INVESTIGATION OF GENOTYPE × ENVIRONMENT INTERACTION WITH CONSIDERINGIMPUTATION IN SIMULATED GENOMIC DATA VIA DIFFERENT ANIMAL MODELS

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NADERI YOUSEF

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Journal: Journal of Animal Production Year:2018 | Volume:20 | Issue:3 Page(s): 375-386

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Title

INVESTIGATION OF GENOTYPE × ENVIRONMENT INTERACTION WITH CONSIDERINGIMPUTATION IN SIMULATED GENOMIC DATA VIA DIFFERENT ANIMAL MODELS

Author(s)

NADERI YOUSEF | Issue Writer Certificate

Keywords

GENOMIC ACCURACYQ1

GENOMIC CORRELATIONQ1

IMPUTATION ACCURACYQ1

LINKAGE DISEQUILIBRIUMQ1

MULTIPLE-TRAITANIMAL MODELQ2

Abstract

The objective of this study was to evaluate single-trait and multiple-trait animal models with considering imputationin simulated genomic data to estimate the accuracies of genomic prediction across various genomic scenarios and todetect genotype × environment (G × E) interaction. Genomic data were simulated to reflect variations in number ofQTL (90 and 900) and LINKAGE DISEQUILIBRIUM (LD = low and high) using 50K SNP panel. Afterwards, 90 percent ofthe markers randomly removed and imputation was performed using FImpute software (version 2. 2). The averageaccuracy of imputation for scenarios with high and low LD was 0. 976 and 0. 943, respectively. In all scenarios, negligible difference on the genomic accuracies was evident, when original genotypes and imputed genotypes werecompared. The GENOMIC ACCURACY reduced with decreasing the LD, heritability and the genetic correlation among thetraits. Comparing to single-trait animal model, using multiple-trait animal model increased GENOMIC ACCURACY. Thelevel of LD and genetic correlation across environments play important roles providing genotype × environmentinteraction exists. On the one hand, considering genotype × environment interaction and its effect on increasing ofGENOMIC ACCURACY and imputation of low to high density marker panels (especially high LD scenarios) to reduce ofthe cost of genomic evaluation on the other hand could be a suitable and practical approach to improve genomicselection application.

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APA: Copy

NADERI, YOUSEF. (2018). INVESTIGATION OF GENOTYPE × ENVIRONMENT INTERACTION WITH CONSIDERINGIMPUTATION IN SIMULATED GENOMIC DATA VIA DIFFERENT ANIMAL MODELS. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), 20(3 ), 375-386. SID. https://sid.ir/paper/209104/en

Vancouver: Copy

NADERI YOUSEF. INVESTIGATION OF GENOTYPE × ENVIRONMENT INTERACTION WITH CONSIDERINGIMPUTATION IN SIMULATED GENOMIC DATA VIA DIFFERENT ANIMAL MODELS. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE)[Internet]. 2018;20(3 ):375-386. Available from: https://sid.ir/paper/209104/en

IEEE: Copy

YOUSEF NADERI, “INVESTIGATION OF GENOTYPE × ENVIRONMENT INTERACTION WITH CONSIDERINGIMPUTATION IN SIMULATED GENOMIC DATA VIA DIFFERENT ANIMAL MODELS,” JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), vol. 20, no. 3 , pp. 375–386, 2018, [Online]. Available: https://sid.ir/paper/209104/en

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