Genomic analysis of the population structure in horses of the Brazilian Mangalarga Marchador breed

Santos, Bruna Aparecida dos; Pereira, Guilherme Luís; Bussiman, Fernando de Oliveira; Paschoal, Victória R.; Júnior, Sérgio M. de Souza; Balieiro, J. C. C.; Chardulo, Luis Artur Loyola; Curi, Rogério Abdallah

doi:10.1016/j.livsci.2019.09.010

Cited by 5 publications

(8 citation statements)

References 39 publications

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“…As we chose not to conduct the study with imputed data from two different platforms, the analyses were conducted with only 192 animals genotyped on Axiom MNEC670. Slight changes were noticed between our results and those of Santos et al [24], which were possibly attributed to the different approaches used in the studies, as well as the reduction in the number of animals.…”

Section: Genetic Structure and Linkage Disequilibrium (Ld)contrasting

confidence: 63%

“…Further detailed aspects of the population structure and LD have been reported in Santos et al [24] using the same database with the inclusion of imputed data. As we chose not to conduct the study with imputed data from two different platforms, the analyses were conducted with only 192 animals genotyped on Axiom MNEC670.…”

Section: Genetic Structure and Linkage Disequilibrium (Ld)mentioning

confidence: 99%

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

Santos

Schettini

Maiorano

et al. 2020

Preprint

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Background: The Mangalarga Marchador horse (MM) is one of the breeds shaped over generations by local adaptations and specific preferences of Brazilian breeders to morphology, functionality, and locomotion. The animals genetically have “batida” or “picada” natural gait trait, which is a trademark of the breed. The movement biomechanics of this breed promote stability during the execution, comfort, and softness of the ride. 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 the identification of genomic regions affected by different selection pressures, mainly highlighting recent selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the MM genome. A broader discussion of genes and traits of importance in this breed, especially traits related to the type and quality of the gait, temperament, conformation, and locomotor system, was also provided.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 670k Axiom ® Equine Genotyping Array (Axiom MNEC670). In total, 169 pruned candidate genes harboring important biological processes were found, highlighting the following: 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: Collectively, our findings revealed for the first time some pieces of evidence for selection signals acting on athletic performance, gait type, and energy to muscle activity in the MM breed, with the particular involvement of the HOX family of genes. Gene network analysis showed no relationship between the signals observed in this population and the DMRT3 gene, a relevant gene associated with gait trait, however candidate genes that were located close (~28Mb) to DMRT3 were identified.

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Section: Genetic Structure and Linkage Disequilibrium (Ld)contrasting

confidence: 63%

Section: Genetic Structure and Linkage Disequilibrium (Ld)mentioning

confidence: 99%

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

Santos

Schettini

Maiorano

et al. 2020

Preprint

View full text Add to dashboard Cite

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“…The first, which used a principal components analysis (PCA), found only one population structure, where the top five‐set eigenvectors explained 54.98% of the cumulative variance, 40.33% of which belonged to cluster 1 for PCA 1 × PCA 2 (Santos, 2020). The second was conducted with imputed population data (Santos et al., 2019), in which some segregations (substructures) were visualized within the breed related to important stallions, but not linked to gait type (marcha batida and marcha picada).…”

Section: Discussionmentioning

confidence: 99%

“…Santos et al. (2019) have also described the current effective population size (Ne) of the MM from the genomic data of 99 animals. The analysis estimated the Ne of 16 generations, demonstrating a marked reduction in recent generations.…”

Section: Discussionmentioning

confidence: 99%

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Fine‐scale estimation of inbreeding rates, runs of homozygosity and genome‐wide heterozygosity levels in the Mangalarga Marchador horse breed

Santos

Schettini

Fonseca

et al. 2020

J Animal Breeding Genetics

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With the availability of high‐density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine‐scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array—670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH) = 0.16; pedigree‐based (FPED) = 0.008; and a method based on excess homozygosity (FHOM) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0–2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0–2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif‐containing 37 (TRIM37), protein phosphatase, Mg2+/Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.

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Structure and genetic variability of the Costa Rican Paso horse

Domínguez-Viveros,

Molina-Villalobos,

Camacho-Sandoval

et al. 2024

Journal of Equine Veterinary Science

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Genomic analysis of the population structure in horses of the Brazilian Mangalarga Marchador breed

Cited by 5 publications

References 39 publications

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

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

Fine‐scale estimation of inbreeding rates, runs of homozygosity and genome‐wide heterozygosity levels in the Mangalarga Marchador horse breed

Structure and genetic variability of the Costa Rican Paso horse

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