Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs
Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant g...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Korea Genome Organization
2018-09-01
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| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-3-59.pdf |
| _version_ | 1818263023591096320 |
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| author | Young-Sup Lee Donghyun Shin |
| author_facet | Young-Sup Lee Donghyun Shin |
| author_sort | Young-Sup Lee |
| collection | DOAJ |
| description | Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2. |
| first_indexed | 2024-12-12T19:12:26Z |
| format | Article |
| id | doaj.art-ba759902dbaa4bc497917bd46284eac1 |
| institution | Directory Open Access Journal |
| issn | 2234-0742 |
| language | English |
| last_indexed | 2024-12-12T19:12:26Z |
| publishDate | 2018-09-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-ba759902dbaa4bc497917bd46284eac12022-12-22T00:14:49ZengKorea Genome OrganizationGenomics & Informatics2234-07422018-09-01163596410.5808/GI.2018.16.3.59514Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire PigsYoung-Sup LeeDonghyun ShinAlthough pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.http://genominfo.org/upload/pdf/gi-2018-16-3-59.pdfbackfat thicknessgenome-wide association studiesLandraceneuronal geneYorkshire |
| spellingShingle | Young-Sup Lee Donghyun Shin Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs Genomics & Informatics backfat thickness genome-wide association studies Landrace neuronal gene Yorkshire |
| title | Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs |
| title_full | Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs |
| title_fullStr | Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs |
| title_full_unstemmed | Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs |
| title_short | Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs |
| title_sort | genome wide association studies associated with backfat thickness in landrace and yorkshire pigs |
| topic | backfat thickness genome-wide association studies Landrace neuronal gene Yorkshire |
| url | http://genominfo.org/upload/pdf/gi-2018-16-3-59.pdf |
| work_keys_str_mv | AT youngsuplee genomewideassociationstudiesassociatedwithbackfatthicknessinlandraceandyorkshirepigs AT donghyunshin genomewideassociationstudiesassociatedwithbackfatthicknessinlandraceandyorkshirepigs |