Mohammad Hossein Fallahi; Hossein Moradi Shahrbabak; Mohammad Moradi Shahrbabak; Rostam Abdollahi Arpanahi
Abstract
The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, ...
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The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, 62,141 SNP markers remained for identification of linkage disequiliberum, haplotype blocks and effective population size. LD was measured by the square of the correlation coefficient (r2) between alleles. The maximum LD measured by r2 varied from 0.25 to 0.29 at a distance of < 2.5 kb, and the minimum average values of r2 varied from 0.012 to 0.014 at distances ranging from 900 to 1000 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. Overall, 1693 blocks were observed through the genome. Eleven percent of all SNPs were clustered into haplotype blocks, covering 202 ±3.4 Mb of the total autosomal genome size. Effective population size (Ne) was estimated based on expected linkage disequilibrium. Ne was estimated to be 422 in our population.
Yousef Naderi
Abstract
Genomic selection using imputed genotypes can have an important role in increasing economic efficiency andthe genetic improvement of the threshold traits. The objective of this study was to: investigate the accuracy of imputation and to evaluate its effect on area under receiver operating characteristic ...
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Genomic selection using imputed genotypes can have an important role in increasing economic efficiency andthe genetic improvement of the threshold traits. The objective of this study was to: investigate the accuracy of imputation and to evaluate its effect on area under receiver operating characteristic (AUROC) of threshold BayesA (TBA) and random forest (RF) algorithms for discrete traits with different genomic architectures. Genomic data were simulated to reflect variations in heritability (0.30 and 0.10), number of QTL (108 and 1080) and linkage disequilibrium (low and high) for 27 chromosomes. To simulate a condition close to reality, we randomly masked markers with 50% and 90% missing rate for each scenario; afterwards, missing genotypes were imputed and imputation accuracy was estimated. In the last step, to evaluate the AUROC of TBA and RF, original or imputed genotypes were used. The accuracy of imputation was improved with increasing level of LD and decreased missing rate. The total average of AUROC values were 0.64 and 0.66 when using RF and TBA, respectively. Comparing to original genotypes, using imputed genotypes with 50% and 90% missing rate decreased the average AUROC about 0.013 and 0.02 for RF and 0.0018 and 0.026 for TBA, respectively. Despite the higher AUROC of TBA at different scenarios, RF showed a better performance in large number QTL. Generally, genomic prediction based on imputed genotypes (5K) can be implemented to reduce of the cost of a genomic evaluation.
Somayeh Barani; Mohammad Moradi-Shahrbabak; Ardeshir Nejati-Javaremi; Mohammad Hosein Moradi; Mohsen Gholizadeh; Majid Khansefid
Abstract
Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative ...
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Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative trait loci (QTL). The aim of this research was to estimate of the extent of LD in three Iranian native sheep breeds. Therefore, 186 blood samples were taken from three sheep breeds (96 Baluchi, 45 lori-Bakhtiari and 45 Zel) and genotyped by Illumina ovine 50K SNPChip, then linkage disequilibrium in any breed were measured using r2. The results showed that the highest average values of r2 at inter marker distance of less than 10Kb were 0.392± 0.323, 0.360±0.308 and 0.340±0.306 in Baluchi, Lori-Bakhtiari and Zel, respectively. The highest average values of r2 in autosome chromosomes of each breed were obtained for chromosome 24 and 25 in Baluchi, 9 and 21 in Lori-Bakhtiari and 23 and 24 in Zel. The amount of LD reduced with increasing the distance between markers, the extent of LD was less than 0.1 at inter marker distances greater than 100Kb. The comparison of correlation coefficients LD between different breeds showed a strong persistence of LD phase between Zel and Lori-Bakhtiari breeds which is probably due to recent common ancestors between these two breeds. Generally, with increase amount of LD means that lower marker density in association studies will be required. The results of this study showed to achieve genomic prediction accuracy of 85% (assuming there is no other accuracy limiting factor) and robust GWAS results, the density of markers must be higher than 50K SNPChip.
