In livestock, selection programs utilizing quantitative genetics are time consuming due to long generation interval and sometimes of lowly heritable traits. Several genes to be used in selection based on their biological actions or those located in genome regions of identified Quantitative Trait Loci (QTLs) have been regarded as candidate genes affecting economic traits in livestock. Such candidate genes have successful application in identifying several DNA markers associated with production traits. Utilization of candidate genes is one of the primary methods to determine the specific genes related to the economic traits in farm animals. Using molecular techniques is a good way to achieve fast genetic improvement through identifying the genes or QTLs that affect the trait of economic importance in farm animals. This approach has enabled opportunities to enhance genetic improvement programs by direct selection on genes or genomic regions through marker-assisted selection (MAS) and gene introgression. Mapping of QTLs was ta crucial approach to identify genes related to complex traits at the genome-wide level. Recently, a genome wide association study (GWAS) succeeded in identifying the casual genes, using the sequence variations by single nucleotide polymorphism (SNP). GWAS is an ideal technique to discover the major genes for complex traits and is a novel way to study the genetic mechanism of such traits. Many genes affecting milk traits such as GHR and PRLR genes were identified in cattle using GWAS method. The objectives of the present reviewed article are: 1) Applying a fine chromosomal mapping for localizing the QTL affecting some economic traits using specific microsatellite markers or SNP's in Egyptian farm animals, 2) Selecting the molecular markers to be considered in genetic variability and genotyping, 3) Identifying the candidate genes and causative mutations associated with economic traits in these animals (e.g. cattle, buffalo, sheep, goats and rabbits), 4) Determining the genetically significant SNP markers associated with the economic traits, 5) To perform GWAS using SNP to detect potential causative mutations and genomic regions affecting some productive and reproductive traits in the Egyptian farm animals. A list of the necessary procedures and executable approach are suggested for a genetic improvement program of Egyptian farm animals using the molecular approaches, that may be outlined as: 1) Determining the main objectives, 2) Collecting and recording the phenotypic data, 3) Evaluating the animals genetically, 4) Determine the list of main equipments and chemicals required, 5) Collecting the blood samples and DNA extraction, 6) Genotyping the animals using SNPs markers, 7) Applying the bioinformatics analyses for candidate genes and detecting QTLs, 8) Preparing and editing the genotyping files, 9) Estimating the average yield deviation for each trait, 10) Applying the Genome-Wide Association Study (GWAS), 11) Applying SNP association test, 12) Applying genome-wide complex trait analysis (GCTA), 13) Estimating the genomic breeding values (GBV) to be applied in genomic selection, 14) Evaluating the prediction accuracy (EBV vs GEBV), 15) Estimating the Genomic Best Linear Unbiased Predictions (GBLUP) and SNP-GBLUP, 16) Estimating the genomic breeding values (GBV) to be applied in genomic selection (GS).
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