Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins

SIMPLE SUMMARY: The ideal body conformation is an important part of the breeding objective of Czech Holsteins to allow high production while improving health and fitness. In this study, we aimed to identify loci that influence these traits. The genome-wide association study (GWAS) was performed using the weighted single-step best linear unbiased prediction (wssGBLUP) method. The multiple comparison test was performed with the Bonferroni correction. Composite traits (dairy capacity composite, feet and legs composite, and total score) and partial linear traits (stature, body depth, angularity, and fore udder attachment) each showed associations with one single nucleotide polymorphism (SNP) that were either statistically significant or approached the significance threshold. The association analysis without the Bonferroni correction (based on the significance level of 1.00 × 10(−6)) showed one significant SNP for total score, and also one for stature, angularity, and fore udder attachment. Moreover, one SNP was of near-significance threshold for the dairy capacity composite, the feet and legs composite, and body depth. ABSTRACT: The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low—dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.