Direct Phenotyping and Principal Component Analysis of Type Traits Implicate Novel QTL in Bovine Mastitis through Genome-Wide Association

Abstract

Our objectives were to robustly characterize a cohort of Holstein cows for udder and teat type traits and perform high-density genome-wide association studies for those traits within the same group of animals, thereby improving the accuracy of the phenotypic measurements and genomic association study. Additionally, we sought to identify a novel udder and teat trait composite risk index to determine loci with potential pleiotropic effects related to mastitis. This approach was aimed at improving the biological understanding of the genetic factors influencing mastitis. Cows (N = 471) were genotyped on the Illumina BovineHD777k beadchip and scored for front and rear teat length, width, end shape, and placement; fore udder attachment; udder cleft; udder depth; rear udder height; and rear udder width. We used principal component analysis to create a single composite measure describing type traits previously linked to high odds of developing mastitis within our cohort of cows. Genome-wide associations were performed, and 28 genomic regions were significantly associated (Bonferroni-corrected p < 0.05). Interrogation of these genomic regions revealed a number of biologically plausible genes whicht may contribute to the development of mastitis and whose functions range from regulating cell proliferation to immune system signaling, including ZNF683, DHX9, CUX1, TNNT1, and SPRY1. Genetic investigation of the risk composite trait implicated a novel locus and candidate genes that have potentially pleiotropic effects related to mastitis.

Keywords: genome-wide association; mastitis; principal component analysis; teat conformation; udder conformation.

Figure 1

Creation of a new mastitis risk trait for genome-wide association (GWA) using principal component (PC) analysis. (A) Loading values for risk PC1 by rear teat width (RTW), rear teat end shape (RTS), fore udder attachment (FUA), and udder height (UH), where cows with higher risk PC1 scores likely have lower mastitis risk. (B) Manhattan plot showing -log₁₀ p-values by chromosome in a linear GWA for risk PC1, with the black line representing the Bonferroni multiple testing correction threshold of 0.05.

Figure 2

Genome-wide association (GWA) for fore udder attachment. Manhattan plot showing -log₁₀ p-values by chromosome in a case–control GWA comparing loose fore udders to tight fore udders (n = 288). The black line represents the Bonferroni multiple testing correction threshold of 0.05.

Figure 3

Genome-wide association (GWA) for udder depth. Manhattan plot showing -log₁₀ p-values by chromosome in (A) a case–control GWA comparing deep (high mastitis risk) versus high udders among the total cohort (N = 458) and (B) a linear GWA with all udder depth scores (deep, intermediate, high) for a primiparous-only subset of cows (n = 144). The black line represents the Bonferroni multiple testing correction threshold of 0.05.

Figure 4

Genome-wide association (GWA) for rear udder height. Manhattan plot showing -log₁₀ p-values by chromosome in a case–control GWA comparing low rear udders to all other udder height classifications (N = 458). The black line represents the Bonferroni multiple testing correction threshold of 0.05.

Figure 5

Genome-wide association (GWA)s for rear teat width. Manhattan plots showing -log₁₀ p-values by chromosome in (A) a case–control GWA for the rear teat width, where cows are divided along the median value, representing extreme differences in morphology, and (B) a linear GWA for the raw measurements of the rear teat width, accounting for continuous variation in the trait. The black line represents the Bonferroni multiple testing correction threshold.

Figure 6

Genome-wide association (GWA) for rear teat end shape. Manhattan plots showing -log₁₀ p-values by chromosome in a case–control GWA comparing flat (high mastitis risk) with pointed (low mastitis risk) rear teat ends. The black line represents the Bonferroni multiple testing correction threshold.