Abstract
BackgroundSingle nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. We compared allele frequency distributions and genetic diversity measures (expected heterozygosity (He), fixation index (FST) values, genetic distances and principal components analysis (PCA)) between the two data types. With the array data, we applied different filtering options (SNPs polymorphic in samples of two Gallus gallus wild populations, linkage disequilibrium (LD) based pruning and minor allele frequency (MAF) filtering, and combinations thereof) to assess their potential to mitigate the ascertainment bias.ResultsRare SNPs were underrepresented in the array data. Array data consistently overestimated He compared to WGS data, however, with a similar ranking of the breeds, as demonstrated by Spearman’s rank correlations ranging between 0.956 and 0.985. LD based pruning resulted in a reduced overestimation of He compared to the other filters and slightly improved the relationship with the WGS results. The raw array data and those with polymorphic SNPs in the wild samples underestimated pairwise FST values between breeds which had low FST (<0.15) in the WGS, and overestimated this parameter for high WGS FST (>0.15). LD based pruned data underestimated FST in a consistent manner. The genetic distance matrix from LD pruned data was more closely related to that of WGS than the other array versions. PCA was rather robust in all array versions, since the population structure on the PCA plot was generally well captured in comparison to the WGS data.ConclusionsAmong the tested filtering strategies, LD based pruning was found to account for the effects of ascertainment bias in the relatively best way, producing results which are most comparable to those obtained from WGS data and therefore is recommended for practical use.
Highlights
Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations
The proportion of SNPs in the frequency bin 0.025–0.125 was slightly higher in the whole genome resequencing (WGS) than the array data while the proportions of SNPs in the bins 0.150–0.3 were slightly higher in the array than the WGS data
The array data had very low but increasing numbers of SNPs at allele frequencies between 0 and 0.175 while the WGS had a very high number of rare variants between 0 and 0.025 and SNP numbers decreased with increasing frequencies, with the exception of the last window which was found to be slightly over-represented
Summary
Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Following the process of animal domestication, evolutionary forces such as selection and genetic drift have played a critical role in animal diversification Such forces led to genomic alterations such as fixation of favorable alleles within a breed or species and differentiation from the ancestral state due to successful selection programs or adaptation. In Europe, an organized and systematic breeding in chickens was developed during the nineteenth century Selection programs in this case were based on producing attractive features (for entertainment) in line with the breed standards; because of this, many fancy breeds were heavily selected for their attractiveness. To date such heavily selected breeds exhibit reduced genetic diversity and high average genetic distances to other breeds [3,4,5]. Major components for the reduced variability within both the commercial and the fancy breeds are due to the fact that the selection was certainly based on small number of founders, small effective population size and/or high degree of inbreeding
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
