Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire
Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide asso...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Asian-Australasian Association of Animal Production Societies
2015-11-01
|
| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-28-11-1537.pdf |
| _version_ | 1811216722188828672 |
|---|---|
| author | Asif Iqbal You-Sam Kim Jun-Mo Kang Yun-Mi Lee Rajani Rai Jong-Hyun Jung Dong-Yup Oh Ki-Chang Nam Hak-Kyo Lee Jong-Joo Kim |
| author_facet | Asif Iqbal You-Sam Kim Jun-Mo Kang Yun-Mi Lee Rajani Rai Jong-Hyun Jung Dong-Yup Oh Ki-Chang Nam Hak-Kyo Lee Jong-Joo Kim |
| author_sort | Asif Iqbal |
| collection | DOAJ |
| description | Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l’Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered. |
| first_indexed | 2024-04-12T06:43:28Z |
| format | Article |
| id | doaj.art-28fc12b4cda849588bf9c2ca6f887e22 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-04-12T06:43:28Z |
| publishDate | 2015-11-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-28fc12b4cda849588bf9c2ca6f887e222022-12-22T03:43:39ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172015-11-0128111537154410.5713/ajas.15.075223397Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in BerkshireAsif IqbalYou-Sam KimJun-Mo KangYun-Mi LeeRajani RaiJong-Hyun Jung0Dong-Yup Oh1Ki-Chang Nam2Hak-Kyo Lee3Jong-Joo Kim Jung P&C Institute, Seoul 16950, Korea Livestock Research Institute, Yeongju, 750-871, Korea Department of Animal Science and Technology, Sunchon National University, Suncheon 540-950, Korea Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, KoreaMeat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l’Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.http://www.ajas.info/upload/pdf/ajas-28-11-1537.pdfGenome Wide Association StudyBerkshireQuantitative Trait LociSingle Nucleotide PolymorphismMeat Quality |
| spellingShingle | Asif Iqbal You-Sam Kim Jun-Mo Kang Yun-Mi Lee Rajani Rai Jong-Hyun Jung Dong-Yup Oh Ki-Chang Nam Hak-Kyo Lee Jong-Joo Kim Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire Asian-Australasian Journal of Animal Sciences Genome Wide Association Study Berkshire Quantitative Trait Loci Single Nucleotide Polymorphism Meat Quality |
| title | Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire |
| title_full | Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire |
| title_fullStr | Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire |
| title_full_unstemmed | Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire |
| title_short | Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire |
| title_sort | genome wide association study to identify quantitative trait loci for meat and carcass quality traits in berkshire |
| topic | Genome Wide Association Study Berkshire Quantitative Trait Loci Single Nucleotide Polymorphism Meat Quality |
| url | http://www.ajas.info/upload/pdf/ajas-28-11-1537.pdf |
| work_keys_str_mv | AT asifiqbal genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT yousamkim genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT junmokang genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT yunmilee genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT rajanirai genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT jonghyunjung genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT dongyupoh genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT kichangnam genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT hakkyolee genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire AT jongjookim genomewideassociationstudytoidentifyquantitativetraitlociformeatandcarcassqualitytraitsinberkshire |