Publications by authors named "Mohammad Moradi Shahrbabak"

13 Publications

  • Page 1 of 1

Genome Diversity and the Origin of the Arabian Horse.

Sci Rep 2020 06 16;10(1):9702. Epub 2020 Jun 16.

Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.

The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the "Straight Egyptian" subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
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http://dx.doi.org/10.1038/s41598-020-66232-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298027PMC
June 2020

Correction to: Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

BMC Genet 2020 Apr 8;21(1):42. Epub 2020 Apr 8.

AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia.

Following publication of the original article [1], the authors flagged that the article had published with the author 'Ali Jalil Sarghale' erroneously omitted from the author list.
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http://dx.doi.org/10.1186/s12863-020-00841-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140384PMC
April 2020

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

BMC Genet 2020 02 10;21(1):16. Epub 2020 Feb 10.

AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia.

Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (F), excess of homozygosity (F), correlation between uniting gametes (F), and diagonal elements of the genomic relationship matrix (F); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies.

Results: In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on F, F and F were higher in AZ than they were in KHZ, which was in contrast to the F estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX).

Conclusion: The calculated F was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that F can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
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http://dx.doi.org/10.1186/s12863-020-0824-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011551PMC
February 2020

Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.

PLoS One 2019 31;14(5):e0217687. Epub 2019 May 31.

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia.

Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217687PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544294PMC
January 2020

Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds.

J Hered 2019 03;110(2):173-182

Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY.

The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicating high genetic diversity in Persian Arabian horses. Analysis of population genetic structure using STRUCTURE and principal component analysis suggested that Persian Arabian horses can be divided into 3 groups, however the groups do not match traditional matrilineal strains. In total, 15 genomic regions were identified by at least 2 of the 3 implemented methods, Tajima's D, H, and H12, as potentially under selection in Persian Arabian horses. Most of these peaks were found on chromosome 9, overlapping with QTLs previously associated with horse temperament. Biological function analysis of identified candidate genes highlighted enrichment of GO term "response to lipopolysaccharide" and KEGG pathway "chemokine-mediated signaling pathway," which are associated with immune responses and may have been targets of selection in Persian Arabian horses. Independent analyses of SNP data from 30 horses of 4 other Iranian breeds suggested distinct population structure between Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the results of this study suggest a rich genetic diversity in the Persian Arabian horses and a clear genetic differentiation with Turkemen and Caspian breeds.
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http://dx.doi.org/10.1093/jhered/esy061DOI Listing
March 2019

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds.

BMC Genomics 2018 Jun 11;19(1):449. Epub 2018 Jun 11.

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.

Background: Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals.

Results: A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (F) was used to detect signatures of selection. In total, 13 regions with outlier F values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2.

Conclusions: Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.
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http://dx.doi.org/10.1186/s12864-018-4759-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996463PMC
June 2018

MHC haplotype diversity in Persian Arabian horses determined using polymorphic microsatellites.

Immunogenetics 2018 05 23;70(5):305-315. Epub 2017 Nov 23.

Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.

Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new. In 47 of the remaining 58 unrelated horses, we could assign one previously identified MHC haplotype, and by default, we gave provisional haplotype status to the remaining constellation of microsatellite alleles. In these horses, we found 21 haplotypes that we had previously defined and 31 provisional haplotypes, two of which had been identified in an earlier study. This gave a total of 78 new MHC haplotypes. The final 11 horses were MHC heterozygotes that we could not phase using information from any of the previously validated or provisional haplotypes. However, we could determine that these horses carried a total of 22 different undefined haplotypes. In the overall population sample, we detected three homozygous horses and one maternally inherited recombinant from 21 informative segregations. Virtually all of the horses tested were MHC heterozygotes, and most unrelated horses (98%) were heterozygous for rare microsatellite-defined haplotypes found less than three times in the sampled horses. This is evidence for a very high level of MHC haplotype variation in the Persian Asil Arabian horse.
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http://dx.doi.org/10.1007/s00251-017-1039-xDOI Listing
May 2018

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

J Theor Biol 2014 Sep 10;356:213-22. Epub 2014 May 10.

Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, Shiraz, Iran; School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia. Electronic address:

Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity. To identify LBPs from non-LBPs, the performances of support vector machine (SVM) and neural network were compared in this study. Comprehensive protein features and various techniques were employed to create datasets. Five-fold cross-validation (CV) and independent evaluation (IE) tests were used to assess the validity of the two methods. The results indicated that SVM outperforms neural network. SVM achieved 89.28% (CV) and 89.55% (IE) overall accuracy in identification of LBPs from non-LBPs and 92.06% (CV) and 92.90% (IE) (in average) for classification of different LBPs classes. Increasing the number and the range of extracted protein features as well as optimization of the SVM parameters significantly increased the efficiency of LBPs class prediction in comparison to the only previous report in this field. Altogether, the results showed that the SVM algorithm can be run on broad, computationally calculated protein features and offers a promising tool in detection of LBPs classes. The proposed approach has the potential to integrate and improve the common sequence alignment based methods.
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http://dx.doi.org/10.1016/j.jtbi.2014.04.040DOI Listing
September 2014

The relation between the genetic architecture of quantitative traits and long-term genetic response.

J Appl Genet 2014 Aug 27;55(3):373-81. Epub 2014 Mar 27.

Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, P. O. Box 31585-4111, Karaj, Iran,

The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.5 × 10(-5) per locus was simulated. Selection of superior animals was done using best linear unbiased prediction (BLUP) with assumption of infinitesimal model. Selection intensity was constant over 30 generations of selection. The highest genetic progress obtained when the allelic frequency had L-shaped distribution and number of trait-affecting loci was high (500). Although quantitative genetic theories predict the extinction of genetic variance due to artificial selection in long time, our results showed that under L- and U-shapped allelic frequency distributions, the additive genetic variance is persistent after 30 generations of selection. Further, presence or absence of selection limit can be an indication of low (<50) or high (>100) number of trait-affecting loci, respectively. It was concluded that the genetic architecture of complex traits is an important subject which should be considered in studies concerning long-term response to selection.
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http://dx.doi.org/10.1007/s13353-014-0205-1DOI Listing
August 2014

Detecting novel SNPs and breed-specific haplotypes at calpastatin gene in Iranian fat- and thin-tailed sheep breeds and their effects on protein structure.

Gene 2014 Mar 5;537(1):132-9. Epub 2014 Jan 5.

Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.

Calpastatin has been introduced as a potential candidate gene for growth and meat quality traits. In this study, genetic variability was investigated in the exon 6 and its intron boundaries of ovine CAST gene by PCR-SSCP analysis and DNA sequencing. Also a protein sequence and structural analysis were performed to predict the possible impact of amino acid substitutions on physicochemical properties and structure of the CAST protein. A total of 487 animals belonging to four ancient Iranian sheep breeds with different fat metabolisms, Lori-Bakhtiari and Chall (fat-tailed), Zel-Atabay cross-bred (medium fat-tailed) and Zel (thin-tailed), were analyzed. Eight unique SSCP patterns, representing eight different sequences or haplotypes, CAST-1, CAST-2 and CAST-6 to CAST-11, were identified. Haplotypes CAST-1 and CAST-2 were most common with frequency of 0.365 and 0.295. The novel haplotype CAST-8 had considerable frequency in Iranian sheep breeds (0.129). All the consensus sequences showed 98-99%, 94-98%, 92-93% and 82-83% similarity to the published ovine, caprine, bovine and porcine CAST locus sequences, respectively. Sequence analysis revealed four SNPs in intron 5 (C24T, G62A, G65T and T69-) and three SNPs in exon 6 (c.197A>T, c.282G>T and c.296C>G). All three SNPs in exon 6 were missense mutations which would result in p.Gln 66 Leu, p.Glu 94 Asp and p.Pro 99 Arg substitutions, respectively, in CAST protein. All three amino acid substitutions affected the physicochemical properties of ovine CAST protein including hydrophobicity, amphiphilicity and net charge and subsequently might influence its structure and effect on the activity of Ca2+ channels; hence, they might regulate calpain activity and afterwards meat tenderness and growth rate. The Lori-Bakhtiari population showed the highest heterozygosity in the ovine CAST locus (0.802). Frequency difference of haplotypes CAST-10 and CAST-8 between Lori-Bakhtiari (fat-tailed) and Zel (thin-tailed) breeds was highly significant (P<0.001), indicating that these two haplotypes might be breed-specific haplotypes that distinguish between fat-tailed and thin-tailed sheep breeds.
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http://dx.doi.org/10.1016/j.gene.2013.12.023DOI Listing
March 2014

Identifying novel SNPs and allelic sequences of the stearoyl-CoA desaturase gene (SCD) in fat-tailed and thin-tailed sheep breeds.

Biochem Genet 2014 Apr 23;52(3-4):153-8. Epub 2013 Nov 23.

Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran,

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http://dx.doi.org/10.1007/s10528-013-9635-4DOI Listing
April 2014

Underlying functional genomics of fat deposition in adipose tissue.

Gene 2013 May 20;521(1):122-8. Epub 2013 Mar 20.

Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.

The objective of this study was to gain insight into the underlying mechanisms of fat deposition. Two sheep breeds with large fat-tail (Lori-Bakhtiari) and with thin-tail (Zel) were used as models. To determine important and key candidate lipid metabolism related genes, comparative genomic approaches were employed. Gene expression profiles of adipose tissues were analyzed in human, pig, and cattle by express sequence tag (EST) analysis. EST analysis determined 65, 102 and 125 transcripts in human, pig and cattle respectively with at least 10 fold over-expression in the adipose tissue. Based on our comparative functional genomic analysis, seven genes were more abundant and common in investigated mammalian adipose tissues promising a conserved novel gene network in mammalian lipid metabolism. The candidate genes including fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), Stearoyl-CoA desaturase (SCD) and Lipoprotein lipase (LPL) were selected for further gene expression investigation within two sheep breeds. The real time PCR results showed that among the genes tested, FABP4 was expressed at higher levels than the others. The expression of FABP4 was significantly higher in the fat-tail of Lori-Bakhtiari than in the fat-tail and visceral adipose tissues of Zel (P<0.05). The findings suggest that the FABP4 gene expression in the fat-tail is an important index of fat deposition.
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http://dx.doi.org/10.1016/j.gene.2013.03.045DOI Listing
May 2013

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.

BMC Genet 2012 Feb 26;13:10. Epub 2012 Feb 26.

Department of Animal Science-Excellent centre for improving sheep carcass quality and quantity, University of Tehran, PO Box 3158711167-4111, Karaj, Iran.

Background: Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds.

Results: Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7.

Conclusions: In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.
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http://dx.doi.org/10.1186/1471-2156-13-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351017PMC
February 2012
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