Comparing subpopulations of plasma progesterone using cluster analyses

The production of progesterone during the luteal phase of the estrous cycle regulates early embryonic development, uterine function, and luteal function. Plasma progesterone concentrations were measured during a spontaneous estrous cycle in lactating Holstein-Friesian cows of New Zealand or North American ancestry, fed either fresh pasture or a total mixed ration. Subpopulations of profiles were identified using 2 approaches: 1) shape-based clustering and 2) trait-based clustering. Subpopulations of profiles were compared using key progesterone profile components, which described the early and late luteal phase of the estrous cycle. The application of resistant nonlinear smoothing functions across raw progesterone profiles resulted in a high degree of agreement between the raw data and smoothed estimates (R(2) = 0.93). Both clustering techniques resulted in the identification of 3 similar subpopulations of progesterone profiles. The distribution of animals in these defined subpopulations and the association with cow strain and diet were examined. The early luteal phase was similar for the shape-based categories, but differed in the trait-based analyses. Differences in the late luteal phase and the onset of functional luteal regression in the different clusters were evident for both the shape- and trait-based analyses. The distribution of animals across the subpopulations identified by shape-based clustering was not associated with either cow strain or diet. However, within the 3 subpopulations identified using trait-based clustering, cow strain affected the shape of the progesterone profile. Isolation of 3 subpopulations within a small data set showed that otherwise normal progesterone profiles exhibit significant variation. The differences in the luteal phase of these subpopulations, in particular progesterone early in the luteal phase and the early onset of functional luteal regression, may provide an insight into factors associated with subfertility.