Translational Genomics For Improving Sow Fertility

Sow fertility traits, such as litter size and number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable, polygenic, sex-limited, and express late in life. Age at puberty is an early indicator of reproductive longevity. Gilts that achieve puberty at an early age have a greater probability to produce more parities over their lifetime. However, measuring age at puberty is time consuming and tedious. Identifying pleiotropic polymorphisms that affect age at puberty and other fertility traits, including reproductive longevity, could help to improve the accuracy of genomic prediction for sow fertility traits. We developed a custom Affymetrix SNP array (SowPro90) including SNPs located in major QTL regions for age at puberty, other fertility and disease related traits, and potential loss of function SNPs. Genetic variants were identified using deep transcriptomic and genomic sequencing, gene network analysis, and genome-wide association (GWAS) carried out at University of Nebraska-Lincoln (UNL) and US Meat Animal Research Center (USMARC). This novel SNP array was used to fine map the genetic sources associated with fertility traits. Using a Bayesian haplotype approach (BayesIM), SowPro90 haplotypes were inferred and assigned to the entire UNL population and were used in an association analysis for age at puberty and other fertility traits. Five major QTL regions located on four chromosomes (SSC2, SSC7, SSC14, SSC18) were discovered for age at puberty. As expected, a negative correlation (r = −0.96 to −0.10; PP2RX3, OAS1, NR2F2, PTPN11). These SNPs showed significant or suggestive effects on age at puberty, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. It will be beneficial to further characterize these SNPs and candidate genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect phenotypic variation of fertility traits. Advisor: Daniel Cioban

Evaluation of genotype quality parameters for \u3ci\u3eSowPro90\u3c/i\u3e, a new genotyping array for swine

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

GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows

Genetic variants associated with traits such as age at puberty and litter size could provide insight into the underlying genetic sources of variation impacting sow reproductive longevity and productivity. Genomewide characterization and gene expression profiling were used using gilts from the University of Nebraska–Lincoln swine resource population (n = 1,644) to identify genetic variants associated with age at puberty and litter size traits. From all reproductive traits studied, the largest fraction of phenotypic variation explained by the Porcine SNP60 BeadArray was for age at puberty (27.3%). In an evaluation data set, the predictive ability of all SNP from highranked 1-Mb windows (1 to 50%), based on genetic variance explained in training, was greater (12.3 to 36.8%) compared with the most informative SNP from these windows (6.5 to 23.7%). In the integrated data set (n = 1,644), the top 1% of the 1-Mb windows explained 6.7% of the genetic variation of age at puberty. One of the high-ranked windows detected (SSC2, 12–12.9 Mb) showed pleiotropic features, affecting both age at puberty and litter size traits. The RNA sequencing of the hypothalami arcuate nucleus uncovered 17 differentially expressed genes (adjusted P \u3c 0.05) between gilts that became pubertal early (180 d of age). Twelve of the differentially expressed genes are upregulated in the late pubertal gilts. One of these genes is involved in energy homeostasis (FFAR2), a function in which the arcuate nucleus plays an important contribution, linking nutrition with reproductive development. Energy restriction during the gilt development period delayed age at puberty by 7 d but increased the probability of a sow to produce up to 3 parities (P \u3c 0.05). Identification of pleotropic functional polymorphisms may improve accuracy of genomic prediction while facilitating a reduction in sow replacement rates and addressing welfare concerns

The roles of age at puberty and energy restriction |in sow reproductive longevity: a genomic perspective

Approximately 50% of sows are culled annually with more than one-third due to poor fertility. Our research demonstrated that age at puberty is an early pre-breeding indicator of reproductive longevity. Age at puberty can be measured early in life, has a moderate heritability, and is negatively correlated with lifetime number of parities. Detection of age at puberty is tedious and time consuming and is therefore not collected by the industry, which limits genetic progress. Genomic prediction is a viable approach to preselect gilts that will express puberty early and have superior reproductive longevity. The hypothesis that genetic variants explaining differences in age at puberty also explain differences in sow reproductive longevity was tested. Phenotypes, genotypes, and tissues from the UNL resource population (n \u3e 1700) were used in genome-wide association analyses, genome, and RNA sequencing to uncover functional polymorphisms that could explain variation in puberty and reproductive longevity. A BeadArray including 56,424 SNP explained 25.2% of the phenotypic variation in age at puberty in a training set (n = 820). Evaluation of major windows and SNPs of subsequent batches of similar genetics (n = 412) showed that if all SNPs located in the major 1-Mb windows were tested, they explained a substantial amount of phenotypic variation (12.3 to 36.8%). Due to differences in linkage disequilibrium status, the most informative SNP from these windows explained a lower proportion of the variation (6.5 to 23.7%). To improve genomic predictive ability, the limited capability of BeadArray was enhanced by potential functional variants uncovered by genome sequencing of selected sires (n = 20; \u3e20X). There were 11.2 mil. SNPs and 2.9 mil. indels discovered across sires and reference genomes. The role of gene expression differences in explaining phenotypic variation in age at puberty was investigated by RNA sequencing of the hypothalamic arcuate nucleus (ARC) in gilts (n = 37) with different pubertal statuses. Seventy genes, including genes involved in reproductive processes, were differentially expressed between gilts with early and late puberty status (Padj \u3c 0.1). Dietary restriction of energy 3 mo before breeding delayed puberty by 7 d but improved the potential of a sow producing up to three parities (P \u3c 0.05). Energy restriction was associated with differential expression in 42 genes in the ARC, including genes involved in energy metabolism. This integrated genomic information will be evaluated in commercial populations to improve the reproductive potential of sows through genomic selection. This project is supported by AFRI Competitive grant no. 2013-68004-20370 from the USDA-NIFA. USDA is an equal opportunity provider and employer

