Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1

Abstract

Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms.

Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

“…This rate was in line with the 98% previously observed [ 34 ], which evaluated a subset of the duplicate pairs evaluated in this study. This rate is also comparable to the 98.8% for humans [ 37 ], the 97.38% observed for sheep [ 38 ], and the 98.4% for swine [ 39 ].…”

“…Concordance rates between the Illumina Infinium 20 K and Affymetrix Axiom Apple 480 K SNP array data were reported as 96 to 98%, based on 53 common individuals [ 34 ]. This high rate is promising and is in line with those found in other organisms: an average concordance of 96 to 98.8% was reported in human [ 37 ], sheep [ 38 ], and swine [ 39 ]. However, levels of concordance were not documented at the individual SNP level, as would be needed for accurate data integration.…”

SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array

“…In this study, we developed the first high throughput genotyping assay for the four main cultured species in the Mytilus genus, a Use of a marker CR of ≥95% as a threshold instead of DQC, as employed in this study, has been successfully demonstrated in GWAS for different taxa to obtain informative results on population structure, admixture and identification of SNPs significant for breeding purposes, including sheep (Davenport et al, 2020), chicken (Liu et al, 2019) and swine (Cheng et al, 2022;Wijesena et al, 2019).…”

“…Use of a marker CR of ≥ 95% as a threshold instead of DQC, as employed in this study, has been successfully demonstrated in GWAS for different taxa to obtain informative results on population structure, admixture and identification of SNPs significant for breeding purposes, including sheep (Davenport et al, 2020), chicken (Liu et al, 2019) and swine (Cheng et al, 2022; Wijesena et al, 2019). Here we chose to apply this alternative filtering method as samples genotyped in the 60 K blue mussel array consistently received low scores with the DQC parameter (ST1) and were removed from the analysis by the software, indicating the existence of polymorphisms present in the DQC 71 bp flanking probes.…”

Functional genomics of reproduction in pigs: Are we there yet?

“…A custom and commercially available SNP array (SowPro90) was designed that included over 50,000 potential functional and loss‐of‐function variants identified from genomic and transcriptomic sequences in QTL regions from three independent GWAS studies for age at puberty (D. J. Nonneman et al, 2016; Tart et al, 2013; Wijesena et al, 2017) and viral disease (Walker et al, 2018) and 50,000 core SNP from the Porcine SNP60 BeadArray to contain a total of 103,476 SNP (Wijesena et al, 2019). Because of the addition of potential functional variants and its higher density of SNP, this array has been used to fine‐map QTL in one of the original discovery populations for age at puberty (Tart et al, 2013; Wijesena et al, 2017) and a large commercial population for reproductive longevity (Wijesena et al, 2020).…”