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SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population.

Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Kojima T, Suzuki K - BMC Genet. (2016)

Bottom Line: Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35-39 Mb, 41-42 Mb, and 103 Mb.The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths.In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.

View Article: PubMed Central - PubMed

Affiliation: National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan. s0sato@nlbc.go.jp.

ABSTRACT

Background: The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree. First, we performed a simulation analysis using real genotype data of this population to compare the power (based on the hypothesis) of the two methods. We then performed GWAS using both methods and real phenotype data comprising 52 traits, which included growth, carcass, and meat quality traits.

Results: In total, 836 animals were genotyped using the Illumina PorcineSNP60 BeadChip and 14 customized SNPs from regions of known candidate genes related to the traits of interest. The power of SNP-based GWAS was greater than that of haplotype-based GWAS in a simulation analysis. In real data analysis, a larger number of significant regions was obtained by SNP-based GWAS than by haplotype-based GWAS. For SNP-based GWAS, 23 genome-wide significant SNP regions were detected for 17 traits, and 120 genome-wide suggestive SNP regions were detected for 27 traits. For haplotype-based GWAS, 6 genome-wide significant SNP regions were detected for four traits, and 11 genome-wide suggestive SNP regions were detected for eight traits. All genome-wide significant SNP regions detected by haplotype-based GWAS were located in regions also detected by SNP-based GWAS. Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35-39 Mb, 41-42 Mb, and 103 Mb. The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths. Mapped QTL regions contain some candidate genes involved in skeletal formation (FUBP3; far upstream element binding protein 3) and fat deposition (METTL3; methyltransferase like 3).

Conclusion: Our results show that a multigenerational pig population is useful for detecting QTL, which are typically segregated in a purebred population. In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.

No MeSH data available.


Related in: MedlinePlus

Regional plots of several loci associated with 13 traits. The x-axis indicates the Mb, and the y-axis indicates -log10 (p-value). Gene loci and their strands were annotated based on Sscrofa10.2 assembly from the Ensemble database (http://asia.ensembl.org/Sus_scrofa/Info/Index?db=core). Dashed line indicates the threshold of the Bonferroni 5 % genome-wide significance level. a Plots in chromosome 1 (304.2–305.0 Mb) for average daily gain (DG), backfat thickness (BF), chest width (CW), and circumference of chest (CC). b Plots in chromosome 7 (102.8–103.9 Mb) for Carcass length (CL), Carcass length I (CL1), Carcass length II (CL2), Carcass length III (CL3), and Thoracic vertebrae number (TVN). c Plots in chromosome 7 (34.2–42.5 Mb) for circumference of cannon bone at front (CCB at F105), circumference of cannon bone at rear (CCB at R105), Subcutaneous fat area of carcass cross section at half-body length (SFA at HBL), and All fat area of carcass cross section at half-body length (ALLFA at HBL)
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Fig4: Regional plots of several loci associated with 13 traits. The x-axis indicates the Mb, and the y-axis indicates -log10 (p-value). Gene loci and their strands were annotated based on Sscrofa10.2 assembly from the Ensemble database (http://asia.ensembl.org/Sus_scrofa/Info/Index?db=core). Dashed line indicates the threshold of the Bonferroni 5 % genome-wide significance level. a Plots in chromosome 1 (304.2–305.0 Mb) for average daily gain (DG), backfat thickness (BF), chest width (CW), and circumference of chest (CC). b Plots in chromosome 7 (102.8–103.9 Mb) for Carcass length (CL), Carcass length I (CL1), Carcass length II (CL2), Carcass length III (CL3), and Thoracic vertebrae number (TVN). c Plots in chromosome 7 (34.2–42.5 Mb) for circumference of cannon bone at front (CCB at F105), circumference of cannon bone at rear (CCB at R105), Subcutaneous fat area of carcass cross section at half-body length (SFA at HBL), and All fat area of carcass cross section at half-body length (ALLFA at HBL)

Mentions: The SNPs showing genome-wide significant association with growth, body measurements, carcass measurements, and fat area in SNP-based GWAS and haplotype-based GWAS are presented in Table 4. In addition, three regional plots associated with multiple traits are shown in Fig. 4. Significant association between rs81352956 on Sus scrofa chromosome (SSC) 1 at 304 Mb and DG (P = 1.22 × 10−8) was evident in both SNP-based and with haplotype-based analyses (Table 4, Fig. 4a). Each copy of effect allele A at rs81352956 was associated with a decrease in DG of 34.75 g/d. Moreover, significant associations between rs81352969 on SSC1 at 304 Mb and BF (P = 6.30 × 10−10) and CC (P = 6.82 × 10−9), respectively, were observed in both SNP-based and haplotype-based analyses (Table 4). However, a significant association between rs81352969 on SSC1 at 304 Mb and CW (P = 1.17 × 10−7) was only detected with SNP-based GWAS. Each copy of effect allele A at rs81352969 was associated with increases in BF of 0.18 cm; CW of 0.45 cm; and CC of 0.87 cm. Both SNPs, rs81352969 and rs81352956 on SSC1 at 304 Mb, were located within close proximity (a distance of 27 kb) of each other.Table 4


SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population.

Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Kojima T, Suzuki K - BMC Genet. (2016)

Regional plots of several loci associated with 13 traits. The x-axis indicates the Mb, and the y-axis indicates -log10 (p-value). Gene loci and their strands were annotated based on Sscrofa10.2 assembly from the Ensemble database (http://asia.ensembl.org/Sus_scrofa/Info/Index?db=core). Dashed line indicates the threshold of the Bonferroni 5 % genome-wide significance level. a Plots in chromosome 1 (304.2–305.0 Mb) for average daily gain (DG), backfat thickness (BF), chest width (CW), and circumference of chest (CC). b Plots in chromosome 7 (102.8–103.9 Mb) for Carcass length (CL), Carcass length I (CL1), Carcass length II (CL2), Carcass length III (CL3), and Thoracic vertebrae number (TVN). c Plots in chromosome 7 (34.2–42.5 Mb) for circumference of cannon bone at front (CCB at F105), circumference of cannon bone at rear (CCB at R105), Subcutaneous fat area of carcass cross section at half-body length (SFA at HBL), and All fat area of carcass cross section at half-body length (ALLFA at HBL)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4837538&req=5

Fig4: Regional plots of several loci associated with 13 traits. The x-axis indicates the Mb, and the y-axis indicates -log10 (p-value). Gene loci and their strands were annotated based on Sscrofa10.2 assembly from the Ensemble database (http://asia.ensembl.org/Sus_scrofa/Info/Index?db=core). Dashed line indicates the threshold of the Bonferroni 5 % genome-wide significance level. a Plots in chromosome 1 (304.2–305.0 Mb) for average daily gain (DG), backfat thickness (BF), chest width (CW), and circumference of chest (CC). b Plots in chromosome 7 (102.8–103.9 Mb) for Carcass length (CL), Carcass length I (CL1), Carcass length II (CL2), Carcass length III (CL3), and Thoracic vertebrae number (TVN). c Plots in chromosome 7 (34.2–42.5 Mb) for circumference of cannon bone at front (CCB at F105), circumference of cannon bone at rear (CCB at R105), Subcutaneous fat area of carcass cross section at half-body length (SFA at HBL), and All fat area of carcass cross section at half-body length (ALLFA at HBL)
Mentions: The SNPs showing genome-wide significant association with growth, body measurements, carcass measurements, and fat area in SNP-based GWAS and haplotype-based GWAS are presented in Table 4. In addition, three regional plots associated with multiple traits are shown in Fig. 4. Significant association between rs81352956 on Sus scrofa chromosome (SSC) 1 at 304 Mb and DG (P = 1.22 × 10−8) was evident in both SNP-based and with haplotype-based analyses (Table 4, Fig. 4a). Each copy of effect allele A at rs81352956 was associated with a decrease in DG of 34.75 g/d. Moreover, significant associations between rs81352969 on SSC1 at 304 Mb and BF (P = 6.30 × 10−10) and CC (P = 6.82 × 10−9), respectively, were observed in both SNP-based and haplotype-based analyses (Table 4). However, a significant association between rs81352969 on SSC1 at 304 Mb and CW (P = 1.17 × 10−7) was only detected with SNP-based GWAS. Each copy of effect allele A at rs81352969 was associated with increases in BF of 0.18 cm; CW of 0.45 cm; and CC of 0.87 cm. Both SNPs, rs81352969 and rs81352956 on SSC1 at 304 Mb, were located within close proximity (a distance of 27 kb) of each other.Table 4

Bottom Line: Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35-39 Mb, 41-42 Mb, and 103 Mb.The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths.In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.

View Article: PubMed Central - PubMed

Affiliation: National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan. s0sato@nlbc.go.jp.

ABSTRACT

Background: The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree. First, we performed a simulation analysis using real genotype data of this population to compare the power (based on the hypothesis) of the two methods. We then performed GWAS using both methods and real phenotype data comprising 52 traits, which included growth, carcass, and meat quality traits.

Results: In total, 836 animals were genotyped using the Illumina PorcineSNP60 BeadChip and 14 customized SNPs from regions of known candidate genes related to the traits of interest. The power of SNP-based GWAS was greater than that of haplotype-based GWAS in a simulation analysis. In real data analysis, a larger number of significant regions was obtained by SNP-based GWAS than by haplotype-based GWAS. For SNP-based GWAS, 23 genome-wide significant SNP regions were detected for 17 traits, and 120 genome-wide suggestive SNP regions were detected for 27 traits. For haplotype-based GWAS, 6 genome-wide significant SNP regions were detected for four traits, and 11 genome-wide suggestive SNP regions were detected for eight traits. All genome-wide significant SNP regions detected by haplotype-based GWAS were located in regions also detected by SNP-based GWAS. Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35-39 Mb, 41-42 Mb, and 103 Mb. The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths. Mapped QTL regions contain some candidate genes involved in skeletal formation (FUBP3; far upstream element binding protein 3) and fat deposition (METTL3; methyltransferase like 3).

Conclusion: Our results show that a multigenerational pig population is useful for detecting QTL, which are typically segregated in a purebred population. In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS.

No MeSH data available.


Related in: MedlinePlus