OTUs EL6924, EL5477 and EL140E with monophyletic group while as the second cluster (C2) consisted of OTUs EL4E4D and EL174A with 2015 Thesis https://eprints.ums.edu.my/id/eprint/38575/ https://eprints.ums.edu.my/id/eprint/38575/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/38575/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QL614-639.8 Fishes
spellingShingle	QL614-639.8 Fishes Ahmad Zaidi Tani Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
description	Grouper (Genus: Epinephe/us) represent one of the high value fisheries resource in Malaysia and several inter-specific hybrids have been developed by the fish breeders. DNA based markers are ideal elucidation of the fundamental associated with inheritance and linkage in determinate hybrids. First generation markers (Microsatellite, RAPD, ISSR etc.) have limitations when applied to characterize intraspecific hybrids. This study set forth to overcome this limitation by developing the second generation of non-coding non informative anonymous nuclear markers (ncni-ANM) for subsequent genetic characterization of Fl grouper hybrids. Smallinsert genomic DNA library of Epinephelus lanceolatus (EL) and Epinephelus fuscoguttatus (EF) were constructed via a shotgun approach following which they were annotated, subjected to a similarity searches using the blastn algorithms and deposited at the GenBank. Annotated genomic sequences of E lanceolatus and E fuscoguttatuswere than used for designation of anonymous nuclear markers (ANM) and further categorized into being non-coding non-informative ANM (ncni-ANM), non-coding informative ANM (nci-ANM) or coding informative ANM (ci-ANM). Intraspecific DNA fingerprinting analysis was carried out using five E lanceo/atus and 12 E fuscoguttatus broodstock, scored as binary matrix and calculated for genetic distance (GD), genetic similarity (GS) and cophenetic correlation index (CCC) via Jaccard's and Dice's coefficient. An unweighted pair-group method with arithmetic mean (UPGMA) phenogram was constructed based on the GD and CCC values to verify the genetic relationship among the grouper broodstock operational taxonomic units (OTUs). Subsequently, thirty two half-sib Fl hybrids obtained by crossing of female E fuscoguttatus and male E /anceo/atus (EFEL) brooders were characterized using 34 male E. lanceolatus and 32 E. fuscoguttatus ncni-ANM in order to evaluate Mendelian segregation pattern based on genetic inheritance and segregation distortion analyses. A library of 127 genomic sequences was developed of which seven E. lanceolatus and 16 E. fuscoguttatus sequences could be mapped back to the Dicentrarchus labrax genome. Locus specific markers were developed using 60 E. lanceolatus and 67 E. fuscoguttatus genomic sequences. A total of 46 £ lanceolatus ANM were designed containing 34 ncni-ANM, 4 nci-ANM and 8 ci-ANM. While as in total of 42 E. fuscoguttatus ANM were designed containing 32 ncni-ANM, 3 nci-ANM and 7 ci-ANM. Polymerase chain reaction (PCR) amplification patterns of ncni-ANM in both £ lanceolatus and £ fuscoguttatus broodstocks revealed 11 £ lanceolatus and 10 E. fuscoguttatus ncni-ANM were reproducible. Among these 13 E. lanceolatus and E. fuscoguttatus ncni-ANM loci ranged in size from 153 to 177 bp and 157 to 624 bp respectively revealing variation across all OTUs through visualization of agarose gel electrophoresis patterns and binary matrix scoring. Clustering comparison based on CCC goodness-of-fit showed both species samples were best presented using Jaccard's coefficient. The phenogram constructed for the five E /anceolatus OTUs showed two clusters with polyphyletic groups. The first cluster (Cl) consisted of OTUs EL6924, EL5477 and EL140E with monophyletic group while as the second cluster (C2) consisted of OTUs EL4E4D and EL174A with
format	Thesis
qualification_level	Master's degree
author	Ahmad Zaidi Tani
author_facet	Ahmad Zaidi Tani
author_sort	Ahmad Zaidi Tani
title	Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
title_short	Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
title_full	Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
title_fullStr	Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
title_full_unstemmed	Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
title_sort	development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2015
url	https://eprints.ums.edu.my/id/eprint/38575/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38575/2/FULLTEXT.pdf
_version_	1804890329298501632

Development and characterization of anonymous nuclear markers to determine genetic variation in two groupers species and their hybrids

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