GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle
It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd e...
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| Format: | Article |
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MDPI AG
2021-07-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/11/7/2050 |
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| author | Beatriz Castro Dias Cuyabano Gabriel Rovere Dajeong Lim Tae Hun Kim Hak Kyo Lee Seung Hwan Lee Cedric Gondro |
| author_facet | Beatriz Castro Dias Cuyabano Gabriel Rovere Dajeong Lim Tae Hun Kim Hak Kyo Lee Seung Hwan Lee Cedric Gondro |
| author_sort | Beatriz Castro Dias Cuyabano |
| collection | DOAJ |
| description | It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs. |
| first_indexed | 2024-03-10T09:47:57Z |
| format | Article |
| id | doaj.art-69da4594efca4866858e119144450261 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T09:47:57Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-69da4594efca4866858e1191444502612023-11-22T03:00:55ZengMDPI AGAnimals2076-26152021-07-01117205010.3390/ani11072050GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef CattleBeatriz Castro Dias Cuyabano0Gabriel Rovere1Dajeong Lim2Tae Hun Kim3Hak Kyo Lee4Seung Hwan Lee5Cedric Gondro6Department of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing, MI 48824, USADepartment of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing, MI 48824, USAAnimal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, KoreaAnimal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, KoreaDepartment of Animal Biotechnology, Chonbuk National University, Jeonju 54896, KoreaDivision of Animal and Dairy Science, Chungnam National University, Daejeon 305764, KoreaDepartment of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing, MI 48824, USAIt is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs.https://www.mdpi.com/2076-2615/11/7/2050genetic evaluationvariance componentscarcass traitsgeographical location |
| spellingShingle | Beatriz Castro Dias Cuyabano Gabriel Rovere Dajeong Lim Tae Hun Kim Hak Kyo Lee Seung Hwan Lee Cedric Gondro GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle Animals genetic evaluation variance components carcass traits geographical location |
| title | GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle |
| title_full | GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle |
| title_fullStr | GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle |
| title_full_unstemmed | GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle |
| title_short | GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle |
| title_sort | gps coordinates for modelling correlated herd effects in genomic prediction models applied to hanwoo beef cattle |
| topic | genetic evaluation variance components carcass traits geographical location |
| url | https://www.mdpi.com/2076-2615/11/7/2050 |
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