LINKAGE DISEQUILIBRIUM AND IDENTIFICATION OF HAPLOTYPE BLOCKS IN SARABI COWS BREED

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MARZBAI HAMID; MORADI SHAHRBABAK HOSSEIN; MORADI SHAHRBABAK MOHAMMAD

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Journal: Journal of Animal Production Year:2018 | Volume:20 | Issue:1 Page(s): 29-40

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Information Journal Paper

Title

LINKAGE DISEQUILIBRIUM AND IDENTIFICATION OF HAPLOTYPE BLOCKS IN SARABI COWS BREED

Author(s)

MARZBAI HAMID | MORADI SHAHRBABAK HOSSEIN | MORADI SHAHRBABAK MOHAMMAD | Issue Writer Certificate

Keywords

AUTOSOMAL CHROMOSOMESQ1

GENOMIC SELECTIONQ1

GENOME-WIDE ASSOCIATION STUDIESQ1

SARABI COWSQ2

SINGLE NUCLEOTIDE POLYMORPHISMQ1

Abstract

This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 SARABI COWS using 40k SNP-chip of Illumina company. After genotyping and quality control, 27386 SNP markers on AUTOSOMAL CHROMOSOMES remained for further analyze. The LD was measured by r2 and D' statistics. The average of r2 and D' for range less than 2. 5 kb were maximum with 0. 505 and 0. 927, respectively. The average of r2 and D' in range of 2-5 Mb were minimum with 0. 064 and 0. 486, respectively. In total, 582 haplotype blocks were observed in the genome of SARABI COWS. About 6. 73% SNPs from all of SNPs and 0. 83% (21. 43 Mb) of the autosomal genome were covered by the haplotype blocks. Population effective size was estimated about 40 that return to four generations ago. The low number of haplotype blocks and also low LD level in Sarabi cow population indicates high variation in this local breed. In refer to the results and the number of haplotype blocks in this breed, applying the haplotype blocks could improve results and high precision on GENOMIC SELECTION studies. So, it is recommended that in application of GENOMIC SELECTION using haplotype blocks is more beneficial than single SNP markers.

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APA: Copy

MARZBAI, HAMID, MORADI SHAHRBABAK, HOSSEIN, & MORADI SHAHRBABAK, MOHAMMAD. (2018). LINKAGE DISEQUILIBRIUM AND IDENTIFICATION OF HAPLOTYPE BLOCKS IN SARABI COWS BREED. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), 20(1 ), 29-40. SID. https://sid.ir/paper/209200/en

Vancouver: Copy

MARZBAI HAMID, MORADI SHAHRBABAK HOSSEIN, MORADI SHAHRBABAK MOHAMMAD. LINKAGE DISEQUILIBRIUM AND IDENTIFICATION OF HAPLOTYPE BLOCKS IN SARABI COWS BREED. JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE)[Internet]. 2018;20(1 ):29-40. Available from: https://sid.ir/paper/209200/en

IEEE: Copy

HAMID MARZBAI, HOSSEIN MORADI SHAHRBABAK, and MOHAMMAD MORADI SHAHRBABAK, “LINKAGE DISEQUILIBRIUM AND IDENTIFICATION OF HAPLOTYPE BLOCKS IN SARABI COWS BREED,” JOURNAL OF ANIMAL PRODUCTION (JOURNAL OF AGRICULTURE), vol. 20, no. 1 , pp. 29–40, 2018, [Online]. Available: https://sid.ir/paper/209200/en

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