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Development, optimisation and validation of a pedigree suite for selective breeding in abalone
Abstracts / Aquaculture 272S1 (2007) S238–S321
S239
conditional maximum likelihood method for estimation of stock compositions indicated that Asian stocks were mainly distributed in the northcentral and western Bering Sea and that the North American stocks were abundant in the North Pacific Ocean south to the Aleutian Islands. These results suggest non-random distribution of Asian and North American stocks of chum salmon in the Bering Sea and North Pacific Ocean, and high potential of the developed DNA microarray for stock identification of mixed ocean aggregation of chum salmon.
using fish from the above 96 populations examined for mtDNA. The observed congruence of the genetic profiles obtained from mtDNA and msDNA analyses suggests that a battery of two DNA markers will become useful for construction of a better baseline for genetic stock identification of chum salmon in high seas. In addition, a high-throughput DNA microarray method was successfully developed to identify the mtDNA haplotypes of chum salmon, which was proven to be useful for rapid detection of haplotypes on board ships.
doi:10.1016/j.aquaculture.2007.07.018
doi:10.1016/j.aquaculture.2007.07.019
Genetic variation and population structure of chum salmon in the North Pacific rim inferred from mitochondrial and microsatellite DNA analyses
Development, optimisation and validation of a pedigree suite for selective breeding in abalone
S. Abe a , M. Yoon a, S. Sato b, S. Moriya c, S. Urawa b, A. Urano d a Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan b Genetics Section, National Salmon Resources Center, 2-2 Nakanoshima, Toyohira-ku, Sapporo 062-0922, Japan c Research and Development Center, Nisshinbo Industries, Inc., 1-2-3, Onodai, Midori-ku, Chiba 267-0056, Japan d Graduate School of Sciences, Hokkaido University, North 10 West 8, Kita-ku, Sapporo 060-0810, Japan Chum salmon (Oncorhnychus keta) have the widest natural geographical distribution among all Pacific salmon species of the genus Oncorhynchus in the North Pacific Rim. Using nucleotide sequence variation in the mitochondrial (mt) DNA control region and allelic variation at several microsatellite (ms) DNA loci, genetic variation and population structure of chum salmon were estimated to address the stock identification problem and related issues. The mtDNA sequence analysis using more than 4200 fish representing a total of 96 populations from Asia and North America disclosed 22 variable nucleotide sites in the analyzed region, which defined a total of 32 haplotypes of three clades (A, B and C). The clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. Besides such a clear geographic association of haplotypes, mtDNA sequence data suggested strong genetic differentiation among Asian and North American populations and a substantial geographic structuring among local populations within regions. Nearly identical population genetic profiles were obtained from msDNA analysis
S.A. Appleyard, N.A. Carr, P.D. Kube, N.G. Elliott CSIRO Marine and Atmospheric Research, Hobart, Tasmania, Australia Reliable and cost-effective DNA pedigree assignment for many terrestrial livestock programs is now a reality. While the cost of genotyping livestock on a commercial scale is starting to decrease, this depends on the species in question and the number of markers implemented in a pedigree suite. Aquaculture of greenlip (Haliotis laevigata) and blacklip (Haliotis rubra) abalone is an emerging primary industry in Australia with selective breeding programs developed for commercial farms. Current DNA technologies present viable tools for these breeding programs although the accurate identification of family members is paramount. For most aquaculture species and indeed for abalone, access to DNA pedigree markers for family assignment and assessment is not fully developed. A robust and costeffective pedigree system must contain loci with high combined exclusion probabilities and polymorphic information content yet balanced with respect to the resources needed to run such a system. This poster details the developmental stages and optimisation steps undertaken to obtain a cost-effective and high-throughput system for DNA pedigree assignment in cultured Australian abalone. We present the results of our study to date based on 50 microsatellite loci and their ability to assign pedigree from multiple family lines. In addition, we outline the utility of these loci for genetic parameter testing within family lines and ongoing assessment of wild abalone genetic diversity. doi:10.1016/j.aquaculture.2007.07.020
S239
conditional maximum likelihood method for estimation of stock compositions indicated that Asian stocks were mainly distributed in the northcentral and western Bering Sea and that the North American stocks were abundant in the North Pacific Ocean south to the Aleutian Islands. These results suggest non-random distribution of Asian and North American stocks of chum salmon in the Bering Sea and North Pacific Ocean, and high potential of the developed DNA microarray for stock identification of mixed ocean aggregation of chum salmon.
