Prospection of genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line

Abstract

Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index ( F ST ) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing line and 68 of the cutting line, were genotyped using single nucleotide polymorphism arrays. On the basis of 27 genomic regions identified as selection signatures by REHH and F ST statistics, functional annotations of genes were made in order to identify those that could have been important during formation of the racing line and that could be used subsequently for the development of selection tools. Genes involved in muscle growth (n = 8), skeletal growth (n = 10), muscle energy metabolism (n = 15), cardiovascular system (n = 14) and nervous system (n = 23) were identified, including the FKTN, INSR, GYS1, CLCN1, MYLK, SYK, ANG, CNTFR and HTR2B.

Exercise-related genes analysis of Mongolian Horse

“…According to the analysis of GO, KEGG and individual gene function, we subsequently put our interest in exercise-related genes of Abaga horse. Twenty-one genes may involve in exercise of Abaga horse while their functions embodied vasoconstriction ( HTR2B ) (Launay et al 2002; Bevilacqua et al 2010; Meira et al 2014), angiogenesis ( CDH5 ) (Sauteur et al 2014), cardiac contraction ( KCNQ1 ) (Jespersen et al 2005; Brown et al 2015; Pedersen et al 2017), cardiac development and muscle structure ( ENAH ) (Franzini-Armstrong 1973; Benz et al 2013), muscle growth ( PIH1D1, SMURF1 ) (Inoue et al 2010; Ponsuksili et al 2014; Dalbo et al 2013), myogenic differentiation ( UNC13C ) (Meyer et al 2015; Langlois and Cowan 2017), skeletal muscle function ( ATP1A3 ) (Aughey et al 2007; Brashear et al 2007), femur strength and bone mineral density ( PPP2R5B, PPP6R3 ) (Alam et al 2009; Medina-Gomez et al 2017), osteoclast growth ( PTPRE, RHOBTB1 ) (Chiusaroli et al 2004; Song et al 2014), chondrogenesis (SCFD) (DeLise et al 2000; Hou et al 2017), lipid and carbohydrate metabolism ( PPARD, GCG, TCF7L2, GALNT13 ) (Yi et al 2005; Bevilacqua et al 2010; Park et al 2012; Ahmetov and Fedotovskaya 2015; Giordano Attianese and Desvergne 2015; Ropka-Molik et al 2017), exercise stress-induced response ( CD69, EIF4G3 ) (Testi et al 1989; Gradi et al 1998; Cappelli et al 2007; Morabito et al 2016), exercise coordination ( GRM1 ) (Conquet et al 1994; Bossi et al 2017) and height ( VGLL4 ) (Gabriel et al 2016). These genes of positive selection were presented simultaneously in Abaga horse, which may be a reason that it runs rapider than Wushen horse.…”

“…We picked up exercise-related genes as candidate genes in positively selected genes, further, presented enriched KEGG pathways and functions with selected exercise-related genes (Figure 7). HTR2B (encoding 5-hydroxytryptamine receptor 2B), has been identified in the genome of Quarter horses of the racing line (Meira et al 2014) and associated with impulsive behavior (Bevilacqua et al 2010) and vasoconstriction (Launay et al 2002). In zebrafish, vascular endothelial cadherin (encoded by CDH5 ) can promote elongation of the endothelial cell interface during angiogenesis (Sauteur et al 2014).…”

“…As an ancient breed, Mongolian horse has gone through a long breeding period (China National Commission of Animal Genetic Resources 2011). With a view to research tendentiousness, researchers pay more attention to traits of Thoroughbred horse (Gim et al 2004; Park et al 2012; Capomaccio et al 2013) and Quarter horse (Doan et al 2012; Meira et al 2014), but not the Mongolian horse and its diverse sub-branch. The preeminent endurance and stress-resistance of Mongolia horse are important factors for it to well adapt to the cold and harsh plateau environment (Li et al 2009).…”

Genomic regions associated with performance in racing line of Quarter Horses

“…In Brazil the effective number of animals in the racing line is relatively small compared to other lines, however its has substantial economic importance. Despite economic and scientific interest in this line and its racing aptitude, few efforts have been made to better understand the genetic mechanisms underlying this trait (Meira et al, 2014a(Meira et al, , 2014bPereira et al, 2016bPereira et al, , 2016a.…”

“…However, Pereira et al (2016bPereira et al ( , 2016a showed that some markers appropriate for the thoroughbred are not suitable for the identification of animals with superior racing performance in the Quarter Horse breed. In an attempt to identify genes and DNA polymorphisms specific for the racing line of Quarter Horses related to speed and performance in horse races, Meira et al (2014aMeira et al ( , 2014b investigated selection signatures and performed a genome-wide association study (GWAS). However, because of the small number of animals used, the results obtained were not conclusive in determining genetic variants associated with racing performance in the breed.…”