Nazari-Ghadikolaei Anahit, Fikse W Freddy, Viklund Åsa Gelinder, Mikko Sofia, Eriksson Susanne
Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Växa, Uppsala, Sweden.
J Anim Breed Genet. 2025 Sep;142(5):499-512. doi: 10.1111/jbg.12923. Epub 2025 Jan 4.
Swedish Warmblood horses (SWB) are bred for show jumping and/or dressage with young horse test scores as indicator traits. This study aimed to investigate possible candidate genes and regions of importance for evaluated and linearly scored young horse test traits. A single-step genome-wide association study (ssGWAS) was done using the BLUPF90 suite of programs for factors scores from factor analysis of traits assessed at young horse tests together with height at withers. The ssGWAS included 20,814 SWB with factors scores for four factors for evaluated traits. A total of 6436 of these horses also had factor scores for 13 factors for linearly scored traits. Genotypes from a 670K SNP array were available for 380 of the horses in this study. All genotyped horses had factor scores for evaluated traits, and 379 also had factors scores for linearly scored traits. Significant SNPs associated with three factors related to size were located on ECA3 within or nearby a well-known region, including the genes ligand dependent nuclear receptor corepressor like (LCORL), non-SMC condensin I complex subunit G (NCAPG), DDB1 and CUL4 Associated Factor 16 (DCAF16), and the Family with Sequence Similarity 184 Member B (FAM184B). Significant SNPs were also detected for two factors for evaluated traits representing conformation and jumping, and four factors for linearly scored traits related to body length, neck conformation, walk and trot (hindleg position and activity), respectively. Among nearby genes, calcium/calmodulin-dependent protein kinase type 1D (CAMK1D) for the factor for linearly scored traits related to neck conformation and GLI Family Zinc Finger 2 (GLI2) for the factor for evaluated jumping traits, were most promising. For these, top associated SNPs were detected within the genes, and the known gene functions seems to be related to the phenotypes. In conclusion, ssGWAS is beneficial to detect plausible candidate genes/regions for desired traits in warmblood horses.
瑞典温血马（SWB）被培育用于场地障碍赛和/或盛装舞步，幼驹测试成绩作为指标性状。本研究旨在调查对于评估和线性评分的幼驹测试性状而言可能的候选基因和重要区域。使用BLUPF90程序套件进行了单步全基因组关联研究（ssGWAS），该程序用于对幼驹测试评估的性状以及肩高进行因子分析得到的因子得分。ssGWAS纳入了20,814匹瑞典温血马，这些马具有针对评估性状的四个因子的因子得分。其中共有6436匹马还具有针对线性评分性状的13个因子的因子得分。本研究中380匹马可获得来自670K SNP芯片的基因型。所有进行基因分型的马都具有针对评估性状的因子得分，379匹马还具有针对线性评分性状的因子得分。与三个与体型相关的因子相关的显著SNP位于ECA3上一个知名区域内或附近，包括配体依赖性核受体共抑制因子样基因（LCORL）、非SMC凝聚素I复合体亚基G基因（NCAPG）、DDB1和CUL4相关因子16基因（DCAF16）以及序列相似性家族184成员B基因（FAM184B）。对于代表 conformation（构象）和跳跃的评估性状的两个因子以及分别与体长、颈部构象、行走和小跑（后肢位置和活动）相关的线性评分性状的四个因子，也检测到了显著SNP。在附近基因中，与颈部构象相关的线性评分性状的因子的钙/钙调蛋白依赖性蛋白激酶1D基因（CAMK1D）以及与评估跳跃性状的因子的GLI家族锌指蛋白2基因（GLI2）最具潜力。对于这些基因，在基因内部检测到了顶级关联SNP，并且已知的基因功能似乎与表型相关。总之，单步全基因组关联研究有利于检测温血马中所需性状的合理候选基因/区域。