Translational Genomics For Improving Sow Fertility

Sow fertility traits, such as litter size and number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable, polygenic, sex-limited, and express late in life. Age at puberty is an early indicator of reproductive longevity. Gilts that achieve puberty at an early age have a greater probability to produce more parities over their lifetime. However, measuring age at puberty is time consuming and tedious. Identifying pleiotropic polymorphisms that affect age at puberty and other fertility traits, including reproductive longevity, could help to improve the accuracy of genomic prediction for sow fertility traits. We developed a custom Affymetrix SNP array (SowPro90) including SNPs located in major QTL regions for age at puberty, other fertility and disease related traits, and potential loss of function SNPs. Genetic variants were identified using deep transcriptomic and genomic sequencing, gene network analysis, and genome-wide association (GWAS) carried out at University of Nebraska-Lincoln (UNL) and US Meat Animal Research Center (USMARC). This novel SNP array was used to fine map the genetic sources associated with fertility traits. Using a Bayesian haplotype approach (BayesIM), SowPro90 haplotypes were inferred and assigned to the entire UNL population and were used in an association analysis for age at puberty and other fertility traits. Five major QTL regions located on four chromosomes (SSC2, SSC7, SSC14, SSC18) were discovered for age at puberty. As expected, a negative correlation (r = −0.96 to −0.10; PP2RX3, OAS1, NR2F2, PTPN11). These SNPs showed significant or suggestive effects on age at puberty, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. It will be beneficial to further characterize these SNPs and candidate genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect phenotypic variation of fertility traits. Advisor: Daniel Cioban

Translational Genomics for Improving Sow Fertility

Sow fertility traits, such as litter size and number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable, polygenic, sex-limited, and express late in life. Age at puberty is an early indicator of reproductive longevity. Gilts that achieve puberty at an early age have a greater probability to produce more parities over their lifetime. However, measuring age at puberty is time consuming and tedious. Identifying pleiotropic polymorphisms that affect age at puberty and other fertility traits, including reproductive longevity, could help to improve the accuracy of genomic prediction for sow fertility traits. We developed a custom Affymetrix SNP array (SowPro90) including SNPs located in major QTL regions for age at puberty, other fertility and disease related traits, and potential loss of function SNPs. Genetic variants were identified using deep transcriptomic and genomic sequencing, gene network analysis, and genome-wide association (GWAS) carried out at University of Nebraska-Lincoln (UNL) and US Meat Animal Research Center (USMARC). This novel SNP array was used to fine map the genetic sources associated with fertility traits. Using a Bayesian haplotype approach (BayesIM), SowPro90 haplotypes were inferred and assigned to the entire UNL population and were used in an association analysis for age at puberty and other fertility traits. Five major QTL regions located on four chromosomes (SSC2, SSC7, SSC14, SSC18) were discovered for age at puberty. As expected, a negative correlation (r = −0.96 to −0.10; P\u3c0.0001) was observed between genomic estimated breeding values for age at puberty and reproductive longevity at these QTL. Some of the SNPs discovered in the major QTL regions for age at puberty were located in candidate genes for fertility traits (e.g. P2RX3, OAS1, NR2F2, PTPN11). These SNPs showed significant or suggestive effects on age at puberty, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. It will be beneficial to further characterize these SNPs and candidate genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect phenotypic variation of fertility trait

