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

Abstract

Background 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.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity‐enriched regions uncover signals of selection in the Quarter Horse racing line

“…The longest shared homozygous segment was detected in ECA 7, with a length of around 25 Mbp. Studies have already reported the same findings in ECA 7, and it is probably an important region conserved for most equine breeds (Ablondi et al, 2019; Grilz‐Seger et al, 2019; Santos, Schettini, et al, 2021). Therefore, selection events and genetic drift initially contribute to the formation of long ROHs (Pemberton et al, 2012).…”

A genome‐wide comparison between selected and unselected Valle del Belice sheep reveals differences in population structure and footprints of recent selection

“…Although we have mainly focused attention on the common candidate regions identified by at least two approaches, it is important to reiterate that each method has specific features implying that non‐overlapping regions of selection signatures across different methods should be treated as complementary information to better understand the different patterns of variation in a population (Santos et al, 2021). In this regard, the Rsb approach identified a region on OAR06 with well‐known candidate genes.…”

Genome‐wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse

“…Two heterozygous and two missing genotypes were permitted within each segment. The scanning window was set to 50 SNPs (Ceballos et al, 2018; Santos et al, 2021). The detailed settings were as follows: –homozyg –density 60 –gap 1000 –kb 250 –snp 20, –window‐het 2, –window‐missing 2, –window‐snp 50, –window‐threshold 0.05.…”

“…Thus, the DNA regions that are ROH in the majority of the animals in a breed can be regarded as selection signatures (Grilz‐Seger et al, 2019; Peripolli et al, 2017). Because TD analysis and ROH analysis rely on different measures of genetic fixation/variation, the methods are often used in combination to avoid missing DNA regions of interest (de Simoni Gouveia et al, 2014; Rajawat et al, 2022; Santos et al, 2021; Xia et al, 2021).…”