The development and application of genetic markers for the Kuruma prawn Penaeus japonicus

Moore, S. S.; Whan, Vicki; Davis, Geoff; Byrne, Keren; Hetzel, David J.; Preston, Nigel P.

doi:10.1016/s0044-8486(98)00461-x

Cited by 125 publications

(86 citation statements)

References 9 publications

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“…Microsatellite analyses have been used to assess genetic variation in several penaeid species, such as L. vannamei (Wolfus et al, 1997), Marsupenaeus japonicus (Moore et al, 1999), L. stylirostris (Bierne et al, 2000), Penaeus monodon (Tassanakajon et al, 1998;Brooker et al, 2000;Pongsomboon et al, 2000, Xu et al, 2001, Litopenaeus schmitti (Maggioni et al, 2003;Borrel et al, Genetics and Molecular Biology, 30, 4, 1156-1160(2007 Copyright by the Brazilian Society of Genetics. Printed in Brazil www.sbg.org.br 2004) and Litopenaeus setiferus (Ball and Chapman, 2003) but, however, little is known on the genetics of the Brazilian L. vannamei broodstocks Galetti Jr 2002, 2005;De Francisco and Galetti Jr, 2005;Gonçalves et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Genetic variation in a closed line of the white shrimp Litopenaeus vannamei (Penaeidae)

2007

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The culture of the marine shrimp Litopenaeus vannamei has recently boosted the Brazilian shrimp industry. However, it is well known that selection methods based solely on phenotypic characteristics, a reduced number of breeders and the practice of inbreeding may promote a significant raise in the genetic similarity of the captive populations, leading to greater disease susceptibility and impairing both the growth and final size of the shrimps. We used four microsatellite loci to investigate genetic variation in three generations (F 5 , F 6 and F 7 ) of a closed and reared L. vannamei lineage. Although an accentuated heterozygosis deficit was detected, we also observed that the captive propagation of this lineage did not lead to a significant loss of genetic variability over the three generations studied. One possible reason for this is that the breeding conditions of this lineage were good enough to prevent any significant loss of genetic variability. However, three generations may have been insufficient to produce detectable changes in genetic frequencies in the loci studied. Alternatively, the microsatellite loci may have been non-neutral (biased) and related to the conditions in which the shrimps were kept, resulting in a similar allele pool in respect to these four microsatellites over the three generations studied. Any generalizations regarding microsatellite variation in closed shrimp lines may thus be incomplete and should be carefully analyzed.

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Section: Introductionmentioning

confidence: 99%

Genetic variation in a closed line of the white shrimp Litopenaeus vannamei (Penaeidae)

2007

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“…All the breeding programs implemented on shrimp species might benefit from the use of molecular markers and linkage maps. In fact two maps have been reported on shrimps (Moore et al, 1999;Wilson et al, 2002;.…”

Section: Introductionmentioning

confidence: 99%

A sex-specific linkage map of the white shrimp Penaeus (Litopenaeus) vannamei based on AFLP markers

et al. 2004

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We report the construction of sex-specific linkage maps for the white shrimp Penaeus (Litopenaeus) vannamei (Penaeidae; Crustacea). Linkage information was generated using amplified fragment length polymorphism (AFLP) markers in a mapping panel consisting of 42 individuals derived from a commercial cross. We used 103 primer combinations that produced 741 segregating bands. From them, 477 segregated in a 1:1 model, 181 in a 3:1 model, 62 fitted both models and 21 fitted neither model. A total of 394 loci with a 1:1 segregation ratio were mapped to unique positions in the male and female maps using a pseudotestcross strategy. A total of 51 and 47 linkage groups were detected for the male and female maps respectively, in comparison to 44 haploid groups expected from the karyotype. The female map covered 2771 Kosambi units (cM) and was 24% longer than the male map (2116 cM long). The distribution of the markers showed that both maps had low saturation and clustering at short linkage distances. Markers with a distorted segregation were observed as previously reported in other shrimp species. The estimated genomic length indicates that the P. vannamei genome has higher recombination rates than closely related species. We demonstrate the feasibility of implementing molecular techniques

