Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs

Wu, Zhongping; Zheng, Danying; Huang, Min; Hou, Yong; Zhang, Hui; Chen, Hao; Ren, Jun

doi:10.3389/fgene.2019.00218

Cited by 22 publications

(35 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An increase in coverage between 41.22 and 41.78 Mb confirmed the presence of a previously reported 560 kb duplication (DUP1; Supplementary Fig. S 3 , [ 25 , 26 ]. The duplication also encompasses a copy of KIT that carries a splice donor site variant (SSC8: 41486012G > A, rs345599765) which manifests in a dominant white phenotype [ 23 , 24 ].…”

Section: Resultssupporting

confidence: 85%

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

et al. 2021

View full text Add to dashboard Cite

Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

show abstract

Section: Resultssupporting

confidence: 85%

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

et al. 2021

View full text Add to dashboard Cite

show abstract

“…An increase in coverage between 41.22 and 41.78 Mb confirmed the presence of a previously reported 560 kb duplication (DUP1; Supplementary Fig. S3, Additional File 4, [25, 26]. The duplication also encompasses a copy of KIT that carries a splice donor site variant (SSC8: 41486012G>A, rs345599765) which manifests in a dominant white phenotype [23, 24].…”

Section: Resultssupporting

confidence: 78%

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Nosková

Bhati

Kadri

et al. 2021

Preprint

View full text Add to dashboard Cite

Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

show abstract

“…An increase in coverage between 41.22 and 41.78 Mb con rmed the presence of a previously reported 560 kb duplication (DUP1; Supplementary Fig. S3, Supplementary File 4, [25,26]. The duplication also encompasses a copy of KIT that carries a splice donor site variant (SSC8: 41486012G>A, rs345599765) which manifests in a dominant white phenotype [23,24].…”

Section: Resultssupporting

confidence: 59%

Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Nosková

Bhati

Kadri

et al. 2021

Preprint

View full text Add to dashboard Cite

Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

show abstract

Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs

Cited by 22 publications

References 38 publications

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Contact Info

Product

Resources

About