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

Hiruni R. Wijesena, Gary A. Rohrer, Dan J. Nonneman, Brittney N. Keel, Jessica L. Petersen, Stephen D. Kachman, Daniel C. Ciobanu

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)3262-3273
Number of pages12
JournalJournal of animal science
Volume97
Issue number8
DOIs
StatePublished - Jul 30 2019

Fingerprint

genotyping
Single Nucleotide Polymorphism
Genotype
genotype
genomics
sows
swine
puberty
transcriptomics
sampling
Fertility
quality control
Swine
quantitative trait loci
animals
genetic polymorphism
Quantitative Trait Loci
genome
prediction
Adaptive Immunity

Keywords

  • SNP genotype
  • SowPro90
  • custom
  • pig
  • puberty
  • quality
  • reproductive longevity

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Genetics

Cite this

Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1. / Wijesena, Hiruni R.; Rohrer, Gary A.; Nonneman, Dan J.; Keel, Brittney N.; Petersen, Jessica L.; Kachman, Stephen D.; Ciobanu, Daniel C.

In: Journal of animal science, Vol. 97, No. 8, 30.07.2019, p. 3262-3273.

Research output: Contribution to journalArticle

Wijesena, Hiruni R. ; Rohrer, Gary A. ; Nonneman, Dan J. ; Keel, Brittney N. ; Petersen, Jessica L. ; Kachman, Stephen D. ; Ciobanu, Daniel C. / Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1. In: Journal of animal science. 2019 ; Vol. 97, No. 8. pp. 3262-3273.
@article{eeecbccecec24bf597f6685e28bd3ace,
title = "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.",
keywords = "SNP genotype, SowPro90, custom, pig, puberty, quality, reproductive longevity",
author = "Wijesena, {Hiruni R.} and Rohrer, {Gary A.} and Nonneman, {Dan J.} and Keel, {Brittney N.} and Petersen, {Jessica L.} and Kachman, {Stephen D.} and Ciobanu, {Daniel C.}",
year = "2019",
month = "7",
day = "30",
doi = "10.1093/jas/skz185",
language = "English (US)",
volume = "97",
pages = "3262--3273",
journal = "Journal of Animal Science",
issn = "0021-8812",
publisher = "American Society of Animal Science",
number = "8",

}

TY - JOUR

T1 - Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1

AU - Wijesena, Hiruni R.

AU - Rohrer, Gary A.

AU - Nonneman, Dan J.

AU - Keel, Brittney N.

AU - Petersen, Jessica L.

AU - Kachman, Stephen D.

AU - Ciobanu, Daniel C.

PY - 2019/7/30

Y1 - 2019/7/30

N2 - 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.

AB - 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.

KW - SNP genotype

KW - SowPro90

KW - custom

KW - pig

KW - puberty

KW - quality

KW - reproductive longevity

UR - http://www.scopus.com/inward/record.url?scp=85070789102&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85070789102&partnerID=8YFLogxK

U2 - 10.1093/jas/skz185

DO - 10.1093/jas/skz185

M3 - Article

C2 - 31150541

AN - SCOPUS:85070789102

VL - 97

SP - 3262

EP - 3273

JO - Journal of Animal Science

JF - Journal of Animal Science

SN - 0021-8812

IS - 8

ER -