Mahdi Mokhber; Mohammad Moradi Shahre Babak; Mostafa Sadeghi; Hossein Moradi Shahrbabak; Javad Rahmani-Nia
Abstract
In order to estimate the effective population size (Ne) in Iranian water buffalo blood and hair samples of 407 individual from Azari (N=260), Khuzestani (N=120) and Mazandrani (N=27) buffalo populations were gathered. After DNA extaraction, the samples were genotyped using Axiom® Buffalo Genotyping ...
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In order to estimate the effective population size (Ne) in Iranian water buffalo blood and hair samples of 407 individual from Azari (N=260), Khuzestani (N=120) and Mazandrani (N=27) buffalo populations were gathered. After DNA extaraction, the samples were genotyped using Axiom® Buffalo Genotyping 90K Array. The Ne was estimated from 700 to 4 generations ago and also for the present generation by linkage disequiblirum data and based on heterozygote-excess method using NeEstimator (V2), respectively. Estimated Ne for Azari, Khuzestani and Mazandarani were calculated 1530, 1375 and 1141, respectively, for 700 generations ago. Ne for the present generation in Azeri, Khuzestani and Mazandarani were estimated 447, 226 and 35, respectively. The Ne for Azeri and Khuzestani were relatively high and these two populations were not endanger to extinction, but their Ne has been declined in the resent generations massively and it is necessary to care about the maintenance of Ne and relatively high diversity for these populations. However, the Mazandarani population is endangered because of low Ne and so it is necessary to carefully monitor their effective population size, improve the profitability of production and planning a suitable mating scheme to control inbreeding and genetically conserve this population.
Amir Hossein Khalt-Abadi Farahani; Mohammad Hossein Moradi
Abstract
The objective of the present study was to estimate the inbreeding values using run of homozygosity and study the evolutionary trend of the effective population size (Ne) in some Asian horse breeds. A total of 99 animal samples consisting 19, 24, 18, 19 and 19 samples from AkhalTake, Arrabian, Caspian, ...
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The objective of the present study was to estimate the inbreeding values using run of homozygosity and study the evolutionary trend of the effective population size (Ne) in some Asian horse breeds. A total of 99 animal samples consisting 19, 24, 18, 19 and 19 samples from AkhalTake, Arrabian, Caspian, Mongolian and Thoroughbred breeds, genotyped by Illumina SNP50K Beadchip assay were used in this study, respectively. This study has been performed in collaboration with the Equine Genetic Diversity Consortium (EGDC) project. The inbreeding values based on the run of homozygosity using FROH and next, Ne using linkage disequilibrium across 5 up to 1000 generations ago were estimated. The result of principal component analysis (PCA) indicated that all breeds will be separated from each other in the first two principal components. Average expected and observed heterozygosity for different breeds ranged 0.278-0.294 and 0.278-0.308 respectively. Estimation of inbreeding based on genomic information showed that the values are ranged between 0.003 in Mongolian up to 0.166 in Thoroughbreds. The Ne results showed a decreasing trend over the last 1000 generations for all breeds, with an increasing slope since about 100 generations ago. The highest historically effective population size in recent generations (5 generations ago) was found in the Arabian breed (53 heads) and the lowest for Caspian and Thoroughbred (33-34 heads) breeds. Generally, the results of this study indicated that despite a reasonable genetic variation and low inbreeding value, however, the Ne is the lowest in Caspian compared to other Asian horse breeds that designing of appropriate programs is necessary to conserve remaining purebred animals of this indigenous Iranian horse breed.
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.
Mohammad Hossein Moradi; Amir Hossein Farahani; Ardeshir Nejati-Javaremi
Abstract
The aim of the present study was to estimate the effective population size (Ne) in some Iranian sheep breeds using genome wide SNP data. A total of 217 animal samples consisting of 45, 37, 34, 35, 45 and 11 samples from Zel, Afshari, Moghani, Qezel, Lori-Bakhtiari and a wild-type of Iranian sheep breeds, ...
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The aim of the present study was to estimate the effective population size (Ne) in some Iranian sheep breeds using genome wide SNP data. A total of 217 animal samples consisting of 45, 37, 34, 35, 45 and 11 samples from Zel, Afshari, Moghani, Qezel, Lori-Bakhtiari and a wild-type of Iranian sheep breeds, genotyped by Illumina OvineSNP50K Beadchip assay were used in this study respectively. This study has been performed in collaboration with the Ovine HapMap project. The Ne was estimated using linkage disequilibrium across 4 up to 3500 generations ago. The result of principal component analysis (PCA) indicated that all breeds will be separated from each other in the first two principal components. Average expected and observed heterozygosity for different breeds ranged 0.36-0.37 and 0.37-0.43 respectively. The Ne results showed a decreasing trend over the last 3500 generations for all breeds, with an increasingly slope since about last 550 generations. The Ne in Iranian sheep breeds for 4 generations ago were ranged from 9 up to 89. The highest historically effective population size was found for Zel breed (89 heads) and the lowest for Afshari (44 heads) and wild_type (9 heads) sheep breeds. Generally, the results indicated that although a considerable genetic variation exists in these populations, however Ne has been decreased strongly in Iranian sheep breeds especially in Afshari and wild-type sheep breeds during recent years and designing of appropriate programs is necessary to conserve remaining purebred animals of these indigenous sheep breeds.
Karim Karimi; Ali Esmaili zadeh koshkueih; Masoud Asadi Fozi
Abstract
The objective of this study was to estimate the effective number of breeders in Sarabi cattle population using heterozygote-excess method based on single nucleotide polymorphism markers. Data consisted of 20 Sarabi cows. SNP genotyping was performed using Illumina High-density Bovine BeadChip designed ...
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The objective of this study was to estimate the effective number of breeders in Sarabi cattle population using heterozygote-excess method based on single nucleotide polymorphism markers. Data consisted of 20 Sarabi cows. SNP genotyping was performed using Illumina High-density Bovine BeadChip designed to genotype 777,962 SNPs. Average observed heterozygosity, expected heterozygosity, minor allele frequencies and percentage of deviation from Hardy-Weinberg test were estimated. Effective number of breeders was estimated per each chromosome using NEESTIMATOR (v2) software based on heterozygote-excess method. Average chromosome-wise effective number of breeders was equal to 28 and corresponding average confidence interval was between 17.3 and 40.2. Results of this study indicated that Sarabi breed is on serious risk of extinction. Design of appropriate programs is necessary to conserve remaining purebred cattles.