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“…Over the last few decades, microsatellite sequences have been widely used in many animal groups, including shrimp, and principally in economically important species (Wolfus et al, 1997;Bierne et al, 2000;Xu et al, 2001). Due to their high level of allelic variation and codominant nature, microsatellite loci have been extremely useful for the determination of genetic diversity, stock discrimination, identification of lineages and individuals, the establishment of pedigrees, the development of breeding programs, linkage map studies and the identification of loci related to commercially important characteristics (Moore et al, 1999;Ozaki et al, 2000).In the past half decade, different research groups have been striving to characterize microsatellite markers in the genome of a number of penaeid shrimp species (Cruz et al, 2002;Meehan et al, 2003;Pérez et al, 2005). However, the validation of these sequences has generally not been easy.…”

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confidence: 99%

“…; (7) number and size of alleles per locus; and (8) results generated by the TRF program during the analysis, including any inconsistencies with the literature concerning the locus in question. Among the main observed inconsistencies in the sequences analyzed were the presence of microsatellites which were not flanked by one or both of the described primers, partially or totally absent repeats in the sequence described, microsatellites described with different motifs than those found by the TRF program and microsatellites with more than one GenBank ID or for which the ID numbers were different to those described in the paper in which it was cited.Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed: Farfantepenaeus notialis (Robainas et al, 2002;Robainas et al, 2003) (Espinosa et al, 2001;Maggioni et al, 2003; Borrel et al, 2004), Litopenaeus setiferus (Ball et al, 1998), Litopenaeus stylirostris (Vonau et al, 1999;Bierne et al, 2000), Litopenaeus vannamei (Wolfus et al, 1997;Cruz et al, 2002;Meehan et al, 2003;Pérez et al, 2005), Marsupenaeus japonicus (Moore et al, 1999), Penaeus esculentus (Meadows et al, 2003) and Penaeus monodon (Xu et al, 1999;Pongsomboon et al, 2000;Brooker et al, 2000;Xu et al, 2001;Wuthisuthimethavee et al, 2003;Pan et al, 2004). Cross-species amplification results are practically inexistent, being limited to a few loci described for L. vannamei that were also efficient in Rimapenaeus byrdi (= Trachypenaeus byrdi) and L. stylirostris (Pérez et al 2005).…”

mentioning

confidence: 99%

“…Due to their high level of allelic variation and codominant nature, microsatellite loci have been extremely useful for the determination of genetic diversity, stock discrimination, identification of lineages and individuals, the establishment of pedigrees, the development of breeding programs, linkage map studies and the identification of loci related to commercially important characteristics (Moore et al, 1999;Ozaki et al, 2000).…”

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In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

et al. 2007

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We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta-and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.Key words: Crustacea, microsatellite structure, Penaeidae, SSR.Received: September 19, 2006; Accepted: May 7, 2007. Over the last few decades, microsatellite sequences have been widely used in many animal groups, including shrimp, and principally in economically important species (Wolfus et al., 1997;Bierne et al., 2000;Xu et al., 2001). Due to their high level of allelic variation and codominant nature, microsatellite loci have been extremely useful for the determination of genetic diversity, stock discrimination, identification of lineages and individuals, the establishment of pedigrees, the development of breeding programs, linkage map studies and the identification of loci related to commercially important characteristics (Moore et al., 1999;Ozaki et al., 2000).In the past half decade, different research groups have been striving to characterize microsatellite markers in the genome of a number of penaeid shrimp species (Cruz et al., 2002;Meehan et al., 2003;Pérez et al., 2005). However, the validation of these sequences has generally not been easy. The penaeid genome seems to contain very long microsatellite repetitions, hindering the cloning and sequencing of microsatellites containing both flanking regions. A few comparisons demonstrate that the microsatellites found in penaeids (Tassanakajon et al., 1998;Cruz et al., 2002) are approximately twice the size of the sequences found in other animal groups (Estoup et al., 1993;Brooker et al., 1994), being four or five times larger in so...

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The development and application of genetic markers for the Kuruma prawn Penaeus japonicus

Cited by 125 publications

References 9 publications

Genetic variation in a closed line of the white shrimp Litopenaeus vannamei (Penaeidae)

Genetic variation in a closed line of the white shrimp Litopenaeus vannamei (Penaeidae)

A sex-specific linkage map of the white shrimp Penaeus (Litopenaeus) vannamei based on AFLP markers

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

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