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Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Wang H, Wang C, Yang K, Liu J, Zhang Y, Wang Y, Xu X, Michal JJ, Jiang Z, Liu B - PLoS ONE (2015)

Bottom Line: Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively.Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs.In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

No MeSH data available.


Related in: MedlinePlus

Heatmap analysis of CNV genes between Chinese and Western domestic pigs.The heatmap boxes show the sliding and nonoverlapping windows, 1 Kb in (A) and (B) and 2 Kb in (C). CN values were plotted within these three regions and correspond to the different colors. On the top of the heatmap is the information of genes affected by CNVs. (A) A region of nearly 8 Kb (chr13: 158,547,001–158,554,500) in PVRL3 gene had higher CN (from 5 to 9 copies), especially in Chinese domestic pigs (15 individuals / 22 totals), which was not found in Western domestic pigs. The last exon of three transcripts and the fourth intron of one transcript of this gene were affected by this CNVR. (B) A 6 Kb region at chromosome 14 from 126,295,501 to 126,301,500 bp had a higher CN in Chinese domestic pigs, but not in Western pigs. In addition, no genes were overlapped within this region. (C) The heatmap of AATK and BAIAP2 genes indicated that CN gain was present in Western domestic pigs in this region, but not in Chinese domestic pigs (chr12: 1,496,701–1,546,473).
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pone.0131522.g004: Heatmap analysis of CNV genes between Chinese and Western domestic pigs.The heatmap boxes show the sliding and nonoverlapping windows, 1 Kb in (A) and (B) and 2 Kb in (C). CN values were plotted within these three regions and correspond to the different colors. On the top of the heatmap is the information of genes affected by CNVs. (A) A region of nearly 8 Kb (chr13: 158,547,001–158,554,500) in PVRL3 gene had higher CN (from 5 to 9 copies), especially in Chinese domestic pigs (15 individuals / 22 totals), which was not found in Western domestic pigs. The last exon of three transcripts and the fourth intron of one transcript of this gene were affected by this CNVR. (B) A 6 Kb region at chromosome 14 from 126,295,501 to 126,301,500 bp had a higher CN in Chinese domestic pigs, but not in Western pigs. In addition, no genes were overlapped within this region. (C) The heatmap of AATK and BAIAP2 genes indicated that CN gain was present in Western domestic pigs in this region, but not in Chinese domestic pigs (chr12: 1,496,701–1,546,473).

Mentions: We also found that some interesting origin specific CNVRs harbored genes. One such example is the poliovirus receptor-related gene PVRL3, also known as NECTIN-3, which is located on chromosome 13 (158,524,401–158,603,720). A 8 Kb region nearby this gene had a high CN (5~9 copies) in Chinese domestic pigs (7 breeds and 15 individuals), but no CN variation was found in Western pigs (Fig 4A). This gene has 4 transcript variants and encodes the cell adhesion protein Nectin 3. We predicted that the CNVR affected different exons and introns in the four transcripts of this gene (Fig 4A). A chromosomal translocation upstream of the PVRL3 gene significantly affects Nectin 3 expression and leads to congenital ocular defects in humans [54]. In addition, PVRL3 as an immune gene plays an important role in the Nectin-Wave pathway and is important in cell-cell adhesion according to the gene ontology analysis. The over-expression of PVRL3 gene could significantly inhibit tumour growth [55]. If CN gain existed in PVRL3 gene and promoted the gene expression, Chinese domestic pigs might be more resistant to some diseases. Another CNVR was a 6 Kb region on chromosome 14 from 126,295,501 to 126,301,500 bp. This region had the highest CN gain, almost 13 copies in some Chinese domestic pigs, but no CN gain in Western domestic pigs. There was no gene annotated in this region (Fig 4B).


Genome Wide Distributions and Functional Characterization of Copy Number Variations between Chinese and Western Pigs.

