Genotypic frequency determination of 6 loci related to mulk production in 3 Iranian native cattle breeds and comparing with Holstein.

Most of quantitative traits are affected by polygenes and environment. Although the number of genes are unknown, but there are some candidate genes for quantitative traits. Finite locus suggests fewer genes might have more genetic variations. Recent progress in molecular genetics has provided possibility of detecting and sequencing of genes. Polymorphisms in coding or regulatory regions of genes can affect on gene expression or differed in sequence, quality or quantity of gene products. Protein milk genes include two parts of casein and whey proteins, which are considered as candidate genes. The first aim of this study was to determine gene frequencies of growth hormone, Pit1, Beta-lactoglobulin, ¥ل-S1 and ¥ê-caseins. it has also investigated the possibility use of molecular gene effects on breeding programs of native breeds. 5 to 9 ml blood was collected by disposable or vacuum injector included EDTA and kept at -20¨¬ temperature. DNA extracted from whole blood by Miller et al. procedure and diluted to100 ng/¥ىl. PCR-RFLP procedure was used to amplify and digest intron 3 and exon 5 of growth hormone, a part of intron 5 and exon 6 of Pit1, exon 4 of ¥ê-casein and Beta-lactoglobulin. PCR product were digested by endonuclease enzymesMspI for intron 3 and DdeI and AluI of growth hormone, HinfI for Pit1 and ¥ê-casein, HaeIII for Beta-lactoglobulin. Three samples of Srabai breed were sequenced to confirm results of PCR-RFLP of Pit1. Also, Beta-lactoglobulin promoter were sequenced by Pyrosequencing method at -435, -424, -422 polymorphic sites. PCR-SSCP and ALF SSCP methods were used for ¥ل-S1 promoter exon 17 of ¥ل-S1 casein, respectively. Gene and genotypic frequencies were calculated by counting method for each breed and compared by Chi-Square test. Results showed significance differences of genotypic frequencies between native and Holstein breeds at MspI, DdeI and exon 17 of ¥ل-S1 casein. Mazandarani and Golpaygani breeds showed significance differences with Holstein at AluI, Pit1, ¥ê-casein and Beta-lactoglobulin. There was no difference between Sarabi and Holstein at these polymorphic sites. Non-parametric Kruskal-Wallis test showed significance difference at least between two breeds at ¥ل-casein gene. Sequencing of exon 6 of Pit1 showed transition mutation of G to A created HinfI restriction site at nucleotide 1256. Haplotypes of promoter and coding region of Beta-lactoglobulin showed linkage disequilibrium. Association of genetic variants of studied genes and milk yield trait were investigated by single trait model. Additive, dominance and gene substitution effects were used to simulate milk yield for Golpaygani breed in Visual Basic 6 software. Base population included 4950 females and 50 sires with 1700 and 422 kg for mean and standard deviation and 0.27 for heritability. Generations were overlapped, females and males stayed in herd until at most 5 lactations records and 4 years, respectively. Females were evaluated by individual records of first lactation and males based on their dam records or individual molecular genetic information. Data were simulated for 20 generations and 40 iterations. Results showed higher total breeding value in molecular based program and higher polygenic breeding value for phenotypic breeding programs. There was significance difference in the 3th generations and later. Although molecular based program showed faster response in early generations, but it decreased and reached to platue. After 20 generations, desirable allele frequencies of Beta-lactoglobulin, ¥ل-S1, growth hormone, ¥ê-caseins and Pit1 increased to twice, 33T 16T 10 and 2 percent, respectively. Inbreeding values reached to 4.5 percent in both method and was not significant.