Abstract：The horse (Equus caballus) temperament traits directly determines whether or how it is trained. Mongolian horse is a natural species, mixes with fewer external genome, which makes it as the most suitable species for researching the association of the polymorphism of candidate genes with the phenotype of temperament traits. The aim of this study was to identify the polymorphisms of the solute carrier family 6 member 4 gene (SLC6A4), dopamine beta-hydroxylase gene (DBH), brain derived neurotrophic factor gene (BDNF) and catechol-O-methyltransferase gene(COMT) and provide insight into the association with the Mongolian horse temperament behavior. The research animals were consisted with 60 Mongolian horses, with the same breeding and training situation, which were numbered and collected peripheral blood, respectively. The 28 temperament behavioral characteristics were described with the questionnaire survey method. The SNP analysis for 4 candidate genes was performed using the single strand conformational polymorphism (SSCP) and gene sequencing. Further, the statistical analysis system (SAS) software was used to analyze the genotype and the association. For BDNF gene, the SNPs in 222 bp (C→T) and 261 bp (G→C) were identified, and the association analysis showed that the biting behavior was significant affected by BDNF genes as C222T and G261C. For DBH gene, the SNP was identified in 758 bp (G→A), and DBH gene (G758A) was significant associated with endurance and on other horse-friendly behavior, which also had remarkable influence on such behaviors as comprehension ability, crossing the river and swimming, sand bath et al. For SLC6A4 gene, the SNP was identified in 1 362 bp (T→C), and gene (T1362C) significantly affected the behavior such as nervousness, panic, the reaction to harness and timid, et al. SLC6A4 gene (T1362C) was remarkable associated with the independence acts else. For COMT gene, the SNP was identified in 217 bp (G→A) and COMT gene (G217A) had a greatly significant associated with the competitiveness. Above information illustrated that BDNF, DBH, SLC6A4 and COMT were associated with the Mongolian horses' behavior trait. This study can provide the theory basis for the Mongolian horse temperament trait's marker assisted selection.
