Genetic diversity, parentage verification, and genetic bottlenecks evaluation in iranian turkmen horse1

Rahimi-Mianji, Ghodrat; Nejati‐Javaremi, A.; Farhadi, Ayoub

doi:10.1134/s1022795415090082

Cited by 6 publications

(3 citation statements)

References 29 publications

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“…Early equine parentage verification techniques utilised antigen-based blood typing markers (Bowling et al 1985) and advancements in molecular technology facilitated a feasible change to using STR markers, which enhanced parentage verification accuracy and process efficiencies in comparison to blood typing methods (Bowling et al 1997). Typical equine STR profiles consist of a minimum 12 markers recommended by The International Society of Animal Genetics (ISAG 2012) and STRs continue to serve as a robust and accurate choice of marker when performing parentage verification and population genetics studies across equine breeds (Lee et al 2006, Tozaki et al 2001, van de Goor et al 2011and Rahimi-Mianji et al 2015. Several analogous species have similar industry-based parentage verification needs i.e.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

Flynn

Morrin-O'Donnell²,

Weld³

et al. 2021

Preprint

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Short tandem repeat (STR), also known as microsatellite markers are currently used for genetic parentage verification within equine. Transitioning from STR to single nucleotide polymorphism (SNP) markers to perform equine parentage verification is now a potentially feasible prospect and a key area requiring evaluation is parentage testing accuracies when using SNP based methods, in comparison to STRs. To investigate, we utilised a targeted equine genotyping by sequencing (GBS) panel of 562 SNPs to SNP genotype 309 Thoroughbred horses - inclusive of 55 previously parentage verified offspring. Availability of STR profiles for all 309 horses, enabled comparison of parentage accuracies between SNP and STR panels. An average sample call rate of 97.2% was initially observed, and subsequent removal of underperforming SNPs realised a pruned final panel of 516 SNPs. Simulated trio and partial parentage scenarios were tested across 12-STR, 16-STR, 147-SNP and 516-SNP panels. False-positives (i.e. expected to fail parentage, but pass) ranged from 0% for 147-SNP and 516-SNP panels to 0.003% when using 12-STRs within trio parentage scenarios, and 0% for 516-SNPs to 1.6% for 12-STRs within partial parentage scenarios. Our study leverages targeted GBS methods to generate low-density equine SNP profiles and demonstrates the value of SNP based equine parentage analysis in comparison to STRs - particularly when performing partial parentage discovery.

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Section: Introductionmentioning

confidence: 99%

Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

Flynn

Morrin-O'Donnell²,

Weld³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Therefore, an optimized selection strategy and mating program has been suggested to maintain genetic diversity (Nazari et al 2022 ). Despite several studies on different native Iranian horse breeds that assessed the genetic diversity, parentage verification, and genetic structure of the populations using microsatellite or single-nucleotide polymorphism (SNP) (Amjadi et al 2021 ; Nazari et al 2022 ; Sadeghi et al 2019 ; Salek Ardestani et al 2022 ; Seyedabadi et al 2006 ; Shahsavarani and Rahimi-Mianji 2010 ), the majority of the studies were performed on a single breed (Ala-Amjadi et al 2017 ; Gharahveysi and Irani 2011 ; Nazari et al 2022 ; Rahimi-Mianji et al 2015 ; Seyedabadi et al 2006 ). However, Moridi et al ( 2013 ) studied the mitochondrial DNA (mtDNA) diversity and origin of five Iranian native horses, including Turkmen, Kurdish, Caspian, Iranian Arabian, and Sistani breeds.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

et al. 2023

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Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.

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“…Therefore, an optimized selection strategy and mating program has been suggested to maintain genetic diversity (Nazari et al, 2022). Despite several studies in different native Iranian horse breeds that assessed the genetic diversity, parentage verification, and genetic structure of the populations using microsatellite or single nucleotide polymorphism (SNP), the majority of the studies were performed on a single breed (Ala-Amjadi et al, 2017;Gharahveysi and Irani, 2011;Nazari et al, 2022;Rahimi-Mianji et al, 2015;Seyedabadi et al, 2006). However, Moridi et al (2013) studied mitochondrial DNA (mtDNA) diversity and origin of five Iranian native horses including Turkmen, Kurdish, Caspian, Iranian Arabian and Sistani breeds.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Razmkabir

Mousavi

Rostamzadeh

et al. 2022

Preprint

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Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades which shaped their genomes in several unique ways. The principal aims of this study were to evaluate genetic diversity and genome-wide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67) and Persian Arabian (n = 52) populations, using genome-wide genotyping data. The contemporary effective population sizes were 59, 98, 102 and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish, respectively. Analysis of population genetic structure classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using de-correlated composite of multiple selection signals (DCMS) statistics based on six pairwise comparisons, we detected different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05), respectively. The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian with a small size and the other studied breeds with a medium size. Using results of studies for human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results suggest that the identified sweeps might have been enriched as an adaptation to environmental conditions or a response to human-mediated artificial selection.

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Genetic diversity, parentage verification, and genetic bottlenecks evaluation in iranian turkmen horse1

Cited by 6 publications

References 29 publications

Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

Genetic diversity and signatures of selection in four indigenous horse breeds of Iran

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