Sustainable cattle breeding through the genomic diversity index

In animal breeding, the balance between genetic gain and diversity is critical, as accelerated progress can erode variability, increase inbreeding, and heighten the risk of genetic load. We present the Genomic Diversity Index (GDI), a composite measure that quantifies an individual's contribution to population genetic diversity. The GDI integrates three complementary components: (i) inbreeding coefficient based on runs of homozygosity longer than 16 Mb (F_ROH>16Mb), reflecting the detrimental genetic load; (ii) average genomic relatedness, promoting the maintenance of overall diversity; and (iii) the individual's impact on the frequency of rare alleles. Using simulations in Holstein cattle, we compared conventional genomic selection with two strategies that incorporated GDI into sire selection. Compared with conventional genomic selection, both GDI strategies improved all major indicators of genetic diversity. Specifically, genomic inbreeding decreased for F_ROH>16Mb (0.042 vs 0.023) and F_ROH>8Mb (0.095 vs 0.051 and 0.049). Effective population size increased from 99 to over 150 when estimated from linkage disequilibrium and from 96 to approximately 300 when estimated from the rate of inbreeding. The number of monomorphic markers fell by about 35%, and heterozygosity remained higher. Additive genetic variance for production traits increased by up to 19%, with only a small reduction in genetic gain (≤ 7%). Overall, the GDI promoted diversity retention while maintaining selection efficiency. By integrating multiple genomic diversity metrics into a single, interpretable index, GDI provides a practical and easily comprehensible tool for balancing short-term progress with long-term sustainability in both commercial and conservation livestock breeding programmes.