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Fill a medium bowl with ice water. Add the sliced fennel and apple and let sit until crisp, about 10 minutes. Drain well and pat dry. In a medium bowl, toss the fennel and apple with 1 teaspoon of the lemon juice.
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Meanwhile, in a small bowl, mix the crème fraîche with the skyr, horseradish, sugar and the remaining 2 teaspoons of lemon juice. Season the horseradish crème with salt.
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Spread butter on the rye bread and arrange the smoked salmon on top. Dollop the horseradish crème on the salmon, then top with the fennel-apple salad. Garnish with dill and sprinkle with flaky sea salt; serve.
Make Ahead
The horseradish crème can be refrigerated overnight.