Reliability of genomic evaluation for egg quality traits in layers

Druet, David Picard; Varenne, Amandine; Herry, Florian; Herault, Frédéric; Allais, Sophie; Burlot, Thierry; Roy, Pascale Le

doi:10.1186/s12863-020-0820-2

Cited by 9 publications

(11 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The LR method has been applied in evaluations with multiple traits, maternally affected traits, and traits where phenotypes are not available on all individuals for all environments (Chu et al 2019;Macedo et al 2020a;Picard Druet et al 2020). As such, the LR method appears to be a useful choice to evaluate the increase in population accuracy when ignoring r dm in the context of beef cattle international evaluations.…”

Section: Discussionmentioning

confidence: 99%

International genetic and genomic evaluations of beef cattle

Bonifazi¹

View full text Add to dashboard Cite

. International genetic and genomic evaluations of beef cattle.PhD thesis, Wageningen University, the Netherlands.In cattle, advancements in reproductive technologies such as artificial insemination allowed breeders to access the genetic material of superior bulls from foreign countries. However, animals' estimated breeding values (EBV) computed from different national evaluations are not directly comparable across countries due to differences in scales and genetic bases, trait and model definitions, and the possible presence of genotype-by-environment interactions. International evaluations account for such differences by jointly analysing all national data and modelling the same trait recorded in different countries as different correlated traits. The resulting international EBV (EBV INT ) facilitate the comparison of domestic and foreign sires and worldwide trading of their genetic material. This thesis aimed to improve and further develop methodologies for international beef cattle evaluations (Interbeef) by addressing various challenges, mainly related to: i) the estimation of across-country genetic correlations (r g ) and their impact on the EBV INT ; ii) the inclusion of national genomic information; and iii) the development of an official procedure for participating countries to integrate the distributed EBV INT back into their national evaluations. First, I showed that both large and small participating countries benefit from current Interbeef pedigree-based evaluations. Second, I showed the feasibility of estimating across-country r g using a multi-trait approach that simultaneously fits data from all countries and proposed data sub-setting strategies to improve computational time. Third, I showed that the current practice of assuming across-country direct-maternal r g to be 0 has limited impact on the EBV INT of animals of interest such as publishable sires, i.e., sires that meet Interbeef publications rules. On the other hand, assuming zero within-country direct-maternal r g impacts the EBV INT of such animals. Fourth, I developed international genomic evaluations for beef cattle using a single-step SNPBLUP approach (ssSNPBLUP). International ssSNPBLUP evaluations lead to higher accuracies compared to both current international pedigree evaluations and either national pedigree or genomic evaluations, while keeping similar or slightly reduced level and dispersion bias. Finally, I developed a generalized procedure to integrate pedigree-based or singlestep EBV INT of publishable sires into national evaluations. The procedure can be easily implemented with current software. Compared to national evaluations without integration, the integration reduces level bias, gives similar dispersion, and increases accuracies of publishable sires' EBV INT . Overall, this thesis contributes to the development of international evaluations of beef cattle.

show abstract

Section: Discussionmentioning

confidence: 99%

International genetic and genomic evaluations of beef cattle

Bonifazi¹

View full text Add to dashboard Cite

show abstract

“…The LR method has been applied in evaluations with multiple traits, maternally affected traits, and traits where phenotypes are not available on all individuals for all environments ( Chu et al, 2019 ; Macedo et al, 2020 ; Picard Druet et al, 2020 ). As such, the LR method appears to be a useful choice to evaluate the increase in population accuracy when ignoring r dm in the context of beef cattle international evaluations.…”

Section: Discussionmentioning

confidence: 99%

The impact of direct-maternal genetic correlations on international beef cattle evaluations for Limousin weaning weight

Bonifazi

Vandenplas

Napel

et al. 2021

Journal of Animal Science

View full text Add to dashboard Cite

In beef cattle maternally influenced traits, estimates of direct-maternal genetic correlations (rdm) are usually reported to be negative. In international evaluations, rdm can differ both within countries (rdm_WC) and between countries (rdm_BC). The rdm_BC are difficult to estimate and are assumed to be zero in the current model for international beef cattle evaluations (Interbeef). Our objective was to investigate re-ranking of international EBV (IEBV) in international beef cattle evaluations between models that either used estimated values for rdm or assumed them to be 0. Age-adjusted weaning weights and pedigree data were available for Limousin beef cattle from ten European countries. International EBV were obtained using a multi-trait animal model with countries modelled as different traits. We compared IEBV from a model that uses estimated rdm_BC (ranging between -0.14 and +0.14) and rdm_WC (between -0.33 and +0.40) with IEBV obtained either from the current model that assumes rdm_BC to be 0, or from an alternative model that assumes both rdm_BC and rdm_WC to be 0. Direct and maternal IEBV were compared across those three scenarios for different groups of animals. The ratio of population accuracies from the Linear Regression method was used to further investigate the impact of rdm on international evaluations, for both the whole set of animals in the evaluation and the domestic ones. Ignoring rdm_BC, i.e. replacing estimated values with 0, resulted in no (rank correlations > 0.99) or limited (between 0.98 and 0.99) re-ranking for direct and maternal IEBV, respectively. Both rdm_BC and rdm_WC had less impact on direct IEBV than on maternal IEBV. Re-ranking of maternal IEBV decreased with increasing reliability. Ignoring rdm_BC resulted in no re-ranking for sires with IEBV that might be exchanged across countries, and limited re-ranking for the top 100 sires. Using estimated rdm_BC values instead of considering them to be to 0, resulted in null to limited increases in population accuracy. Ignoring both rdm_BC and rdm_WC resulted in considerable re-ranking of animals’ IEBV in all groups of animals evaluated. This study showed the limited impact of the current practice of ignoring rdm_BC in international evaluations for Limousin weaning weight, most likely because the estimated rdm_BC were close to 0. We expect that these conclusions can be extended to other traits that have reported rdm values in the range of rdm_WC values for weaning weight in Limousin.

show abstract

“…ESC was determined by a chromameter, ESS was determined by a compression instrument, EW was determined by a weighing scale, ESshape is calculated from egg diameter and EW, HV was determined by a tripod methodology, and BW was determined by a weighing scale. Further details on the measurements are available on the ontology website (Picard Druet et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

600. No G×E on egg qualities and body weight between cage and floor systems, implications for breeding programmes in laying hens

Bédère

Bécot

Burlot³

et al. 2022

Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)

View full text Add to dashboard Cite

The main objective of this study was to quantify genotype-by-environment interactions for egg quality traits and body weight in laying hens between cage and cage-free systems. Records of 18,524 eggs for quality traits and 10,266 hens for body weight from a pedigreed Rhode Island Red line were used. Hens were hatched across 5 batches from 2018 to 2020, siblings are housed in two systems: a cage and a floor system. Random regressions were modelled to estimate variance components. Heritability estimates were moderate to high in both systems (0.29-0.77). Genetic correlations between the cage and the floor system were high (≥0.79), and genetic correlations between the intercept and the slope of the reaction norm ranged from -0.69 to 0.27. The results indicate that there is no need to maintain a dedicated breeding programme per system, if the breeding goals are identical, which is unlikely.

show abstract

Reliability of genomic evaluation for egg quality traits in layers

Cited by 9 publications

References 23 publications

International genetic and genomic evaluations of beef cattle

International genetic and genomic evaluations of beef cattle

The impact of direct-maternal genetic correlations on international beef cattle evaluations for Limousin weaning weight

600. No G×E on egg qualities and body weight between cage and floor systems, implications for breeding programmes in laying hens

Contact Info

Product

Resources

About