INVESTIGATIONS OF LINKAGE DISEQUILIBRIUM PHASE IN CHROMOSOME 6 OF HOLSTEIN BREED

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NOSRATI M.; TAHMOORESPUR M.; FONTANESI L.; NASSIRY M.R.

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Journal: JOURNAL OF AGRICULTURAL BIOTECHNOLOGY Year:2016 | Volume:8 | Issue:2 Page(s): 83-98

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Title

INVESTIGATIONS OF LINKAGE DISEQUILIBRIUM PHASE IN CHROMOSOME 6 OF HOLSTEIN BREED

Author(s)

NOSRATI M. | TAHMOORESPUR M. | FONTANESI L. | NASSIRY M.R. | Issue Writer Certificate

Keywords

HOLSTEINQ1

LINKAGE DISEQUILIBRIUMQ3

CHROMOSOME 6Q1

NEQ1

Abstract

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 Bead Chip 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 rP 2 P and Dˊ by Haploview v4.2. The extent of LD in this study was 40 kb with r P 2 P=0.3. The r P 2 P 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.

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APA: Copy

NOSRATI, M., TAHMOORESPUR, M., FONTANESI, L., & NASSIRY, M.R.. (2016). INVESTIGATIONS OF LINKAGE DISEQUILIBRIUM PHASE IN CHROMOSOME 6 OF HOLSTEIN BREED. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, 8(2), 83-98. SID. https://sid.ir/paper/224515/en

Vancouver: Copy

NOSRATI M., TAHMOORESPUR M., FONTANESI L., NASSIRY M.R.. INVESTIGATIONS OF LINKAGE DISEQUILIBRIUM PHASE IN CHROMOSOME 6 OF HOLSTEIN BREED. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY[Internet]. 2016;8(2):83-98. Available from: https://sid.ir/paper/224515/en

IEEE: Copy

M. NOSRATI, M. TAHMOORESPUR, L. FONTANESI, and M.R. NASSIRY, “INVESTIGATIONS OF LINKAGE DISEQUILIBRIUM PHASE IN CHROMOSOME 6 OF HOLSTEIN BREED,” JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, vol. 8, no. 2, pp. 83–98, 2016, [Online]. Available: https://sid.ir/paper/224515/en

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