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A genome scan for selection signatures in pigs.

Ma Y, Wei J, Zhang Q, Chen L, Wang J, Liu J, Ding X - PLoS ONE (2015)

Bottom Line: The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang.Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang.Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.

ABSTRACT
Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima's D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74-5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

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Genome-wide distribution of selection signatures detected by LRH, Tajima’s D, XPEHH and FST cross all autosomes in Rongchang.
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pone.0116850.g002: Genome-wide distribution of selection signatures detected by LRH, Tajima’s D, XPEHH and FST cross all autosomes in Rongchang.

Mentions: Fig. 2 (S3–S5 Figs.) depicts the genome-wide distribution of the outliers on each autosome that were detected separately by four approaches in Rongchang, Landrace, Songliao and Yorkshire. We divided the assigned allele/core haplotypes into a series of 0.05 bins according to their frequencies and used box-and-whisker plots to depict the distribution of the outliers (Fig. 3, S6–S8 Figs.). For LRH, it is obviously from Fig. 3A that the outliers were concentrated in the bins with low to moderate haplotype frequencies. This proved that LRH is effective for the detection of haplotypes under ongoing or incomplete selective sweeps, as reported by Sabeti et al. (2002) [25]. In contrast, other outliers detected by Tajima’s D, XPEHH and FST were concentrated on loci with low or high frequencies in all breeds (Fig. 3, S6–S8 Figs.), indicating that these methods are efficient for the identification of selection signatures under the complete selective sweeps.


A genome scan for selection signatures in pigs.

Ma Y, Wei J, Zhang Q, Chen L, Wang J, Liu J, Ding X - PLoS ONE (2015)

Genome-wide distribution of selection signatures detected by LRH, Tajima’s D, XPEHH and FST cross all autosomes in Rongchang.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4355907&req=5

pone.0116850.g002: Genome-wide distribution of selection signatures detected by LRH, Tajima’s D, XPEHH and FST cross all autosomes in Rongchang.
Mentions: Fig. 2 (S3–S5 Figs.) depicts the genome-wide distribution of the outliers on each autosome that were detected separately by four approaches in Rongchang, Landrace, Songliao and Yorkshire. We divided the assigned allele/core haplotypes into a series of 0.05 bins according to their frequencies and used box-and-whisker plots to depict the distribution of the outliers (Fig. 3, S6–S8 Figs.). For LRH, it is obviously from Fig. 3A that the outliers were concentrated in the bins with low to moderate haplotype frequencies. This proved that LRH is effective for the detection of haplotypes under ongoing or incomplete selective sweeps, as reported by Sabeti et al. (2002) [25]. In contrast, other outliers detected by Tajima’s D, XPEHH and FST were concentrated on loci with low or high frequencies in all breeds (Fig. 3, S6–S8 Figs.), indicating that these methods are efficient for the identification of selection signatures under the complete selective sweeps.

Bottom Line: The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang.Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang.Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.

ABSTRACT
Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima's D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74-5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.

Show MeSH
Related in: MedlinePlus