Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

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

doi:10.3390/ani10010053

Cited by 16 publications

(12 citation statements)

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“…Overlapping homozygous regions, highly shared among individuals belonging to the same population, are thought to be potential signs of selection around a target locus. Several examples of ROH analyses in horses are available, and they address key aspects of the breed history and selection pressure [17,35,46,61,63,66]. In this study, we detected three ROH islands shared in over the 70% of the animals, highlighting potential signatures of selection in two regions on ECA3 and one region on ECA11.…”

Section: Discussionmentioning

confidence: 55%

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Mancin

Ablondi

Mantovani

et al. 2020

Animals

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This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

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Section: Discussionmentioning

confidence: 55%

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Mancin

Ablondi

Mantovani

et al. 2020

Animals

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“…A popular strategy to overcome these issues is to prioritize selection signals detected by several single statistical tests e.g. [11,12]; but following this strategy, we may lose some loci that show weak signals [9]. Hence, strategies based on combining p-values of different test statistics (composite measures of selection) have been developed [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

et al. 2020

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Background: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8,

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“…Since directional artificial selection reduces genomic variability, ROH islands are thought to be potential signs of selection around a target locus [ 16 , 24 , 25 ]. Several recent examples of ROH and population structure analyses applied to European horse breeds show key aspects of history and selection pressure [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. However, few studies were conducted in the framework of European small native horse breeds [ 29 , 31 , 32 , 34 ] and, to the best of our knowledge, none of them specifically analyzed Italian autochthonous horse breeds.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

Ablondi

Dadousis

Vasini

et al. 2020

Animals

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Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.

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Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

Cited by 16 publications

References 50 publications

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

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