Translational Genomics for Improving Sow Fertility

Sow fertility traits, such as litter size and number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable, polygenic, sex-limited, and express late in life. Age at puberty is an early indicator of reproductive longevity. Gilts that achieve puberty at an early age have a greater probability to produce more parities over their lifetime. However, measuring age at puberty is time consuming and tedious. Identifying pleiotropic polymorphisms that affect age at puberty and other fertility traits, including reproductive longevity, could help to improve the accuracy of genomic prediction for sow fertility traits. We developed a custom Affymetrix SNP array (SowPro90) including SNPs located in major QTL regions for age at puberty, other fertility and disease related traits, and potential loss of function SNPs. Genetic variants were identified using deep transcriptomic and genomic sequencing, gene network analysis, and genome-wide association (GWAS) carried out at University of Nebraska-Lincoln (UNL) and US Meat Animal Research Center (USMARC). This novel SNP array was used to fine map the genetic sources associated with fertility traits. Using a Bayesian haplotype approach (BayesIM), SowPro90 haplotypes were inferred and assigned to the entire UNL population and were used in an association analysis for age at puberty and other fertility traits. Five major QTL regions located on four chromosomes (SSC2, SSC7, SSC14, SSC18) were discovered for age at puberty. As expected, a negative correlation (r = −0.96 to −0.10; P\u3c0.0001) was observed between genomic estimated breeding values for age at puberty and reproductive longevity at these QTL. Some of the SNPs discovered in the major QTL regions for age at puberty were located in candidate genes for fertility traits (e.g. P2RX3, OAS1, NR2F2, PTPN11). These SNPs showed significant or suggestive effects on age at puberty, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. It will be beneficial to further characterize these SNPs and candidate genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect phenotypic variation of fertility trait

Data from: A missense mutation in SLC45A2 is associated with albinism in several small long haired dog breeds

Homozygosity for a large deletion in the solute carrier family 45, member 2 (SLC45A2) gene causes oculocutaneous albinism (OCA) in the Doberman Pinscher breed. An albino Lhasa Apso did not have this g.27141_31223del (CanFam2) deletion in her SLC45A2 sequence. Therefore, SLC45A2 was investigated in this female Lhasa Apso to search for other possible variants that caused her albinism. The albino Lhasa Apso was homozygous for a nonsynonymous substitution in the seventh exon, a c.1478G>A base change that resulted in a glycine to aspartic acid substitution (p.G493D). This mutation was not found in a wolf, a coyote, or any of the 15 other Lhasa Apso dogs or 32 other dogs of breeds related to the Lhasa Apso. However, an albino Pekingese, 2 albino Pomeranians, and an albino mixed breed dog that was small and long haired were also homozygous for the 493D allele. The colored puppies of the albino Lhasa Apso and the colored dam of the 2 albino Pomeranians were heterozygous for this allele. However, an albino Pug was homozygous for the 493G allele and therefore although we suggest the 493D allele causes albinism when homozygous in several small, long haired dog breeds, it does not explain all albinism in dogs. A variant effect prediction for the albino Lhasa Apso confirms that p.G493D is a deleterious substitution, and a topology prediction for SLC45A2 suggests that the 11th transmembrane domain where the 493rd amino acid was located, has an altered structure

Data from: A missense mutation in SLC45A2 is associated with albinism in several small long haired dog breeds

Homozygosity for a large deletion in the solute carrier family 45, member 2 (SLC45A2) gene causes oculocutaneous albinism (OCA) in the Doberman Pinscher breed. An albino Lhasa Apso did not have this g.27141_31223del (CanFam2) deletion in her SLC45A2 sequence. Therefore, SLC45A2 was investigated in this female Lhasa Apso to search for other possible variants that caused her albinism. The albino Lhasa Apso was homozygous for a nonsynonymous substitution in the seventh exon, a c.1478G>A base change that resulted in a glycine to aspartic acid substitution (p.G493D). This mutation was not found in a wolf, a coyote, or any of the 15 other Lhasa Apso dogs or 32 other dogs of breeds related to the Lhasa Apso. However, an albino Pekingese, 2 albino Pomeranians, and an albino mixed breed dog that was small and long haired were also homozygous for the 493D allele. The colored puppies of the albino Lhasa Apso and the colored dam of the 2 albino Pomeranians were heterozygous for this allele. However, an albino Pug was homozygous for the 493G allele and therefore although we suggest the 493D allele causes albinism when homozygous in several small, long haired dog breeds, it does not explain all albinism in dogs. A variant effect prediction for the albino Lhasa Apso confirms that p.G493D is a deleterious substitution, and a topology prediction for SLC45A2 suggests that the 11th transmembrane domain where the 493rd amino acid was located, has an altered structure

Supplemental Table 1:Primers, annealing temperatures and the fragment of the SLC45A2 gene amplified.

Supplemental Table 1:Primers, annealing temperatures and the fragment of the SLC45A2 gene amplified