Limits...
A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment.

Glover KA, Hansen MM, Lien S, Als TD, Høyheim B, Skaala O - BMC Genet. (2010)

Bottom Line: Global FST was similar among 28 linkage groups when averaging data from mapped SNPs.The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Marine Research, PO Box 1870, Nordnes N- 5817 Bergen, Norway. kevin.glover@imr.no

ABSTRACT

Background: Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations.

Results: Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global FST was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global FST for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.

Conclusion: Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.

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Correct self-assignment percentage plotted against cumulative number of STR loci selecting loci displaying the highest global FST (dotted line), highest number of alleles (solid line), least number of alleles (double line), and greatest assignment power when ranked by the program BELS (broken line). Overall assignment reached a maximum of 65%.
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Figure 3: Correct self-assignment percentage plotted against cumulative number of STR loci selecting loci displaying the highest global FST (dotted line), highest number of alleles (solid line), least number of alleles (double line), and greatest assignment power when ranked by the program BELS (broken line). Overall assignment reached a maximum of 65%.

Mentions: Using Geneclass, the overall accuracy of self-assignment was 65%, 73% and 73% for the data sets consisting of 14 STR, 300 SNPs and 195 mapped SNPs respectively (Figures 3 and 4). In the STR data set, with the exception of selecting loci starting with the least polymorphic first, the various selection methods only gave small differences in increase of assignment with number of loci (Figure 3), and, almost no further gain in assignment was observed past four loci. In the 300 SNP data set, large differences in the cumulative assignment curve were observed between the different selection methods (Figure 4), furthermore, selection of loci from the 195 mapped SNPs gave the highest overall assignment when approximately 100 loci were included in the analysis (80% assignment). Past this number of loci, the assignment accuracy dropped. Comparing the two marker types, the "best" 15 SNPs selected by BELS matched the level of assignment achieved by the best 4 STR loci selected by allelic variation (and BELS).


A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment.

Glover KA, Hansen MM, Lien S, Als TD, Høyheim B, Skaala O - BMC Genet. (2010)

Correct self-assignment percentage plotted against cumulative number of STR loci selecting loci displaying the highest global FST (dotted line), highest number of alleles (solid line), least number of alleles (double line), and greatest assignment power when ranked by the program BELS (broken line). Overall assignment reached a maximum of 65%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2818610&req=5

Figure 3: Correct self-assignment percentage plotted against cumulative number of STR loci selecting loci displaying the highest global FST (dotted line), highest number of alleles (solid line), least number of alleles (double line), and greatest assignment power when ranked by the program BELS (broken line). Overall assignment reached a maximum of 65%.
Mentions: Using Geneclass, the overall accuracy of self-assignment was 65%, 73% and 73% for the data sets consisting of 14 STR, 300 SNPs and 195 mapped SNPs respectively (Figures 3 and 4). In the STR data set, with the exception of selecting loci starting with the least polymorphic first, the various selection methods only gave small differences in increase of assignment with number of loci (Figure 3), and, almost no further gain in assignment was observed past four loci. In the 300 SNP data set, large differences in the cumulative assignment curve were observed between the different selection methods (Figure 4), furthermore, selection of loci from the 195 mapped SNPs gave the highest overall assignment when approximately 100 loci were included in the analysis (80% assignment). Past this number of loci, the assignment accuracy dropped. Comparing the two marker types, the "best" 15 SNPs selected by BELS matched the level of assignment achieved by the best 4 STR loci selected by allelic variation (and BELS).

Bottom Line: Global FST was similar among 28 linkage groups when averaging data from mapped SNPs.The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Marine Research, PO Box 1870, Nordnes N- 5817 Bergen, Norway. kevin.glover@imr.no

ABSTRACT

Background: Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations.

Results: Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global FST was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global FST for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.

Conclusion: Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.

Show MeSH