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Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations.

Qiao R, Gao J, Zhang Z, Li L, Xie X, Fan Y, Cui L, Ma J, Ai H, Ren J, Huang L - Genet. Sel. Evol. (2015)

Bottom Line: This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1).Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. qrm480@hotmail.com.

ABSTRACT

Background: Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population.

Results: We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.

Conclusions: We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

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Manhattan plots for the analyses of growth traits in F2and Sutai pigs. (A): GWAS for birth weight (BW0), body weight at day 46 (BW46) and body weight at day 240 (BW240) in F2 animals. (B): GWAS for BW0, BW21 and BW240 in Sutai pigs. In the Manhattan plots, negative log10P-values of the filtered high-quality SNPs SNPs were plotted against their genomic positions; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively.
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Fig2: Manhattan plots for the analyses of growth traits in F2and Sutai pigs. (A): GWAS for birth weight (BW0), body weight at day 46 (BW46) and body weight at day 240 (BW240) in F2 animals. (B): GWAS for BW0, BW21 and BW240 in Sutai pigs. In the Manhattan plots, negative log10P-values of the filtered high-quality SNPs SNPs were plotted against their genomic positions; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively.

Mentions: Four major loci that affect fat deposition and growth were identified on SSC2, 4, 7 and X in the F2 population, which confirmed our previously published QTL mapping results [28]. Of these, the most striking locus was located at about 34 to 36 Mb on SSC7 (referred to hereafter as the SSC7 locus; Table 1) and was significantly associated with all fatness traits (Figure 1) and body weight at day 240 (Figure 2). The top SNP for the associated traits was ss107837325 at 34 803 564 bp on this chromosome. At this location, the allele substitution effect accounted for more than 5 mm of backfat thickness and 5.44 kg of body weight at day 240 (Table 1), explaining ~ 40% of phenotypic variance in these traits. By applying the LDLA and LOD-drop-off-2 approaches, we defined the 95% CI of the SSC7 locus as a 2.1-Mb region that was flanked by ss131342658 (33 299 125 bp) and ss131344365 (35 422 882 bp) (Figure 3A). Next, we conducted a haplotype analysis of a ~3.2-Mb region (between 33 299 125 and 36 475 968 bp) surrounding the 95% CI of the SSC7 locus, using 17 founder sows and two founder boars from the F2 population. We showed that a ~1.7-Mb segment between 34 673 190 (ss131343640) and 36 329 680 bp (ss478941605) was shared by 30 Erhualian founder chromosomes (Figure 3B). We then reconstructed haplotypes corresponding to this 1.7-Mb segment in all F2 animals and evaluated the effects of these haplotypes on average backfat thickness (ABFT) and leaf fat weight (LFW) in the F2 animals. The shared haplotype appeared to be a haplotype that was significantly associated with decreased fat deposition (referred to hereafter as Q haplotype) (see Additional file 4: Figure S2). This result was in accordance with previous reports [3,4,29-31], but was also unexpected considering that the Erhualian is an obese Chinese pig breed.Figure 1


Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations.

Qiao R, Gao J, Zhang Z, Li L, Xie X, Fan Y, Cui L, Ma J, Ai H, Ren J, Huang L - Genet. Sel. Evol. (2015)

Manhattan plots for the analyses of growth traits in F2and Sutai pigs. (A): GWAS for birth weight (BW0), body weight at day 46 (BW46) and body weight at day 240 (BW240) in F2 animals. (B): GWAS for BW0, BW21 and BW240 in Sutai pigs. In the Manhattan plots, negative log10P-values of the filtered high-quality SNPs SNPs were plotted against their genomic positions; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358731&req=5

Fig2: Manhattan plots for the analyses of growth traits in F2and Sutai pigs. (A): GWAS for birth weight (BW0), body weight at day 46 (BW46) and body weight at day 240 (BW240) in F2 animals. (B): GWAS for BW0, BW21 and BW240 in Sutai pigs. In the Manhattan plots, negative log10P-values of the filtered high-quality SNPs SNPs were plotted against their genomic positions; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively.
Mentions: Four major loci that affect fat deposition and growth were identified on SSC2, 4, 7 and X in the F2 population, which confirmed our previously published QTL mapping results [28]. Of these, the most striking locus was located at about 34 to 36 Mb on SSC7 (referred to hereafter as the SSC7 locus; Table 1) and was significantly associated with all fatness traits (Figure 1) and body weight at day 240 (Figure 2). The top SNP for the associated traits was ss107837325 at 34 803 564 bp on this chromosome. At this location, the allele substitution effect accounted for more than 5 mm of backfat thickness and 5.44 kg of body weight at day 240 (Table 1), explaining ~ 40% of phenotypic variance in these traits. By applying the LDLA and LOD-drop-off-2 approaches, we defined the 95% CI of the SSC7 locus as a 2.1-Mb region that was flanked by ss131342658 (33 299 125 bp) and ss131344365 (35 422 882 bp) (Figure 3A). Next, we conducted a haplotype analysis of a ~3.2-Mb region (between 33 299 125 and 36 475 968 bp) surrounding the 95% CI of the SSC7 locus, using 17 founder sows and two founder boars from the F2 population. We showed that a ~1.7-Mb segment between 34 673 190 (ss131343640) and 36 329 680 bp (ss478941605) was shared by 30 Erhualian founder chromosomes (Figure 3B). We then reconstructed haplotypes corresponding to this 1.7-Mb segment in all F2 animals and evaluated the effects of these haplotypes on average backfat thickness (ABFT) and leaf fat weight (LFW) in the F2 animals. The shared haplotype appeared to be a haplotype that was significantly associated with decreased fat deposition (referred to hereafter as Q haplotype) (see Additional file 4: Figure S2). This result was in accordance with previous reports [3,4,29-31], but was also unexpected considering that the Erhualian is an obese Chinese pig breed.Figure 1

Bottom Line: This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1).Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China. qrm480@hotmail.com.

ABSTRACT

Background: Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population.

Results: We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits.

Conclusions: We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.

Show MeSH
Related in: MedlinePlus