Effect of minor allele frequency on the number of single nucleotide polymorphisms needed for accurate parentage assignment: A methodology illustrated using Atlantic salmon

Dussault, Forest; Boulding, Elizabeth G.

doi:10.1111/are.13566

Cited by 21 publications

(18 citation statements)

References 23 publications

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“…This study began by assessing the informativeness of 17 QC cowpea SNP markers based on allele frequencies and PIC. The minor allele frequencies refer to the proportion of the secondmost-common alleles at a genetic locus in a population and play a key role in determining allele diversity and heritability in the population (Dussault and Boulding, 2018;Hernandez et al, 2019). Dussault and Boulding (2018) reported that markers with high minor allele frequencies have high resolving power in distinguishing between individuals.…”

Section: Discussionmentioning

confidence: 99%

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

et al. 2021

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Optimization of a breeding program for increased genetic gain requires quality assurance (QA) and quality control (QC) at key phases of the breeding process. One vital phase in a breeding program that requires QC and QA is the choice of parents and successful hybridizations to combine parental attributes and create variations. The objective of this study was to determine parental diversity and confirm hybridity of cowpea F1 progenies using KASP (Kompetitive Allele-Specific PCR)-based single nucleotide polymorphism (SNP) markers. A total of 1,436 F1 plants were derived from crossing 220 cowpea breeding lines and landraces to 2 elite sister lines IT99K-573-1-1 and IT99K-573-2-1 as male parents, constituting 225 cross combinations. The progenies and the parents were genotyped with 17 QC SNP markers via high-throughput KASP genotyping assay. The QC markers differentiated the parents with mean efficiency of 37.90% and a range of 3.4–82.8%, revealing unique fingerprints of the parents. Neighbor-Joining cladogram divided the 222 parents into 3 clusters. Genetic distances between parents ranged from 0 to 3.74 with a mean of 2.41. Principal component analysis (PCA) depicted a considerable overlap between parents and F1 progenies with more scatters among parents than the F1s. The differentiation among parents and F1s was best contributed to by 82% of the markers. As expected, parents and F1s showed a significant contrast in proportion of heterozygous individuals, with mean values of 0.02 and 0.32, respectively. KASP markers detected true hybridity with 100% success rate in 72% of the populations. Overall, 79% of the putative F1 plants were true hybrids, 14% were selfed plants, and 7% were undetermined due to missing data and lack of marker polymorphism between parents. The study demonstrated an effective application of KASP-based SNP assay in fingerprinting, confirmation of hybridity, and early detection of false F1 plants. The results further uncovered the need to deploy markers as a QC step in a breeding program.

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Section: Discussionmentioning

confidence: 99%

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

et al. 2021

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“…Indeed, low-density SNP panels with relatively high polymorphism are testified to be able to conduct accurate parentage analysis. Dussault and Boulding explored how different values of MAF influence the number of SNPs required for accurate parentage assignment, demonstrating that larger panels with low average MAF are needed to achieve the same accuracy as smaller panels with high average MAF [ 21 ].…”

Section: Discussionmentioning

confidence: 99%

“…Nevertheless, the majority of SNPs are biallelic contrast to multi-allelic microsatellites, which undermines the potential of per SNP locus applying to parentage analysis because of relatively lower polymorphism and heterozygosity [ 20 ]. This problem usually can be alleviated by increasing the number of SNPs involved in analysis, and also, selecting the loci with higher minimum allele frequency (MAF) can enhance the power of markers for parentage exclusion [ 21 ]. However, the increase of loci also results in the increase of investment of time and money.…”

Section: Introductionmentioning

confidence: 99%

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng

Yang

Wang

et al. 2021

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Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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“…This pattern is especially evident among breeders of domestic cattle and sheep (Table ). Not coincidentally, the cattle breeding field has arrived at a preliminary consensus that 500 or more SNPs are required to resolve parentage confidently (e.g., McClure et al, ; McClure et al, ), whereas fields using modern analytical methods tend to conclude that 100–200 SNPs are usually more than adequate (Abadía‐Cardoso, Anderson, Pearse, & Garza, ; Dussault & Boulding, ; Steele et al, ). The reason that exclusion performs less well than formal maximum‐likelihood approaches is that it requires implicit assumptions that are ill defined and it discards much of the data.…”

Section: Approaches To Parentage Analysismentioning

confidence: 99%

The future of parentage analysis: From microsatellites to SNPs and beyond

2019

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Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next‐generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next‐generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next‐generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP‐based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100–500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next‐generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next‐generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

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Effect of minor allele frequency on the number of single nucleotide polymorphisms needed for accurate parentage assignment: A methodology illustrated using Atlantic salmon

Cited by 21 publications

References 23 publications

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

The future of parentage analysis: From microsatellites to SNPs and beyond

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