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Single-step GWAS using chip 65k for racing performance in Quarter Horses

Amanda Dias Assoni ; Guilherme L. Pereira ; Rogério Abdallah Curi ; Josineudson Augusto II Vasconcelos Silva ; Henrique N. de Oliveira ; Luis Arthur Loyola Chardulo
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Quarter Horses are characterized by great sprinting speed over short distances on straight tracks. The speed index (SI) is commonly used to both classify and compare racing performance under different conditions. The objective of this study was to identify the chromosomal regions responsible for racing performance (Speed Index maximum - SI max) through a single-step genome wide association study (ssGWAS) in Quarter Horses. A total of 654 horses were included in the pedigree database, which of 218 had SI records and were genotyped with Equine SNP70 BeadChip (65k). The model used for the analysis included the fixed effects of sex, racing year (1988 to 2015), and age at racing (2-5 years). SNP effects and weights for GWAS were derived as follows: 1) let D = I in the first step; 2) calculate G = ZDZ?q; 3) calculate the GEBVs for the entire dataset using ssGBLUP; 4) use GEBVs to get the SNP effects (?): ? = qDZ?(ZDZ?q)-1?, where ? is the GEBVs for genotyped animals; 5) calculate the weights for each i-th SNP: di = ?2i2pi(1-pi); 6) normalize the SNP weights in order to keep the total genetic variance constant (iterate through steps 2 to 6). The SNP weights were refined by three iterations. Genomic regions were compared considering genetic variance explained by six SNPs adjacent windows. Eight regions in eight different equine chromosomes (ECA), where 39 genes were found, explained 12% of the total genetic variance: ECA 3 (2.45%), ECA15 (1.99%), ECA29 (1.70%), ECA28 (1.56%), ECA19 (1.35%), ECA11 (1.24%), ECA14 (1.08%) and ECA9 (1.02%). As expected many regions and genes were associated explaining small percentage of the genetic variance of the SI, suggesting SI as a polygenic trait. It is noteworthy, however, that top 30 regions explained approximately 30% of the total genetic variance, many of these regions are close and can be linked to the same genes or causal effects. Although the consistent results, there is a further investigation using 110 genotyped horses (54k SNPs) in progress, and should allow us to confirm the results found by the present study.