Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine
The purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri, U.S. Individu...
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| Format: | Article |
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MDPI AG
2022-02-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/3/388 |
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| author | Gabriella Roby Dodd Kent Gray Yijian Huang Breno Fragomeni |
| author_facet | Gabriella Roby Dodd Kent Gray Yijian Huang Breno Fragomeni |
| author_sort | Gabriella Roby Dodd |
| collection | DOAJ |
| description | The purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri, U.S. Individuals were from a commercial cross of a Duroc sire and a dam resulting from a Landrace and Large White cross. Genotypic information was available for 8232 animals with 33,581 SNPs. The pedigree file contained a total of 553,448 animals. A threshold of 78 on the Temperature Humidity Index (THI) was used to signify heat stress. A two-trait analysis was used with the phenotypes heat stress (Trait One) and non-heat stress (Trait Two). Variance components were calculated via AIREML and breeding values were calculated using single step GBLUP (ssGBLUP). The heritability for Traits One and Two were calculated at 0.25 and 0.20, respectively, and the genetic correlation was calculated as 0.63. Validation was calculated for 163 genotyped sires with progeny in the last generation. The benchmark was the GEBV with complete data, and the accuracy was determined as the correlation between the GEBV of the reduced and complete data for the validation sires. Weighted ssGBLUP did not increase the accuracies. Both methods showed a maximum accuracy of 0.32 for Trait One and 0.54 for Trait Two. Manhattan Plots for Trait One, Trait Two, and the difference between the two were created from the results of the two-trait analysis. Windows explaining more than 0.8% of the genetic variance were isolated. Chromosomes 1 and 14 showed peaks in the difference between the two traits. The genetic correlation suggests a different mechanism for Hot Carcass Weight under heat stress. The GWAS results show that both traits are highly polygenic, with only a few genomic regions explaining more than 1% of variance. |
| first_indexed | 2024-03-10T00:16:39Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T00:16:39Z |
| publishDate | 2022-02-01 |
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| series | Animals |
| spelling | doaj.art-207e6eb7a1db4312bcdbf51e43e2cf772023-11-23T15:48:58ZengMDPI AGAnimals2076-26152022-02-0112338810.3390/ani12030388Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in SwineGabriella Roby Dodd0Kent Gray1Yijian Huang2Breno Fragomeni3Animal Science Department, University of Connecticut, Storrs, CT 06269, USASmithfield Premium Genetics, Rose Hill, NC 28458, USASmithfield Premium Genetics, Rose Hill, NC 28458, USAAnimal Science Department, University of Connecticut, Storrs, CT 06269, USAThe purpose of this study was to perform a genome-wide association study to determine the genomic regions associated with heat stress tolerance in swine. Phenotypic information on carcass weight was available for 227,043 individuals from commercial farms in North Carolina and Missouri, U.S. Individuals were from a commercial cross of a Duroc sire and a dam resulting from a Landrace and Large White cross. Genotypic information was available for 8232 animals with 33,581 SNPs. The pedigree file contained a total of 553,448 animals. A threshold of 78 on the Temperature Humidity Index (THI) was used to signify heat stress. A two-trait analysis was used with the phenotypes heat stress (Trait One) and non-heat stress (Trait Two). Variance components were calculated via AIREML and breeding values were calculated using single step GBLUP (ssGBLUP). The heritability for Traits One and Two were calculated at 0.25 and 0.20, respectively, and the genetic correlation was calculated as 0.63. Validation was calculated for 163 genotyped sires with progeny in the last generation. The benchmark was the GEBV with complete data, and the accuracy was determined as the correlation between the GEBV of the reduced and complete data for the validation sires. Weighted ssGBLUP did not increase the accuracies. Both methods showed a maximum accuracy of 0.32 for Trait One and 0.54 for Trait Two. Manhattan Plots for Trait One, Trait Two, and the difference between the two were created from the results of the two-trait analysis. Windows explaining more than 0.8% of the genetic variance were isolated. Chromosomes 1 and 14 showed peaks in the difference between the two traits. The genetic correlation suggests a different mechanism for Hot Carcass Weight under heat stress. The GWAS results show that both traits are highly polygenic, with only a few genomic regions explaining more than 1% of variance.https://www.mdpi.com/2076-2615/12/3/388genomic selectiongenotype × environment interactiongenome-wide association studygene identificationQTLssGBLUP |
| spellingShingle | Gabriella Roby Dodd Kent Gray Yijian Huang Breno Fragomeni Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine Animals genomic selection genotype × environment interaction genome-wide association study gene identification QTL ssGBLUP |
| title | Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine |
| title_full | Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine |
| title_fullStr | Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine |
| title_full_unstemmed | Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine |
| title_short | Single-Step GBLUP and GWAS Analyses Suggests Implementation of Unweighted Two Trait Approach for Heat Stress in Swine |
| title_sort | single step gblup and gwas analyses suggests implementation of unweighted two trait approach for heat stress in swine |
| topic | genomic selection genotype × environment interaction genome-wide association study gene identification QTL ssGBLUP |
| url | https://www.mdpi.com/2076-2615/12/3/388 |
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