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| Title |
Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data
|
|---|---|
| Published in |
Journal of Animal Science and Technology, December 2015
|
| DOI | 10.1186/s40781-015-0080-2 |
| Pubmed ID | |
| Authors |
Karim Karimi, Ali Esmailizadeh Koshkoiyeh, Cedric Gondro |
| Abstract |
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. A total of 70 samples, representing seven Iranian indigenous cattle breeds, were genotyped for 777962 SNPs. The average values of LD based on the r(2) criterion were computed by grouping all syntenic SNP pairwises for inter-marker distances from 0 Kb up to 1 Mb using three distance sets. Average r(2) 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. 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. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 12 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 12 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 3 | 25% |
| Lecturer > Senior Lecturer | 1 | 8% |
| Other | 1 | 8% |
| Student > Bachelor | 1 | 8% |
| Student > Doctoral Student | 1 | 8% |
| Other | 2 | 17% |
| Unknown | 3 | 25% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 6 | 50% |
| Environmental Science | 1 | 8% |
| Unknown | 5 | 42% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 January 2016.
All research outputs
#20,656,820
of 25,374,647 outputs
Outputs from Journal of Animal Science and Technology
#101
of 190 outputs
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#292,364
of 396,492 outputs
Outputs of similar age from Journal of Animal Science and Technology
#3
of 6 outputs
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