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Zhu Z.Y.,Molecular Population Genetics Group | Wang C.M.,Molecular Population Genetics Group | Lo L.C.,Molecular Population Genetics Group | Lin G.,Molecular Population Genetics Group | And 7 more authors.
Animal Genetics | Year: 2010

Summary Microsatellites are the most popular markers for parentage assignment and population genetic studies. To meet the demand for international comparability for genetic studies of Asian seabass, a standard panel of 28 microsatellites has been selected and characterized using the DNA of 24 individuals from Thailand, Malaysia, Indonesia and Australia. The average allele number of these markers was 10.82 ± 0.71 (range: 6-19), and the expected heterozygosity averaged 0.76 ± 0.02 (range: 0.63-1.00). All microsatellites showed Mendelian inheritance. In addition, eight standard size controls have been developed by cloning a set of microsatellite alleles into a pGEM-T vector to calibrate allele sizes determined by different laboratories, and are available upon request. Seven multiplex PCRs, each amplifying 3-5 markers, were optimized to accurately and rapidly genotype microsatellites. Parentage assignment using 10 microsatellites in two crosses (10-10 and 20-20) demonstrated a high power of these markers for revealing parent-sibling connections. This standard set of microsatellites will standardize genetic diversity studies of Asian seabass, and the multiplex PCR sets will facilitate parentage assignment. © 2009 The Authors. Source


Shen X.,Reproductive Genomics Group | Cui J.,National University of Singapore | Gong Q.,Ocean University of China
Genome | Year: 2011

Members of the Fox gene family of transcriptional regulators are essential for animal development and have been extensively studied in vertebrates. The mouse and human genomes contain at least 40 FOX genes which are divided into 19 subclasses based on the sequence similarity of the highly conserved forkhead domain. Using the genome sequence of the Takifugu rubripes and Tetraodon nigroviridis, we examined the genomic complement of fox genes in these organisms to gain insight into the evolutionary relationship of this gene family. We identified 53 fox genes in Tetraodon nigroviridis and Takifugu rubripes genome by searching the forkhead domain. These genes are divided into 18 subclasses as follows: 8 fox genes in subclass O; 6 in subclass P; 4 in subclasses D, J, and N; 3 in subclasses A, B, C, E, F, and I; 2 in subclasses K, L, and Q; and 1 in subclasses G, H, M, and R. Together with the forkhead domain sequences of human, chicken, frog, zebrafish, medaka, and Caenorhabditis elegans, the phylogenetic relationship of the fox genes in Takifugu rubripes and Tetraodon nigroviridis were analyzed and compared. The genes structure, general features, and the three-dimensional model of these genes were also discussed. © 2011 Published by NRC Research Press. Source


Liew W.C.,Reproductive Genomics Group
Briefings in functional genomics | Year: 2014

In this review, we provide a detailed overview of studies on the elusive sex determination (SD) and gonad differentiation mechanisms of zebrafish (Danio rerio). We show that the data obtained from most studies are compatible with polygenic sex determination (PSD), where the decision is made by the allelic combinations of several loci. These loci are typically dispersed throughout the genome, but in some teleost species a few of them might be located on a preferential pair of (sex) chromosomes. The PSD system has a much higher level of variation of SD genotypes both at the level of gametes and the sexual genotype of individuals, than that of the chromosomal sex determination systems. The early sexual development of zebrafish males is a complicated process, as they first develop a 'juvenile ovary', that later undergoes a transformation to give way to a testis. To date, three major developmental pathways were shown to be involved with gonad differentiation through the modulation of programmed cell death. In our opinion, there are more pathways participating in the regulation of zebrafish gonad differentiation/transformation. Introduction of additional powerful large-scale genomic approaches into the analysis of zebrafish reproduction will result in further deepening of our knowledge as well as identification of additional pathways and genes associated with these processes in the near future. Source


Wang C.M.,National University of Singapore | Lo L.C.,National University of Singapore | Zhu Z.Y.,National University of Singapore | Pang H.Y.,National University of Singapore | And 6 more authors.
Marine Biotechnology | Year: 2011

The caudal fin represents a fundamental design feature of fishes and plays an important role in locomotor dynamics in fishes. The shape of caudal is an important parameter in traditional systematics. However, little is known about genes involved in the development of different forms of caudal fins. This study was conducted to identify and map quantitative trait loci (QTL) affecting the length of caudal fin and the ratio between tail length and standard body length in Asian seabass (Lates calcarifer). One F1 family containing 380 offspring was generated by crossing two unrelated individuals. One hundred and seventeen microsatellites almost evenly distributed along the whole genome were genotyped. Length of caudal fin at 90 days post-hatch was measured. QTL analysis detected six significant (genome-wide significant) and two suggestive (linkage-group-wide significant) QTL on seven linkage groups. The six significant QTL explained 5.5-16.6% of the phenotypic variance, suggesting these traits were controlled by multiple genes. Comparative genomics analysis identified several potential candidate genes for the length of caudal fin. The QTL for the length of caudal fin detected for the first time in marine fish may provide a starting point for the future identification of genes involved in the development of different forms of caudal fins in fishes. © 2010 Springer Science+Business Media, LLC. Source


Cui J.,National University of Singapore | Shen X.,Reproductive Genomics Group | Zhao H.,Central China Normal University | Nagahama Y.,Japan National Institute for Basic Biology
Cytogenetic and Genome Research | Year: 2011

Genes of the Sox family encode evolutionarily conserved high-mobility group box containing transcription factors, which play key roles in various events of developmental contexts. In this study, we identified 15 sox genes by searching for the high-mobility group domain in the medaka genome and by polymerase chain reaction using primers designed from the results obtained from homology protein alignment. All medaka sox genes except a novel sox gene, Olsox32, are encoded in 5 groups as follows: 4 sox genes in group B; 3 sox genes in group D and F, respectively; 2 sox genes in group C and E, respectively, while no sox genes were found in groups A, G, H, I, and J. The medaka Olsox32 does not fall within any of the previously defined groups A-J. Here we have assigned it to a new group K. Together with the Sox protein sequences of other species, the phylogenetic relationship was analyzed and compared. Our findings point to recent sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages. The expression pattern shows that sox genes play a variety of roles in the early embryonic development of medaka. Copyright © 2011 S. Karger AG, Basel. Source

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