Use genetic modification indicator to increase the precision and accuracy of genomic analysis

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Pubblicato: Ιουλ 18, 2024
Aggiornato: 2024-07-18
Versioni:
2024-07-18 (5)
DOI: https://doi.org/10.12681/jhvms.35220
M Safarzadeh
Department of Medicine, Islamic Azad University, Tabriz Branch, Tabriz, Iran
MH Kalani
Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
M Nezafat
Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
M Ouni
Department of Chemical and Polymer Engineering, Central Tehran Branch, Islamic Azad University, Tehran, Iran
P Ghadermarzi
Department of New Technologies, Zabol University, Zabol, Iran
H Aghazadeh
Tabriz University of Medical Sciences, Tabriz, Iran
S Rajabi
Department of Natural Sciences, ‎Tabriz university, Tabriz, Iran
J Pish Jang Aghajeri
Assistant Professor, Department of Animal Sciences, Maragheh Branch, Islamic Azad University, Maragheh, Iran
Abstract

The high expense of genotype determination and the low accuracy of the evaluation in a small number of genotyped samples when using genomic data and genetic markers to perform genomic evaluations are two major problems. The effect of levels of genetic markers in an F2 population obtained from Two-way crossing of native Iran chicken with low growth rate and Arian meat strain with high growth rate was investigated in this study in order to isolate SNPs with higher effect and use these markers in genomic evaluation as a suitable method of screening SNPs in order to increase the accuracy of the evaluation and reduce genotyping costs. In this study, the prediction accuracy of correction values in five marker groups with various MAFs was studied in addition to demonstrating the superiority of the ssGBLUP approach over the BLUP method from the 5-fold cross-validation (CV) method in the single-step assessment strategy. This group of markers (MAF 0.4 - 0.5) was introduced as the best level of allelic frequency to perform genomic evaluations for the growth trait after the results showed that using SNPs with an allelic frequency of 0.4-0.5 in each of the second to seventh weeks showed higher predictive accuracy than the information of all SNPs. In addition to enforcing a low genotype cost, using SNPs with an allelic frequency of 0.4–0.5 and developing low-density SNP chips with markers with the aforementioned properties can be utilized to reliably evaluate individuals based on genetic merit.

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