Development and validation of a low-density SNP panel for paternity and kinship analysis and evaluation of genetic variability and structure of commercial Pacific white shrimp (Litopenaeus vannamei) populations from Brazil

Silva, Nayelle MeyreLisboa; Ianella, P.; Yamagishi, M. E. B.; Rocha, J. L.; Teixeira, Ana Karina; Farias, Flávio Galvão; Guerrelhas, Ana C.; Caetano, Alexandre Rodrigues

doi:10.1016/j.aquaculture.2022.738540

Cited by 7 publications

(3 citation statements)

References 34 publications

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“…It was reported that the minimum number of 36 SNPs (average MAF = 0.42, 85 sires, 162 dams) was able to correctly assign more than 92% of offspring to their true parents, and the assignment accuracy reached 100% when using 68 SNPs (average MAF = 0.37) in farmed rainbow trout (Oncorhynchus mykiss) [22]; a similar study showed that 72-188 polymorphic SNPs were able to obtain assignment accuracy of above 95% in farmed steelhead [33]. The effectiveness of SNPs for parentage assignment using small SNP subsets was also proved in Pacific white shrimp when 88 SNPs with an average MAF of 0.38 (44 sires, four dams) were able to completely assign offspring to correct sires and dams with a confidence higher than 95% [24]. High assignment accuracy, however, should not be the only criterion to assess effectiveness of SNPs for sibship assignment unless assignment rate has also been considered.…”

Section: Maf and Snp Number For Sibship Assignmentmentioning

confidence: 92%

“…Many studies have shown the effectiveness of SNPs for parentage assignment in wild fish population [14,15] and aquaculture species [16][17][18] as well as for brood-stock differentiation [19] and traceability [20]. Effective applications of SNPs have led to the recent development of SNP arrays in high-value farmed species, including Atlantic salmon [21], rainbow trout [22] and Pacific white shrimp [23,24]. In farmed shrimp, SNPs have been reported to show better performances than microsatellites for parentage assignment in black tiger shrimp (Penaeus monodon) [18] and Pacific white shrimp (Penaeus vannamei) [9]; however, comparisons between microsatellite and SNP markers for parentage assignment in banana shrimp remained unknown.…”

Section: Introductionmentioning

confidence: 99%

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Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Phuthaworn

Nguyen

Knibb

2023

JMSE

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Pedigrees are essential components in selective breeding programs to manage genetic diversity and obtain accurate genetic parameter estimates to ensure long-term response to selection in captive populations. High throughput and cost-effective sequencing technologies has offered opportunities of using single nucleotide polymorphisms (SNPs) to resolve penaeid shrimp pedigrees from mass spawning cohorts and communal rearing. Effects of SNPs for sibship assignment were investigated on 546 shrimp using two software programs, Colony and Sequoia. Assignment rates and accuracies using SNP subsets with six different minor allele frequencies (MAFs), four sets of SNPs, and five genotyping error rates were compared to the microsatellite-based pedigree established in a previous study. High MAFs and numbers of SNPs contributed to significant increases in assignment rates and accuracies, whereas genotyping error rates showed negligible impacts on assignment results. Sibship assignments achieved rates and accuracies of 98% and 83%, respectively, with a minimum number of 91 SNPs (average MAF ≥ 0.14), and the two different programs exhibited similar resulting patterns for different SNP subsets. High consistencies between SNP-based and microsatellite-based pedigrees showed that accurate pedigrees could be achieved by using SNPs and thus contribute to the long-term response to selection in farmed banana shrimp.

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Section: Maf and Snp Number For Sibship Assignmentmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Phuthaworn

Nguyen

Knibb

2023

JMSE

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“…The advantages of using microsatellites and SNPs in parentage assignment have been reviewed with an indication that the SNP-based method can benefit from the development of genomics [ 456 ]. The parentage analysis with the close-kin mark–recapture (CKMR) method based usually on a large number of SNP loci, has recently been worked out for a few species, such as salmon, thornback ray, Raja clavate , and the Pacific white shrimp, L. vannamei , with high potential for further applications [ 457 , 458 , 459 ]. Nevertheless, microsatellites remain the most accessible marker system in the preset day kinship analyses of cultured and wild populations [ 460 , 461 , 462 ].…”

Section: Kinship Analysis Of Aquacultured Stocksmentioning

confidence: 99%

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

Wenne

2023

Genes

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A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

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Low-density AgriSeq targeted genotyping-by-sequencing markers are efficient for pedigree quality control in Pinus taeda L. breeding

Lin

Shalizi

Walker

et al. 2023

Tree Genetics & Genomes

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Development and validation of a low-density SNP panel for paternity and kinship analysis and evaluation of genetic variability and structure of commercial Pacific white shrimp (Litopenaeus vannamei) populations from Brazil

Cited by 7 publications

References 34 publications

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

Low-density AgriSeq targeted genotyping-by-sequencing markers are efficient for pedigree quality control in Pinus taeda L. breeding

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