Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals
Abstract Background Preselection of candidates, hereafter referred to as preselection, is a common practice in breeding programs. Preselection can cause bias and accuracy loss in subsequent pedigree-based best linear unbiased prediction (PBLUP). However, the impact of preselection on subsequent sing...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2020-07-01
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| Series: | Genetics Selection Evolution |
| Online Access: | http://link.springer.com/article/10.1186/s12711-020-00562-6 |
| _version_ | 1818506755201564672 |
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| author | Ibrahim Jibrila Jan ten Napel Jeremie Vandenplas Roel F. Veerkamp Mario P. L. Calus |
| author_facet | Ibrahim Jibrila Jan ten Napel Jeremie Vandenplas Roel F. Veerkamp Mario P. L. Calus |
| author_sort | Ibrahim Jibrila |
| collection | DOAJ |
| description | Abstract Background Preselection of candidates, hereafter referred to as preselection, is a common practice in breeding programs. Preselection can cause bias and accuracy loss in subsequent pedigree-based best linear unbiased prediction (PBLUP). However, the impact of preselection on subsequent single-step genomic BLUP (ssGBLUP) is not completely clear yet. Therefore, in this study, we investigated, across different heritabilities, the impact of intensity and type of preselection on subsequent ssGBLUP evaluation of preselected animals. Methods We simulated a nucleus of a breeding programme, in which a recent population of 15 generations was produced with PBLUP-based selection. In generation 15 of this recent population, the parents of the next generation were preselected using several preselection scenarios. These scenarios were combinations of three intensities of preselection (no, high or very high preselection) and three types of preselection (genomic, parental average or random), across three heritabilities (0.5, 0.3 or 0.1). Following each preselection scenario, a subsequent evaluation was performed using ssGBLUP by excluding all the information from the preculled animals, and these genetic evaluations were compared in terms of accuracy and bias for the preselected animals, and in terms of realized genetic gain. Results Type of preselection affected selection accuracy at both preselection and subsequent evaluation stages. While preselection accuracy decreased, accuracy in the subsequent ssGBLUP evaluation increased, from genomic to parent average to random preselection scenarios. Bias was always negligible. Genetic gain decreased from genomic to parent average to random preselection scenarios. Genetic gain also decreased with increasing intensity of preselection, but only by a maximum of 0.1 additive genetic standard deviation from no to very high genomic preselection scenarios. Conclusions Using ssGBLUP in subsequent evaluations prevents preselection bias, irrespective of intensity and type of preselection, and heritability. With GPS, in addition to reducing the phenotyping effort considerably, the use of ssGBLUP in subsequent evaluations realizes only a slightly lower genetic gain than that realized without preselection. This is especially the case for traits that are expensive to measure (e.g. feed intake of individual broiler chickens), and traits for which phenotypes can only be measured at advanced stages of life (e.g. litter size in pigs). |
| first_indexed | 2024-12-10T22:08:50Z |
| format | Article |
| id | doaj.art-8cd2b025f0484d039b73545172cd34dc |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-10T22:08:50Z |
| publishDate | 2020-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-8cd2b025f0484d039b73545172cd34dc2022-12-22T01:31:40ZdeuBMCGenetics Selection Evolution1297-96862020-07-0152111010.1186/s12711-020-00562-6Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animalsIbrahim Jibrila0Jan ten Napel1Jeremie Vandenplas2Roel F. Veerkamp3Mario P. L. Calus4Wageningen University and Research Animal Breeding and GenomicsWageningen University and Research Animal Breeding and GenomicsWageningen University and Research Animal Breeding and GenomicsWageningen University and Research Animal Breeding and GenomicsWageningen University and Research Animal Breeding and GenomicsAbstract Background Preselection of candidates, hereafter referred to as preselection, is a common practice in breeding programs. Preselection can cause bias and accuracy loss in subsequent pedigree-based best linear unbiased prediction (PBLUP). However, the impact of preselection on subsequent single-step genomic BLUP (ssGBLUP) is not completely clear yet. Therefore, in this study, we investigated, across different heritabilities, the impact of intensity and type of preselection on subsequent ssGBLUP evaluation of preselected animals. Methods We simulated a nucleus of a breeding programme, in which a recent population of 15 generations was produced with PBLUP-based selection. In generation 15 of this recent population, the parents of the next generation were preselected using several preselection scenarios. These scenarios were combinations of three intensities of preselection (no, high or very high preselection) and three types of preselection (genomic, parental average or random), across three heritabilities (0.5, 0.3 or 0.1). Following each preselection scenario, a subsequent evaluation was performed using ssGBLUP by excluding all the information from the preculled animals, and these genetic evaluations were compared in terms of accuracy and bias for the preselected animals, and in terms of realized genetic gain. Results Type of preselection affected selection accuracy at both preselection and subsequent evaluation stages. While preselection accuracy decreased, accuracy in the subsequent ssGBLUP evaluation increased, from genomic to parent average to random preselection scenarios. Bias was always negligible. Genetic gain decreased from genomic to parent average to random preselection scenarios. Genetic gain also decreased with increasing intensity of preselection, but only by a maximum of 0.1 additive genetic standard deviation from no to very high genomic preselection scenarios. Conclusions Using ssGBLUP in subsequent evaluations prevents preselection bias, irrespective of intensity and type of preselection, and heritability. With GPS, in addition to reducing the phenotyping effort considerably, the use of ssGBLUP in subsequent evaluations realizes only a slightly lower genetic gain than that realized without preselection. This is especially the case for traits that are expensive to measure (e.g. feed intake of individual broiler chickens), and traits for which phenotypes can only be measured at advanced stages of life (e.g. litter size in pigs).http://link.springer.com/article/10.1186/s12711-020-00562-6 |
| spellingShingle | Ibrahim Jibrila Jan ten Napel Jeremie Vandenplas Roel F. Veerkamp Mario P. L. Calus Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals Genetics Selection Evolution |
| title | Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals |
| title_full | Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals |
| title_fullStr | Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals |
| title_full_unstemmed | Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals |
| title_short | Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals |
| title_sort | investigating the impact of preselection on subsequent single step genomic blup evaluation of preselected animals |
| url | http://link.springer.com/article/10.1186/s12711-020-00562-6 |
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