Wang H, Wang C, Yang K, Liu J, Zhang Y, Wang Y, Xu X, Michal JJ, Jiang Z, Liu B - PLoS ONE (2015)

Heatmap analysis of CNV genes between Chinese and Western domestic pigs.The heatmap boxes show the sliding and nonoverlapping windows, 1 Kb in (A) and (B) and 2 Kb in (C). CN values were plotted within these three regions and correspond to the different colors. On the top of the heatmap is the information of genes affected by CNVs. (A) A region of nearly 8 Kb (chr13: 158,547,001–158,554,500) in PVRL3 gene had higher CN (from 5 to 9 copies), especially in Chinese domestic pigs (15 individuals / 22 totals), which was not found in Western domestic pigs. The last exon of three transcripts and the fourth intron of one transcript of this gene were affected by this CNVR. (B) A 6 Kb region at chromosome 14 from 126,295,501 to 126,301,500 bp had a higher CN in Chinese domestic pigs, but not in Western pigs. In addition, no genes were overlapped within this region. (C) The heatmap of AATK and BAIAP2 genes indicated that CN gain was present in Western domestic pigs in this region, but not in Chinese domestic pigs (chr12: 1,496,701–1,546,473).
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pone.0131522.g004: Heatmap analysis of CNV genes between Chinese and Western domestic pigs.The heatmap boxes show the sliding and nonoverlapping windows, 1 Kb in (A) and (B) and 2 Kb in (C). CN values were plotted within these three regions and correspond to the different colors. On the top of the heatmap is the information of genes affected by CNVs. (A) A region of nearly 8 Kb (chr13: 158,547,001–158,554,500) in PVRL3 gene had higher CN (from 5 to 9 copies), especially in Chinese domestic pigs (15 individuals / 22 totals), which was not found in Western domestic pigs. The last exon of three transcripts and the fourth intron of one transcript of this gene were affected by this CNVR. (B) A 6 Kb region at chromosome 14 from 126,295,501 to 126,301,500 bp had a higher CN in Chinese domestic pigs, but not in Western pigs. In addition, no genes were overlapped within this region. (C) The heatmap of AATK and BAIAP2 genes indicated that CN gain was present in Western domestic pigs in this region, but not in Chinese domestic pigs (chr12: 1,496,701–1,546,473).
Mentions: We also found that some interesting origin specific CNVRs harbored genes. One such example is the poliovirus receptor-related gene PVRL3, also known as NECTIN-3, which is located on chromosome 13 (158,524,401–158,603,720). A 8 Kb region nearby this gene had a high CN (5~9 copies) in Chinese domestic pigs (7 breeds and 15 individuals), but no CN variation was found in Western pigs (Fig 4A). This gene has 4 transcript variants and encodes the cell adhesion protein Nectin 3. We predicted that the CNVR affected different exons and introns in the four transcripts of this gene (Fig 4A). A chromosomal translocation upstream of the PVRL3 gene significantly affects Nectin 3 expression and leads to congenital ocular defects in humans [54]. In addition, PVRL3 as an immune gene plays an important role in the Nectin-Wave pathway and is important in cell-cell adhesion according to the gene ontology analysis. The over-expression of PVRL3 gene could significantly inhibit tumour growth [55]. If CN gain existed in PVRL3 gene and promoted the gene expression, Chinese domestic pigs might be more resistant to some diseases. Another CNVR was a 6 Kb region on chromosome 14 from 126,295,501 to 126,301,500 bp. This region had the highest CN gain, almost 13 copies in some Chinese domestic pigs, but no CN gain in Western domestic pigs. There was no gene annotated in this region (Fig 4B).

Bottom Line: Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively.Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs.In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Copy number variations (CNVs) refer to large insertions, deletions and duplications in the genomic structure ranging from one thousand to several million bases in size. Since the development of next generation sequencing technology, several methods have been well built for detection of copy number variations with high credibility and accuracy. Evidence has shown that CNV occurring in gene region could lead to phenotypic changes due to the alteration in gene structure and dosage. However, it still remains unexplored whether CNVs underlie the phenotypic differences between Chinese and Western domestic pigs. Based on the read-depth methods, we investigated copy number variations using 49 individuals derived from both Chinese and Western pig breeds. A total of 3,131 copy number variation regions (CNVRs) were identified with an average size of 13.4 Kb in all individuals during domestication, harboring 1,363 genes. Among them, 129 and 147 CNVRs were Chinese and Western pig specific, respectively. Gene functional enrichments revealed that these CNVRs contribute to strong disease resistance and high prolificacy in Chinese domestic pigs, but strong muscle tissue development in Western domestic pigs. This finding is strongly consistent with the morphologic characteristics of Chinese and Western pigs, indicating that these group-specific CNVRs might have been preserved by artificial selection for the favored phenotypes during independent domestication of Chinese and Western pigs. In this study, we built high-resolution CNV maps in several domestic pig breeds and discovered the group specific CNVs by comparing Chinese and Western pigs, which could provide new insight into genomic variations during pigs' independent domestication, and facilitate further functional studies of CNV-associated genes.

No MeSH data available.


Related in: MedlinePlus