Genetic variation and population structure of Asian seabass (Lates calcarifer) in the Asia-Pacific region

Yue, Gen Hua; Zhu, Ze Yuan; Lo, Loong Chueng; Wang, Chun Ming; Lin, Grace; Feng, Felicia; Pang, Hong Yan; Li, Jian; Gong, Ping; Liu, Hui Ming; Tan, Jinsong; Chou, R.; Lim, Huansein; Orbán, László

doi:10.1016/j.aquaculture.2009.03.053

Cited by 92 publications

(81 citation statements)

References 37 publications

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“…They consist of repeated core sequences of 2~6 bp in length. Microsatellite markers have been proven to be an efficient tool for evaluating the level of genetic variation in a species with limited genetic information available (Liu and Cordes, 2004;Yue et al, 2004Yue et al, , 2009Liu et al, 2009) because of the high variability, abundance, neutrality, and co-dominance of microsatellite DNA. Polymorphic microsatellites have frequently been applied to genetic analysis and breeding programs of freshwater prawn populations (Wolfus et al, 1997;Chand et al, 2005;Chareontawee et al, 2007;.…”

Section: Introductionmentioning

confidence: 99%

Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China

Y¹,

Feng²,

Li³

2012

Genet. Mol. Res.

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ABSTRACT. The oriental river prawn (Macrobrachium nipponense) is an important freshwater prawn species in China. We collected 236 oriental river prawns from four wild stocks from Qiandao Lake, Zhejiang, China, and used nine polymorphic microsatellite markers to investigate their genetic diversity and structure, to facilitate the development of a selective breeding program. We found 185 alleles at nine loci in this sample. The observed heterozygosity (H O ) and expected heterozygosity (H E ) ranged from 0.43 to 0.89 and 0.56 to 0.95, respectively. The four stocks of M. nipponense displayed high genetic diversity (14.33-15.89 alleles/locus, H O = 0.66-0.77 and H E = 0.78-0.88). Genetic diversity of the stock from Weiping town was lower than the stocks from the other locations. Mutation-drift equilibrium analysis showed no significant bottleneck effect. F-statistics among stocks ranged from 0.03 to 0.07, indicating a moderate level of differentiation. Based on genetic structure analysis, the 236 individuals from the four wild stocks could be divided into two potential populations. Overall, the 09CA, 09AY and 09JJ wild stocks had higher allelic and genetic diversity than the upstream 09WP stock. These three wild stocks could be used as founders for selective breeding.

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Section: Introductionmentioning

confidence: 99%

Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China

Y¹,

Feng²,

Li³

2012

Genet. Mol. Res.

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“…The Asian seabass (called Barramundi in Australia) Lates calcarifer, belonging to the family Lachidae, is widely distributed in coastal and freshwater regions of the tropical Indo-West Pacific, from the Persian Gulf to India to northern Australia (Nelson, 2006;Yue et al, 2009). This species is an important marine food fish and is cultured in Southeast Asia and Australia (Chou and Lee, 1997;Frost et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Cloning and characterization of the calreticulin gene in Asian seabass (Lates calcarifer)

Bai

Zhu

Wang

et al. 2012

Animal

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Calreticulin (CRT) is a Ca 21 -binding molecular chaperone in the endoplasmic reticulum. We cloned and characterized the CRT gene in an important marine food fish species Asian seabass (Lates calcarifer). The full-length DNA of the CRT gene was 2194 bp, including a complete open reading frame encoding 420 amino acid residues, a 113 bp 5 0 -untranslated region and an 818 bp 3 0 -untranslated region. The CRT gene contained nine exons and eight introns covering a total of 2772 bp genomic DNA from the start to stop codon. Ten single nucleotide polymorphisms (SNPs) were detected in introns and an exon in six individuals collected from five different locations. The CRT gene was assigned to linkage group 4 of the linkage map of Asian seabass. Quantitative real-time PCR revealed that the CRT gene was highly expressed in liver at the age of 1, 3 and 7 months under normal conditions, whereas its expression in liver reduced sharply after 0.5 to 2 h cold challenge at 168C, and then increased slowly. A preliminary association analysis showed a significant (P , 0.001) association between the SNP6 in the CRT gene and the mortality after cold challenge at 168C. Our results suggest that the CRT gene is associated with cold tolerance of Asian seabass and further investigation will be necessary to illustrate the underlying mechanisms.Keywords: Barramundi, polymorphism, cold tolerance, QTL ImplicationsWe have isolated the whole length of the complementary DNA of the Calreticulin (CRT ) gene in the Asian seabass, studied the expression levels under normal condition and after 168C cold challenge, analyzed the genomic organization and polymorphism, and identified the association between the single nucleotide polymorphism6 and cold tolerance. Our results suggest that the CRT gene may be involved in cold tolerance in the Asian seabass. Further investigation will be required to illustrate the underlying mechanisms.

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“…Molecular markers can be used to effectively estimate genetic variation and population structure in different populations, thereby providing a basis for better management of whole populations and thence sustainable fisheries (Liu et al, 2009;Yue et al, 2009). The COI gene is well characterized and is frequently used for genetic studies in invertebrates and vertebrates (Ward et al, 2005;Spies et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Analysis of Indian Salmon, <i>Eleutheronema tetradactylum</i> from South Asian Countries Based on Mitochondrial COI Gene Sequences

Thirumaraiselvi

Thangaraj

2015

Not Sci Biol

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Eleutheronema tetradactylum is an important commercial fish species exposed to intense exploitation both in Southeast Asian countries and Northern parts of Australia. Research on the population structure of E. tetradactylum in these coastal waters is substantial in order to ensure sustainable use and appropriate resource management. In this study, genetic variation, diversity and population structure of E. tetradactylum among four FAO fishing areas, along South Asian countries, were evaluated using cytochrome c oxidase subunit I (COI) gene. Totally 30 sequences of COI gene were collected from four FAO fishing areas. Among these 30 individuals, 18 distinct haplotypes were defined. High levels of haplotype diversity (hd = 0.952 ± 0.096) and nucleotide diversity (π = 0.01536 ± 0.00312) were observed in the population within the Bay of Bengal. No haplotype and nucleotide diversity were observed in South China Sea population. Hierarchical analysis of molecular variance (AMOVA) indicated that whereas 0.81% of the genetic variation occurred within the populations, 7.09% occurred among populations. Significant genealogical branches were recognized in North Australian populations (one clade), South China Sea populations (one clade), Arabian Sea and Bay of Bengal populations (one clade on the neighbor-joining tree). These results suggested that E. tetradactylum populations in FAO fishing areas 51, 57 and 61 have developed different genetic structures. Tests of neutral evolution and mismatch distribution suggest that a population growth of E. tetradactylum may take place in these fishing areas.

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Genetic variation and population structure of Asian seabass (Lates calcarifer) in the Asia-Pacific region

Cited by 92 publications

References 37 publications

Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China

Genetic variation based on microsatellite analysis of the oriental river prawn, Macrobrachium nipponense from Qiandao Lake in China

Cloning and characterization of the calreticulin gene in Asian seabass (Lates calcarifer)

Genetic Diversity Analysis of Indian Salmon, <i>Eleutheronema tetradactylum</i> from South Asian Countries Based on Mitochondrial COI Gene Sequences

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