Abstract
Composite crosses result from the mating of two or more distinct cattle breeds. Breeding performance may improve rapidly using a well-organized composite breeding system and a clear selection index. The KiwiCross(®) is a popular composite cross in New Zealand, combining Holstein-Friesian (high milk production) and Jersey (high milk fat). Production efficiency (PR), a key selection index, is calculated by dividing milk solids produced by mature live weight. Over decades of genetic improvement, KiwiCross(®) increased milk production significantly. We hypothesized that certain genomic regions from Holstein-Friesian or Jersey breeds were preserved due to artificial selection based on PR. Analysis of genomic regions using XP-EHH, hapFLK, and ROH haplotype statistics revealed selection signatures on BTA 7 and 20 in both high- and low-performance animals, with distinct regions linked to Holstein-Friesian and Jersey ancestry. Our findings suggest that selection acted on different genomic regions across generations and that preserving key ancestry-specific haplotypes is crucial for maintaining performance in composite breeds. Breeders must recognize that selection for specific traits can alter allele frequencies and lead to the loss of beneficial breed-specific haplotypes over time.