A selection signatures study among Middle Eastern and European sheep breeds

Eydivandi, Sirous; Roudbar, Mahmoud Amiri; Ardestani, Siavash Salek; Momen, Mehdi; Sahana, Goutam

doi:10.1111/jbg.12536

Cited by 16 publications

(10 citation statements)

References 102 publications

(125 reference statements)

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“…The genomes of local breeds have been under natural and artificial selection for centuries to transmit the desired properties to the descendants. These genetic changes shaped recent gene pools, and can be used for investigating genetic relatedness among breeds (Eydivandi et al, 2021a;Ju et al, 2019). Our study showed that the genomes of Iranian horse breeds contain multiple genomic regions under selective pressures (adaptation and/or breeding), representing an opportunity for a more detailed investigation the genes involved in these procedures.…”

Section: Selection Signaturementioning

confidence: 81%

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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Section: Selection Signaturementioning

confidence: 81%

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

Razmkabir

Mousavi

Rostamzadeh

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The genomes of local breeds have been under natural and artificial selection for centuries to transmit the desired properties to the descendants. These genetic changes shaped recent gene pools, and can be used for investigating the genetic relatedness among breeds (Eydivandi et al 2021a ; Ju et al 2019 ; Rajawat et al 2022 ). Our study showed that the genomes of Iranian horse breeds contain multiple genomic regions under selective pressures (adaptation and/or breeding), representing an opportunity for a more detailed investigation of the genes involved in these procedures.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

View full text Add to dashboard Cite

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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“…Fst was a basic indicator for traditionally measuring genetic differentiation among populations. Understanding population structure and genetic background in an evolutionary context [13][14][15] . The corresponding gene loci and their functions were found by analyzing the selected regions with the Fst value in the top 1%.…”

Section: Fst Analysismentioning

confidence: 99%

Analysis of differences between different sheep breeds based on whole-genome resequencing technology

Liu

Guo

Zhang

et al. 2022

Preprint

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The Inner Mongolia Autonomous Region is the region with the highest mutton production in China, but researchers know very little about the genetic evolution of local sheep. In this experiment, whole-genome resequencing technology was used to investigate the genetic distance and single nucleotide polymorphism (SNP) of Chahar sheep, Ujimqin sheep and Xiqi sheep. The results showed that the distribution of SNPs in different regions of the genome was different, thus affecting the function of some genes. Insertion-Deletion (INDEL) also suggested an evolutionary distance between these three types of sheep. The genetic distance between Chahar sheep and the other two types of sheep is relatively far. During the construction of three sheep differential loci, it was found that they could be distinguished by the difference of bases at a certain position on the three chromosomes, which improved the identification of mutton. This suggests that the differences in meat quality between the three types of sheep are not only due to differences in the living environment but also may be influenced by genetic evolution. The research on differential genes can improve the data and theoretical basis for future precise nutrition.

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A selection signatures study among Middle Eastern and European sheep breeds

Cited by 16 publications

References 102 publications

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

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

Analysis of differences between different sheep breeds based on whole-genome resequencing technology

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