A genome-wide signatures of selection study of Welsh ponies and draft horses revealed five genes associated with horse type variation

Ardestani, Siavash Salek; Aminafshar, Mehdi; Maryam, Mohammad Bagher Zandi Baghche; Banabazi, Mohammad Hossein; Sargolzaei, Mehdi; Miar, Younes

doi:10.1016/j.genrep.2020.100833

Cited by 6 publications

(6 citation statements)

References 40 publications

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“…Previous studies reported that LCORL and NCAPG are closely related to body size traits in other species (26)(27)(28)(29). We also found a well-known gene, FAM184B, which is related to the body size traits on the 3 chromosomes from the π-ratio (30,31). In addition, 11 and 5 nonsynonymous sites were found on LCORL and NCAPG, respectively, through mutation site analysis.…”

Section: Genome-wide Differential Selection In Small and Large Body Sizesupporting

confidence: 65%

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Shen

Dai

et al. 2021

Journal of Genetics and Genomics

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Section: Genome-wide Differential Selection In Small and Large Body Sizesupporting

confidence: 65%

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Shen

Dai

et al. 2021

Journal of Genetics and Genomics

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“…Genetic population structure analyses, such as principal component analysis (PCA), Bayesian model‐based (admixture) approach, and phylogenic have been three efficient methods to explain the genetic distance and variation among horse populations (Asadollahpour Nanaei et al, 2019; Asadollahpour Nanaei et al, 2020; Cosgrove et al, 2020; Petersen, Mickelson, Cothran, et al, 2013; Salek Ardestani et al, 2020a, 2020b). For PCA, admixture, TreeMix, and Neighbor‐Net analyses, we downloaded publicly available datasets of 20 different breeds (Al Abri et al, 2017; Kader et al, 2015; Mack et al, 2017; Petersen, Mickelson, Rendahl, et al, 2013; Staiger, Abri, et al, 2016) from online databases (https://www.animalgenome.org, https://datadryad.org and Table S1) and merged them to the aforementioned Iranian horse dataset to have a comprehensive conception of genetic relationships among Iranian and other breeds.…”

Section: Methodsmentioning

confidence: 99%

“…The Asil, Caspian, Dareshuri, Kurdish, and Turkoman are five major Iranian native horse breeds (Yousefi‐Mashouf et al, 2021), which bear historical and cultural importance and play an important role in Iran's horse breeding industry. High throughput genotyping technologies have made it possible to conduct detailed studies on the population structure of livestock species, such as horse (Al Abri et al, 2017; Petersen, Mickelson, Cothran, et al, 2013; Salek Ardestani et al, 2020a), cattle (Ghoreishifar et al, 2020; Gobena et al, 2018), and sheep (Deniskova et al, 2019; Ghoreishifar et al, 2021). A former study illuminated the genetic structure of numerous ( n = 36) horse populations (Petersen, Mickelson, Cothran, et al, 2013) and Ablondi et al (2019) revealed genetic divergence within the Swedish Warmblood horse, due to their specialization in different equestrian disciplines using several selection signatures methods (Ablondi et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Population structure and genomic footprints of selection in five major Iranian horse breeds

et al. 2022

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The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, three haplotype-based methods including haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length were applied to trace genomic footprints of selection of Asil, Caspian, Dareshuri, Kurdish, and Turkoman groups. Then, the Mahalanobis distance based on the negative-log 10 rankbased P-values was estimated based on the haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length values. Asil, Caspian, Dareshuri, Kurdish, and Turkoman can be categorized into five different genetic clusters. Based on the top 1% of Mahalanobis distance based on the negative-log 10 rank-based P-values of SNPs, we identified 24 SNPs formerly reported to be associated with different traits and >100 genes undergoing selection pressures in Asil, Caspian, Dareshuri, Kurdish, and Turkoman. The detected QTL undergoing selection pressures were associated with withers height, equine metabolic syndrome, overall body size, insect bite hypersensitivity, guttural pouch tympany, white markings, Rhodococcus equi infection, jumping test score, alternate gaits, and body weight traits. Our findings will aid to have a better perspective of the genetic characteristics and population structure of Asil, Caspian, Dareshuri, Kurdish, and Turkoman horses as Iranian native horse breeds.

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“…After annotating these variants, we found that 36 candidate genes overlap with them. Of which genes PLAG1 and XKR4 had previously been identified to affect pig body size 16 , 52 ; genes ZNF521 , ATP6V1H , CCSER1 , and FAM184B were shown to influence the stature of cattle, sheep, or horses 53 – 57 . Notably, one of the candidate genes, NPR3 , is not only associated with human height and skeletal frame size but also regulates mouse skeletal overgrowth 58 – 60 .…”

Section: Resultsmentioning

confidence: 99%

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

Tong,

Chen,

et al. 2023

Nat Commun

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High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retrieve 207 resequencing datasets, and form a panel of worldwide distributed wild boars, aboriginal and highly selected pigs with pedigree structures, amounting to 1096 genomes from 43 breeds. Combining with their haplotype-informative reads and pedigree structure, we accurately construct a panel of 1874 haploid genomes with 41,964,356 genetic variants. We further demonstrate its valuable applications in GWAS by identifying five novel loci for intramuscular fat content, and in genomic selection by increasing the accuracy of estimated breeding value by 36.7%. In evolutionary selection, we detect MUC13 gene under a long-term balancing selection, as well as NPR3 gene under positive selection for pig stature. Our study provides abundant genomic variations for robust selection-signature detection and accurate haplotypes for deciphering complex traits in pigs.

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A genome-wide signatures of selection study of Welsh ponies and draft horses revealed five genes associated with horse type variation

Cited by 6 publications

References 40 publications

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Population structure and genomic footprints of selection in five major Iranian horse breeds

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences

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