Genomic dissection and prediction of feed intake and residual feed intake traits using a longitudinal model in F2 chickens

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    Hakimeh Emamgholi Begli, Department of Animal Science, Faculty of Agriculture, University of Tehran, IranRasoul vaez Torshizi, Department of Animal Science, Faculty of Agriculture, University of Tehran, Tarbiat Modares University, IranAli Akbar Masoudi, Department of Animal Science, Faculty of Agriculture, University of Tehran, Tarbiat Modares University, IranAlireza Ehsani, Department of Animal Science, Faculty of Agriculture, University of Tehran, Tarbiat Modares University, Iran
  • Just Jensen
Feed efficiency trait s (FETs) ar e import ant economic indicators in poultry production. Because feed intake (FI) is a time -dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome- wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lea d to an increase in accuracy of selection. Thus, the objectives of this study w ere to evaluate the accuracy o f estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (S N P ) genotypes , a nd to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a tot al of 312 chick ens with phenotype and genotype in the F 2 population. The GWA and GS studies reported in this pap er were conducted using β-spline random regression models f or FI and RFI traits in a chick en F 2 population, with FI and BW recorded for each bird weekly between 2 an d 10 wee ks of ag e. A single SNP regression approach was used on spline coefficients for weekly FI an d RF I traits , with results showing that two significant SNPs for FI occur in the synuclein ( SNCAIP ) gene. Results also show that these regions are significantly associate d wit h the spline co efficient s ( q 2 ) for 5- and 6-week-old birds, while GWA study results showed no SNP association with RFI in F 2 chick ens. Estimated breeding value predictions obtain ed using a pedigree -base d best linear unbiased prediction (ABLUP) m o del were then compared with predictions based on genomic best line ar unbiased prediction (GBL UP). The accuracy was measured as correlation between genomic EBV and EBV with the phenotypic value corrected for fixed effects divided by the square root of heritability. The regression of observed on predicted values was used to estimate bias of methods. Results show that prediction accuracies using GBLUP and ABLUP for the FI measured from 2 nd to 10th week w ere between 0.06 and 0.46 and 0.03 and 0 .37, respectively. These results demonstrate that genomic methods are able to increase the accuracy of predicted breeding values at later ages on the basis of both traits , and indicate that use of a longitudinal model can improve selection accuracy for the trajectory of trait s in F 2 chickens when compared with conventional methods.
OriginalsprogEngelsk
TidsskriftAnimal
Vol/bind12
Tidsskriftsnummer9
Sider (fra-til)1792-1798
Antal sider7
ISSN1751-7311
DOI
StatusUdgivet - sep. 2018

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