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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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Neighbor-joining tree of 27 major haplotypes for a 750-kb critical region of the major QTL on SSC7. Haplotypes with frequencies greater than 0.05 were used to construct a NJ tree using the 750-kb critical region of SSC7. Hap 1 is the Q-bearing haplotype; haplotypes specific to Chinese indigenous breeds are indicated in red blocks; haplotypes present in both Chinese and Western breeds are highlighted in blue blocks; haplotypes prominently occurring in Chinese breeds and Western breeds are marked in red and green triangular blocks, respectively; haplotypes specific to Chinese indigenous breeds and Chinese synthetic breeds are indicated by red inverted triangular blocks.
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Fig4: Neighbor-joining tree of 27 major haplotypes for a 750-kb critical region of the major QTL on SSC7. Haplotypes with frequencies greater than 0.05 were used to construct a NJ tree using the 750-kb critical region of SSC7. Hap 1 is the Q-bearing haplotype; haplotypes specific to Chinese indigenous breeds are indicated in red blocks; haplotypes present in both Chinese and Western breeds are highlighted in blue blocks; haplotypes prominently occurring in Chinese breeds and Western breeds are marked in red and green triangular blocks, respectively; haplotypes specific to Chinese indigenous breeds and Chinese synthetic breeds are indicated by red inverted triangular blocks.

Mentions: We were particularly interested in a ~750-kb region on SSC7 (between 34 673 190 and 35 422 882 bp) that was contained within both the 2.1-Mb 95% CI and the 1.7-Mb Q-sharing segment (Figure 3C). It is most likely that this region encompasses the gene responsible for the SSC7 locus. To investigate the population genetics and evolutionary history at this SSC7 locus, we reconstructed haplotypes corresponding to the critical 750-kb region for 589 individuals from 31 diverse Chinese and Western breeds (Table 2), which had been genotyped for 62 163 SNPs using the Illumina Porcine 60 K DNA chip [25]. A total of 27 haplotypes with frequencies greater than 0.05 were subsequently used to construct a neighbor-joining (NJ) tree. The phylogenetic tree clearly illustrated that the Q-type haplotype is of Chinese origin (Figure 4). Of the 27 haplotypes, 14 occurred exclusively in Chinese indigenous pigs, and two were predominately (>0.8) present in Western pigs. Notably, the Q-type haplotype that we identified in the F2 population was present in multiple Chinese indigenous breeds, many of which carry the Q allele at considerably high frequencies (Table 2). Conversely, this haplotype was nearly absent in Western breeds and Chinese wild boars, which suggests that the causal variants underlying the SSC7 QTL originated after the domestication of Chinese wild boars. Further investigations in multiple Chinese breeds of the minimal shared haplotype that carries the Q allele would be useful to identify the causative mutation underlying the SSC7 locus. Given that a number of Chinese breeds segregate for this major locus, characterization of the causal variant would greatly contribute to the genetic improvement of growth and fatness traits in Chinese indigenous pigs.Table 2


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)

Neighbor-joining tree of 27 major haplotypes for a 750-kb critical region of the major QTL on SSC7. Haplotypes with frequencies greater than 0.05 were used to construct a NJ tree using the 750-kb critical region of SSC7. Hap 1 is the Q-bearing haplotype; haplotypes specific to Chinese indigenous breeds are indicated in red blocks; haplotypes present in both Chinese and Western breeds are highlighted in blue blocks; haplotypes prominently occurring in Chinese breeds and Western breeds are marked in red and green triangular blocks, respectively; haplotypes specific to Chinese indigenous breeds and Chinese synthetic breeds are indicated by red inverted triangular blocks.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Neighbor-joining tree of 27 major haplotypes for a 750-kb critical region of the major QTL on SSC7. Haplotypes with frequencies greater than 0.05 were used to construct a NJ tree using the 750-kb critical region of SSC7. Hap 1 is the Q-bearing haplotype; haplotypes specific to Chinese indigenous breeds are indicated in red blocks; haplotypes present in both Chinese and Western breeds are highlighted in blue blocks; haplotypes prominently occurring in Chinese breeds and Western breeds are marked in red and green triangular blocks, respectively; haplotypes specific to Chinese indigenous breeds and Chinese synthetic breeds are indicated by red inverted triangular blocks.
Mentions: We were particularly interested in a ~750-kb region on SSC7 (between 34 673 190 and 35 422 882 bp) that was contained within both the 2.1-Mb 95% CI and the 1.7-Mb Q-sharing segment (Figure 3C). It is most likely that this region encompasses the gene responsible for the SSC7 locus. To investigate the population genetics and evolutionary history at this SSC7 locus, we reconstructed haplotypes corresponding to the critical 750-kb region for 589 individuals from 31 diverse Chinese and Western breeds (Table 2), which had been genotyped for 62 163 SNPs using the Illumina Porcine 60 K DNA chip [25]. A total of 27 haplotypes with frequencies greater than 0.05 were subsequently used to construct a neighbor-joining (NJ) tree. The phylogenetic tree clearly illustrated that the Q-type haplotype is of Chinese origin (Figure 4). Of the 27 haplotypes, 14 occurred exclusively in Chinese indigenous pigs, and two were predominately (>0.8) present in Western pigs. Notably, the Q-type haplotype that we identified in the F2 population was present in multiple Chinese indigenous breeds, many of which carry the Q allele at considerably high frequencies (Table 2). Conversely, this haplotype was nearly absent in Western breeds and Chinese wild boars, which suggests that the causal variants underlying the SSC7 QTL originated after the domestication of Chinese wild boars. Further investigations in multiple Chinese breeds of the minimal shared haplotype that carries the Q allele would be useful to identify the causative mutation underlying the SSC7 locus. Given that a number of Chinese breeds segregate for this major locus, characterization of the causal variant would greatly contribute to the genetic improvement of growth and fatness traits in Chinese indigenous pigs.Table 2

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