Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 8 2 2016 08 22 Investigations of linkage disequilibrium phase in chromosome 6 of Holstein breed Investigations of linkage disequilibrium phase in chromosome 6 of Holstein breed 83 98 1523 10.22103/jab.2016.1523 FA Maryam Nosrati 2Department of Agriculture, Payame Noor University, PO BOX 19395-3697 Tehran, Iran Mojtaba Tahmoorespur Professor, Department of animal science, Faculty of agriculture, Ferdowsi University of Mashhad, Mashhad, Iran Luca Fontanesi Department of Agri-Food Science and Technology, University of Bologna, Bologna, Italy Mohamadreza Nassiri Professor, Department of animal science, Faculty of agriculture, Ferdowsi University of Mashhad, Mashhad, Iran 0000-0001-7119-8155 Journal Article 2013 03 11 In whole genome association study, genomic selection, Determining of extent and level of linkage disequilibrium (LD) is important in sample size and marker density. In this experiment, the blood and sperm samples were collected form 1089 Holstein bulls and 2030 markers on chromosome 6 were genotyped by using Illumina Bovine SNP50K BeadChip based on UMD3.1 genome assembly. Data were corrected for missing genotyped SNP and individual with unknown genotype by Plink. After correction 1606 markers remained (79%). The average observed heterozygosity was 0.37 and 80% of the markers had minor all frequency more than 0.2. The LD was calculated with r² and Dˊ by Haploview v4.2. The extent of LD in this study was 40 kb with r²=0.3. The r² value was decreasing to 0.2 (moderate level) in 80kb and 0.1 (background level) in 300 kb. The effective population size has been decreased to 100 individual in 10 generations ago. The 49 haplotype blocks with range 18-472 kb were detected that covering the 10.6 Mb of whole chromosome. These results showed that between 4000-70000 markers or one marker per 40-75 kb will be need for whole genome association study in this Holstein population. In whole genome association study, genomic selection, Determining of extent and level of linkage disequilibrium (LD) is important in sample size and marker density. In this experiment, the blood and sperm samples were collected form 1089 Holstein bulls and 2030 markers on chromosome 6 were genotyped by using Illumina Bovine SNP50K BeadChip based on UMD3.1 genome assembly. Data were corrected for missing genotyped SNP and individual with unknown genotype by Plink. After correction 1606 markers remained (79%). The average observed heterozygosity was 0.37 and 80% of the markers had minor all frequency more than 0.2. The LD was calculated with r² and Dˊ by Haploview v4.2. The extent of LD in this study was 40 kb with r²=0.3. The r² value was decreasing to 0.2 (moderate level) in 80kb and 0.1 (background level) in 300 kb. The effective population size has been decreased to 100 individual in 10 generations ago. The 49 haplotype blocks with range 18-472 kb were detected that covering the 10.6 Mb of whole chromosome. These results showed that between 4000-70000 markers or one marker per 40-75 kb will be need for whole genome association study in this Holstein population. https://jab.uk.ac.ir/article_1523_df12ecd077efc8c23881028604dbb8cc.pdf