Department of Animal Production, Faculty of Agriculture, Benha University
Abstract
The experimental chicken populations (F0, F1, F2 and F3) have been constructed all-over the world to be used in gene and quantitative trait loci (QTL) mapping studies in different breeds. The genome-wide QTL are located on seven macro-chromosomes (chromosome 1, 2, 3, 4, 6, 8 and Z) and on one micro-chromosome (chromosome 11) for body weights and gains, on chromosomes 1 and 5 for egg weight, on chromosomes 5 and 7 for number of eggs and on chromosome 1 for age at first egg. The total chromosomal map length for body weight is 1901 cM ranging from 25 cM on chromosome 11 to 568 cM on chromosome 1, while the total chromosomal map length for egg production and egg quality traits was 1949 cM ranging from 52 cM on chromosome 11 to 542 cM on chromosome 1. The majority of molecular markers used nowadays in poultry are microsatellite markers, STRs (short tandem repeats) and SNPs (single nucleated polymorphism). The microsatellites are used as the most widely markers for the analysis of genetic diversity and population structure in poultry. To detect the genetic diversity in poultry, definite number of microsatellite markers covering nine autosomal linkage groups and the sex Z chromosome are considered in genotyping of F0 grandparents and F1 and F2 offspring. Detailed information about selected microsatellites are available at the FAO website (www.dad.fao.org/en/refer/library/guidelin/marker.pdf). Primarily, the chickens' breeds must be characterized on molecular bases in terms of allelic and genotypic frequencies, the effective number of alleles (Ne), the observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE), the polymorphism information content (PIC) and the F-statistics of the reduction in heterozygosity due to inbreeding within each population (FIS). The candidate genes located on 18 chromosomes (number 1, 2, 3, 4, 5, 7, 8, 9, 10, 15, 16, 17, 19, 20, 21, 26, 27 and Z) are associated with growth traits of body weights and gains and feed intakes and conversion in chickens, while the candidate genes located on 11 chromosomes (number 1, 3, 4, 5, 7, 9, 13, 20, 24, 27 and Z) are associated with egg production and egg quality traits. The immune candidate genes located on 15 chromosomes (number 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 24, 26 and 27) are associated with immune responses against Salmonella in chickens. Recently, genome-wide association studies (GWAS) have been used successfully to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with quantitative traits in chickens since a remarkable range of discoveries from GWASs have been detected in production, reproduction and disease resistance traits. To perform a genetic improvement program for the Arabian breeds of chickens using the molecular applications, the following necessary steps are summarized as: 1) Recording the phenotypic data from full pedigree file to evaluate the birds genetically through estimating the breeding values for chicks, hens and cocks, 2) Determining the list of main equipments required and the main list of chemicals for DNA extraction, 3) Collecting the blood samples from birds and performing DNA extraction, 4) Reporting candidate genes from QTLs data base (http://www.animalgenome.org/QTLdb), 5) Preparing the genotyping files using SNP markers, 6) Applying SNP association test to detect the genes closely associated with economic traits in poultry, 7) Estimating the genomic breeding values (GBV) to be applied in genomic selection, 8) Applying the Genome-Wide Association Study (GWAS) using PLINK software, 9) Applying genomic selection program (GS) using GBV of cocks and hens to be the parents of the next generation.
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