Development of a microsatellite DNA parentage marker suite for black tiger shrimp Penaeus monodon

Jerry, Dean R.; Evans, Brad S.; Kenway, Matthew; Wilson, Kate

doi:10.1016/j.aquaculture.2005.11.026

Cited by 45 publications

(40 citation statements)

References 20 publications

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“…In contrast, studies in the eastern oyster, Crassostrea virginica, and the black tiger shrimp, P. monodon, found a higher percentage of useful loci (i.e. C. virginica, 37%; P. monodon, 30%-50%) (Jerry et al, 2006;Reece, Ribeiro, Gaffney, Carnegie & Allen, 2004).…”

Section: Discussionmentioning

confidence: 81%

“…Over the past decades, farming mud crabs has developed rapidly in China as well as in other South East Asian countries, such as Vietnam, Indonesia, the Philippines and Thailand, which could partially be attributed to improvements in hatchery seed production in recent years. In fact, the annual aquaculture production of For the long-term sustainability of a selective breeding programme, maintenance of reliable pedigree information is imperative (Jerry, Evans, Kenway & Wilson, 2006). In situations where mass selection is practiced, the absence of parentage information will increase the risk of inbreeding by choosing consanguineous breeding candidates.…”

Section: Introductionmentioning

confidence: 99%

“…They have been used extensively for parentage assignment and pedigree tracing in aquaculture studies (Estoup et al, 1998;Hara & Sekino, 2003;Jerry et al,2006;Ma et al, 2013;Vandeputte et al, 2004). As microsatellite technique is based on PCR method, it only requires trace DNA samples, hence it also has the advantage of no need to scarify the study animals.…”

Section: Introductionmentioning

confidence: 99%

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Parentage determination of the mud crab Scylla paramamosain using microsatellite markers

Wang

Zeng

et al. 2017

Aquac Res

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This study evaluated the properties of nine Scylla paramamosain microsatellite loci screened by us previously for inclusion in a parentage assignment marker suite. These nine highly polymorphic markers (mean He=0.847 and PIC=0.830) were determined as being suitable for parentage assignment. Simulations based on allele frequency data from 15 known maternal families (165 individuals) demonstrated that at least four loci were required to assign >95% of offspring to maternal parents with 95% confidence.In actual parentage assignments, all progenies were assigned to the maternal parents with six or more loci, which was similar to the simulation predictions. Our results suggest that this set of microsatellites provide a powerful and efficient tool for identifying pedigree information for selective breeding programmes of S. paramamosain. K E Y W O R D Smicrosatellite, offspring, parentage determination, Scylla paramamosain

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Section: Discussionmentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Parentage determination of the mud crab Scylla paramamosain using microsatellite markers

Wang

Zeng

et al. 2017

Aquac Res

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“…The tiger shrimp Penaeus monodon data set (Jerry et al 2006) consisted of 59 individuals from 13 families with seven loci. There were 16 missing alleles among all the loci.…”

Section: Data Setmentioning

confidence: 99%

New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers

Chaovalitwongse

Chou

Berger-Wolf

et al. 2010

INFORMS Journal on Computing

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W ith improved tools for collecting genetic data from natural and experimental populations, new opportunities arise to study fundamental biological processes, including behavior, mating systems, adaptive trait evolution, and dispersal patterns. Full use of the newly available genetic data often depends upon reconstructing genealogical relationships of individual organisms, such as sibling reconstruction. This paper presents a new optimization framework for sibling reconstruction from single generation microsatellite genetic data. Our framework is based on assumptions of parsimony and combinatorial concepts of Mendel's inheritance rules. Here, we develop a novel optimization model for sibling reconstruction as a large-scale mixed-integer program (MIP), shown to be a generalization of the set covering problem. We propose a new heuristic approach to efficiently solve this large-scale optimization problem. We test our approach on real biological data as presented in other studies as well as simulated data, and compare our results with other state-of-the-art sibling reconstruction methods. The empirical results show that our approaches are very efficient and outperform other methods while providing the most accurate solutions for two benchmark data sets. The results suggest that our framework can be used as an analytical and computational tool for biologists to better study ecological and evolutionary processes involving knowledge of familial relationships in a wide variety of biological systems.

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“…As a result, molecular markers and associated tools, such as genetic maps, are currently available for some crustacean species, particularly for shrimps. Molecular markers have been applied, for example, for analyzing the genetic diversity of wild shrimp resources (Xu et al, 2001), for strain and species identification in penaeids (Calo-Mata et al, 2009), and for parentage analysis in the black tiger shrimp Penaeus monodon (Jerry et al, 2006). In addition, linkage maps have been generated for several penaeid shrimp species, in most cases by using amplified fragment length polymorphism (AFLP) (Li et al, 2003;Zhang et al, 2007;Staelens et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of a female-specific DNA marker in the giant freshwater prawn Macrobrachium rosenbergii

et al. 2011

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In this study, a female-specific DNA marker in the freshwater prawn Macrobrachium rosenbergii was identified through amplified fragment length polymorphism (AFLP). The AFLPderived sequence-characterized amplified region (SCAR) marker was tested in over 200 individuals, giving reproducible sex identification. Further molecular characterization of the sex-marker's genomic region (B3 kb long) revealed the presence of tandem and inverted repeats. The B3-kb sequence was identified both in male and female prawns, but with subtle differences: a deletion of 3 bp (present in female prawn but absent in male prawn) identified upstream of the SCAR marker sequence and two female-specific single-nucleotide polymorphisms, both indicating that male prawns are homozygous, whereas female prawns are heterozygous in this locus. Fluorescent in situ hybridization showed the B3-kb sequence to be unique: to the best of our knowledge, this is the first report of a unique sex-specific sequence observed in situ in crustaceans. The sex-specific marker identified in M. rosenbergii may have considerable applied merit for crustacean culture in that it will enable the determination of genetic sex at early developmental stages when phenotypic differences are not identifiable.

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Development of a microsatellite DNA parentage marker suite for black tiger shrimp Penaeus monodon

Cited by 45 publications

References 20 publications

Parentage determination of the mud crab Scylla paramamosain using microsatellite markers

Parentage determination of the mud crab Scylla paramamosain using microsatellite markers

New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers

Isolation and characterization of a female-specific DNA marker in the giant freshwater prawn Macrobrachium rosenbergii

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