using fish from the above 96 populations examined for mtDNA. The observed congruence of the genetic profiles obtained from mtDNA and msDNA analyses suggests that a battery of two DNA markers will become useful for construction of a better baseline for genetic stock identification of chum salmon in high seas. In addition, a high-throughput DNA microarray method was successfully developed to identify the mtDNA haplotypes of chum salmon, which was proven to be useful for rapid detection of haplotypes on board ships.
doi:10.1016/j.aquaculture.2007.07.018
doi:10.1016/j.aquaculture.2007.07.019
Genetic variation and population structure of chum salmon in the North Pacific rim inferred from mitochondrial and microsatellite DNA analyses
Development, optimisation and validation of a pedigree suite for selective breeding in abalone
S. Abe a , M. Yoon a, S. Sato b, S. Moriya c, S. Urawa b, A. Urano d a Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato-cho, Hakodate 041-8611, Japan b Genetics Section, National Salmon Resources Center, 2-2 Nakanoshima, Toyohira-ku, Sapporo 062-0922, Japan c Research and Development Center, Nisshinbo Industries, Inc., 1-2-3, Onodai, Midori-ku, Chiba 267-0056, Japan d Graduate School of Sciences, Hokkaido University, North 10 West 8, Kita-ku, Sapporo 060-0810, Japan Chum salmon (Oncorhnychus keta) have the widest natural geographical distribution among all Pacific salmon species of the genus Oncorhynchus in the North Pacific Rim. Using nucleotide sequence variation in the mitochondrial (mt) DNA control region and allelic variation at several microsatellite (ms) DNA loci, genetic variation and population structure of chum salmon were estimated to address the stock identification problem and related issues. The mtDNA sequence analysis using more than 4200 fish representing a total of 96 populations from Asia and North America disclosed 22 variable nucleotide sites in the analyzed region, which defined a total of 32 haplotypes of three clades (A, B and C). The clade A and C haplotypes characterized Asian populations and clade B haplotypes distinguished North American populations. Besides such a clear geographic association of haplotypes, mtDNA sequence data suggested strong genetic differentiation among Asian and North American populations and a substantial geographic structuring among local populations within regions. Nearly identical population genetic profiles were obtained from msDNA analysis
S.A. Appleyard, N.A. Carr, P.D. Kube, N.G. Elliott CSIRO Marine and Atmospheric Research, Hobart, Tasmania, Australia Reliable and cost-effective DNA pedigree assignment for many terrestrial livestock programs is now a reality. While the cost of genotyping livestock on a commercial scale is starting to decrease, this depends on the species in question and the number of markers implemented in a pedigree suite. Aquaculture of greenlip (Haliotis laevigata) and blacklip (Haliotis rubra) abalone is an emerging primary industry in Australia with selective breeding programs developed for commercial farms. Current DNA technologies present viable tools for these breeding programs although the accurate identification of family members is paramount. For most aquaculture species and indeed for abalone, access to DNA pedigree markers for family assignment and assessment is not fully developed. A robust and costeffective pedigree system must contain loci with high combined exclusion probabilities and polymorphic information content yet balanced with respect to the resources needed to run such a system. This poster details the developmental stages and optimisation steps undertaken to obtain a cost-effective and high-throughput system for DNA pedigree assignment in cultured Australian abalone. We present the results of our study to date based on 50 microsatellite loci and their ability to assign pedigree from multiple family lines. In addition, we outline the utility of these loci for genetic parameter testing within family lines and ongoing assessment of wild abalone genetic diversity. doi:10.1016/j.aquaculture.2007.07.020