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Home / Equine Research Bank / BMC Genomics / Genome-wide scans for signatures of selection in Mangalarga ...
BMC genomics2021; 22(1); 737; doi: 10.1186/s12864-021-08053-8

Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping.

Abstract: The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifying genomic regions affected by different selection pressures, mainly highlighting the recent positive selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the Mangalarga Marchador genome. Besides, we seek to direct the discussion about genes and traits of importance in this breed, especially traits related to the type and quality of gait, temperament, conformation, and locomotor system. Results: Three different methods were used to search for signals of selection: Tajima's D (TD), the integrated haplotype score (iHS), and runs of homozygosity (ROH). The samples were composed of males (n = 62) and females (n = 130) that were initially chosen considering well-defined phenotypes for gait: picada (n = 86) and batida (n = 106). All horses were genotyped using a 670 k Axiom® Equine Genotyping Array​ (Axiom MNEC670). In total, 27, 104 (chosen), and 38 candidate genes were observed within the signatures of selection identified in TD, iHS, and ROH analyses, respectively. The genes are acting in essential biological processes. The enrichment analysis highlighted the following functions: anterior/posterior pattern for the set of genes (GLI3, HOXC9, HOXC6, HOXC5, HOXC4, HOXC13, HOXC11, and HOXC10); limb morphogenesis, skeletal system, proximal/distal pattern formation, JUN kinase activity (CCL19 and MAP3K6); and muscle stretch response (MAPK14). Other candidate genes were associated with energy metabolism, bronchodilator response, NADH regeneration, reproduction, keratinization, and the immunological system. Conclusions: Our findings revealed evidence of signatures of selection in the MM breed that encompass genes acting on athletic performance, limb development, and energy to muscle activity, with the particular involvement of the HOX family genes. The genome of MM is marked by recent positive selection. However, Tajima's D and iHS results point also to the presence of balancing selection in specific regions of the genome.
© 2021. The Author(s).
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Publication Date: 2021-10-14 PubMed ID: 34645387PubMed Central: PMC8515666DOI: 10.1186/s12864-021-08053-8Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article discusses the use of genome-wide scans to identify signs of selective breeding in Mangalarga Marchador horses. The researchers used high-throughput single nucleotide polymorphism (SNP) genotyping to locate regions of the genome affected by selective pressures, primarily recent positive selection, and identified genes and functional pathways associated with these selected traits.

Understanding the Research

  • The study sought to identify areas of the genome in Mangalarga Marchador horses that have been impacted by selective pressures. This includes any breed traits related to the type and quality of gait, temperament, physique, and the locomotor system.
  • Three analytical methods were employed to identify these selection signals: Tajima’s D, Integrated Haplotype Score (iHS), and Runs of Homozygosity (ROH). These methods help to provide a genomic snapshot of the breed’s history and the selection processes that have shaped their genetic makeup.
  • The sampling population consisted of both male and female horses specifically chosen based on their well-defined gait phenotype, labeled as ‘picada’ or ‘batida’.
  • The genetic information was obtained using a 670 k Axiom® Equine Genotyping Array, which is a robust tool for high-throughput SNP genotyping.

Results of the Study

  • Different genes identified as under positive selection across the three methods. In total, 27 (Tajima’s D), 104 (iHS), and 38 (ROH) candidate genes were caught within the selection signatures.
  • These genes were linked to essential biological processes. Among them, several genes (GLI3, HOXC9, HOXC6, HOXC5, HOXC4, HOXC13, HOXC11, and HOXC10) were associated with anterior/posterior pattern formation related to limb development.
  • Other genes were found to be involved in skeletal system development, proximal/distal pattern formation, JUN kinase activity, and muscle stretch response, all of which could potentially impact the horse’s athletic performance.
  • Additional candidate genes were linked to energy metabolism, bronchodilator response, NADH regeneration (potentially affecting energy availability and utilization), reproduction, keratinization (probably affecting skin or coat traits), and the immunological system.

Conclusions from the Research

  • It was concluded that the Mangalarga Marchador horse breed has been significantly shaped by recent positive selection, targeting genes affecting athletic performance, limb development, and energy to muscle activity. Certain HOX family genes, which play a crucial role in organism development, were notably present.
  • Notably, the results of Tajima’s D and iHS also indicated the presence of balancing selection in specific genome regions. Balancing selection is a process by which genetic diversity is maintained in a population, suggesting that beside the active selection for certain desired traits, other genomic areas are under selective pressures to maintain variability.

Cite This Article

APA
Santos WB, Schettini GP, Maiorano AM, Bussiman FO, Balieiro JCC, Ferraz GC, Pereira GL, Baldassini WA, Neto ORM, Oliveira HN, Curi RA. (2021). Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping. BMC Genomics, 22(1), 737. https://doi.org/10.1186/s12864-021-08053-8

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 22
Issue: 1
Pages: 737
PII: 737

Researcher Affiliations

Santos, Wellington B
  • Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil. wellington.bizarria@unesp.br.
Schettini, Gustavo P
  • Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil.
Maiorano, Amanda M
  • Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil.
Bussiman, Fernando O
  • Department of Animal Science, University of São Paulo (USP) - FZEA, Pirassununga, Brazil.
Balieiro, Júlio C C
  • Department of Animal Science, University of São Paulo (USP) - FZEA, Pirassununga, Brazil.
Ferraz, Guilherme C
  • Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil.
Pereira, Guilherme L
  • Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil.
Baldassini, Welder Angelo
  • Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil.
Neto, Otávio R M
  • Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil.
Oliveira, Henrique N
  • Department of Animal Science, São Paulo State University (Unesp) - FCAV, Via de Acesso Professor Paulo Donato Castelane, NN, CEP: 14884-900, Jaboticabal, SP, Brazil.
Curi, Rogério A
  • Department of Breeding and Animal Nutrition, São Paulo State University (Unesp) - FMVZ, Botucatu, Brazil.

MeSH Terms

  • Animals
  • Female
  • Genome
  • Genotype
  • Haplotypes
  • Homozygote
  • Horses / genetics
  • Male
  • Polymorphism, Single Nucleotide
  • Selection, Genetic

Conflict of Interest Statement

The author(s) certify that they have no conflict of interest.

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Citations

This article has been cited 2 times.
  1. Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A. The Genetic Diversity of Stallions of Different Breeds in Russia.. Genes (Basel) 2023 Jul 24;14(7).
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  2. Abondio P, Cilli E, Luiselli D. Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods.. Genes (Basel) 2022 May 22;13(5).
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