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Title: Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data
Contributor(s): Karimi, Karim (author); Esmailizadeh Koshkoiyeh, Ali (author); Gondro, Cedric  (author)orcid 
Publication Date: 2015
Open Access: Yes
DOI: 10.1186/s40781-015-0080-2Open Access Link
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Abstract: Background: Knowledge of linkage disequilibrium (LD) levels among different populations can be used to detect genetic diversity and to investigate the historical changes in population sizes. Availability of large numbers of SNP through new sequencing technologies has provided opportunities for extensive researches in quantifying LD patterns in cattle breeds. The aim of this study was to compare the extent of linkage disequilibrium among Iranian cattle breeds using high density SNP genotyping data. Results: A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r2 criterion were computed by grouping all syntenic SNP pairwises for intermarker distances from 0 Kb up to 1 Mb using three distance sets. Average r2 above 0.3 was observed at distances less than 30 Kb for Sistani and Kermani, 20 Kb for Najdi, Taleshi, Kurdi and Sarabi, and 10 Kb for Mazandarani. The LD levels were considerably different among the Iranian cattle breeds and the difference in LD extent was more detectable between the studied breeds at longer distances. Lower level of LD was observed for Mazandarani breed as compared to other breeds indicating larger ancestral population size in this breed. Kermani breed continued to have more slowly LD decay than all of the other breeds after 3 Kb distances. More slowly LD decay was observed in Kurdi and Sarabi breeds at larger distances (>100 Kb) showing that population decline has been more intense in more recent generations for these populations. Conclusions: A wide genetic diversity and different historical background were well reflected in the LD levels among Iranian cattle breeds. More LD fluctuation was observed in the shorter distances (less than 10 Kb) in different cattle populations. Despite of the sample size effects, High LD levels found in this study were in accordance with the presence of inbreeding and population decline in Iranian cattle breeds.
Publication Type: Journal Article
Source of Publication: Journal of Animal Science and Technology, v.57, p. 1-10
Publisher: BioMed Central Ltd
Place of Publication: United Kingdom
ISSN: 2055-0391
Fields of Research (FoR) 2008: 070201 Animal Breeding
Fields of Research (FoR) 2020: 300305 Animal reproduction and breeding
Socio-Economic Objective (SEO) 2008: 830302 Dairy Cattle
830301 Beef Cattle
Socio-Economic Objective (SEO) 2020: 100402 Dairy cattle
100401 Beef cattle
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Journal Article

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