Correcting within-family pre-selection in genetic evaluation of growth—A simulation study on rainbow trout

Janhunen, Matti; Kause, Antti; Vehviläinen, Harri; Nousiainen, Antti; Koskinen, Heikki

doi:10.1016/j.aquaculture.2014.08.020

Cited by 17 publications

(8 citation statements)

References 25 publications

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“…Selection of the parents of the next generation usually takes place in two or more stages (e.g. [ 1 – 3 ]. ), and the term ‘preselection’ is used to refer to the early stages of selection (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…), and the term ‘preselection’ is used to refer to the early stages of selection (e.g. [ 3 – 5 ]). Preselection is a common practice in the nuclei of breeding programs, where only a few hundred to a few thousand replacement animals are required per generation.…”

Section: Introductionmentioning

confidence: 99%

“…Traditionally, preselection has mostly been based on correlated trait(s) that can be measured easily and cheaply early in life (e.g. [ 1 , 3 , 6 – 8 ]). In the genomic era, preselection is often based on genomic estimated breeding values (GEBV) of young selection candidates, and in the literature this type of preselection is called genomic or genotypic preselection (GPS; e.g.…”

Section: Introductionmentioning

confidence: 99%

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Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals

et al. 2020

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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).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals

et al. 2020

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“…In animal breeding programs, parents of the next generation are usually selected in multiple stages (e.g., Árnason et al., 2012; Meyer & Thompson, 1984; Xu et al., 1995), and the initial stages of this selection are referred to as preselection (e.g., Janhunen et al., 2014; Masuda et al., 2018; Patry & Ducrocq, 2011). Impact of preselection on subsequent genetic evaluations has been a subject of research for a long time in the field of animal breeding (e.g., Appel et al., 1998; Henderson, 1975; Masuda et al., 2018; Patry & Ducrocq, 2011a).…”

Section: Introductionmentioning

confidence: 99%

Avoiding preselection bias in subsequent single‐step genomic BLUP evaluations of genomically preselected animals

Jibrila

Vandenplas

Napel

et al. 2020

J Animal Breeding Genetics

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In animal breeding, parents of the next generation are usually selected in multiple stages, and the initial stages of this selection are called preselection. Preselection reduces the information available for subsequent evaluation of preselected animals and this sometimes leads to bias. The objective of this study was to establish the minimum information required to subsequently evaluate genomically preselected animals without bias arising from preselection, with single‐step genomic best linear unbiased prediction (ssGBLUP). We simulated a nucleus of a breeding program in which a recent population of 15 generations was produced. In each generation, parents of the next generation were selected in a single‐stage selection based on pedigree BLUP. However, in generation 15, 10% of male and 15% of female offspring were preselected on their genomic estimated breeding values (GEBV). These GEBV were estimated using ssGBLUP, including the pedigree of all animals in generations 0–15, genotypes of all animals in generations 13–15 and phenotypes of all animals in generations 11–14. In subsequent ssGBLUP evaluation of these preselected animals, genotypes and phenotypes from various groups of animals were excluded one after another. We found that GEBV of the preselected animals were only estimated without preselection bias when genotypes and phenotypes of all animals in generations 13 and 14 and of the preselected animals were included in the subsequent evaluation. We also found that genotypes of the animals discarded at preselection only helped in reducing preselection bias in GEBV of their preselected sibs when genotypes of their parents were absent or excluded from the subsequent evaluation. We concluded that to prevent preselection bias in subsequent ssGBLUP evaluation of genomically preselected animals, information representative of the reference data used in the evaluation at preselection and genotypes and phenotypes of the preselected animals are needed in the subsequent evaluation.

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“…There have been numerous studies on genetic parameter estimations of growth-related traits in fi sh, such as Japanese fl ounder, Paralichthys olivaceus (Liu et al, 2011;Tian et al, 2011), Atlantic salmon, Salmo salar L. (Powell et al, 2008), rainbow trout, Oncorhynchus mykiss (Sae-Lim et al, 2013;Janhunen et al, 2014), common carp, Cyprinus carpio L. (Nielsen et al, 2009(Nielsen et al, , 2010Wang et al, 2009;Ninh et al, 2011), striped catfi sh, Pangasianodon hypophthalmus (Van Sang et al, 2012), and Nile tilapia, Oreochromis niloticus L. (Thodesen et al, 2011;Bentsen et al, 2012). However, to our knowledge, there is no study on C. semilaevis estimating the genetic parameters for growth-related traits.…”

Section: Introductionmentioning

confidence: 99%

Analysis of phenotypic and genetic parameters for growthrelated traits in the half smooth tongue sole, Cynoglossus semilaevis

Liu

et al. 2015

Chin. J. Ocean. Limnol.

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A bstractPhenotypic and genetic parameters for growth-related traits in the half-smooth tongue sole, Cynoglossus semilaevis , were estimated in 22 full-sib families produced by normal and neo-male breeding stocks. As phenotypic males with female genotypes, neo-males are harmful in C. semilaevis aquaculture because they reduce overall production. The present study evaluated the difference in the growth-related traits: total length (TL), body weight (BW) and square root of body weight (SQ_BW) at the age of 570 days between normal and neo-male offspring (neo-males used as male parents). The difference in the proportion of females between normal and neo-male offspring was also assessed. Based on the linear mixed model, restricted maximum likelihood (REML) and best linear unbiased prediction (BLUP) were used to estimate various (co)variance components and estimated breeding values (EBVs) of growth-related traits. As a result, all the mean values of the three studied traits were signifi cantly larger in normal offspring than in neo-male offspring. Additionally, the female proportion was signifi cantly larger in normal offspring than in neo-male offspring. Heritability was 0.128±0.066 2 for TL, 0.128±0.065 5 for BW and 0.132±0.062 9 for SQ_BW, all of which were low level heritabilities. The correlation coeffi cients of EBVs and phenotypic values of the target traits were 0.516 for TL, 0.524 for BW and 0.506 for SQ_BW, all of which were highly signifi cant ( P <0.01). Genetic correlations among TL, BW and SQ_BW were positive high (0.921-0.969) and higher than those of phenotype (0.711-0.748), both of which had low standard errors (0.063-0.123 for genotype, and 0.010-0.018 for phenotype). Compared with normal offspring, neo-male offspring have lower breeding values for each studied trait through EBVs comparison. Therefore, neo-male offspring should not be used as broodstock in a C. semilaevis breeding programs.

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Correcting within-family pre-selection in genetic evaluation of growth—A simulation study on rainbow trout

Cited by 17 publications

References 25 publications

Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals

Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals

Avoiding preselection bias in subsequent single‐step genomic BLUP evaluations of genomically preselected animals

Analysis of phenotypic and genetic parameters for growthrelated traits in the half smooth tongue sole, Cynoglossus semilaevis

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