Genomic insights into the admixture and diversity of Kerala crossbred cattle

The crossbred cattle population of Kerala, primarily consisting of the Sunandini breed, was developed through systematic crossbreeding of indigenous cattle with exotic breeds (Brown Swiss, Jersey, and Holstein Friesian) to enhance milk production. This study aimed to assess the genetic diversity, population structure, and admixture proportions in this population using medium-density SNP genotyping (50 K array) on 2,273 genotyped animals. The study revealed an observed heterozygosity (Ho) of 0.34 ± 0.14 and expected heterozygosity (He) of 0.35 ± 0.14, indicating substantial genetic diversity. Linkage disequilibrium (LD) decayed rapidly with increasing inter-marker distance, averaging r2 = 0.26 at 0–10 kb and dropping to 0.05 at 200–500 kb, suggesting moderate LD levels suitable for genomic selection. The effective population size (Ne) was estimated at 216 one generation ago, indicating a low risk of immediate inbreeding. The genomic inbreeding estimates (FROH) revealed the presence of ancient inbreeding, with the prevalence of short ROH segments (1–8 Mb). Admixture analysis confirmed that the Kerala crossbred population consists of 37% Holstein Friesian, 31% Brown Swiss, 13% Jersey, and 19% indigenous gene pools, aligning with state breeding policies that promote high exotic inheritance in commercial herds. These findings underscore the success of crossbreeding in enhancing productivity while preserving genetic diversity. However, increasing exotic ancestry may affect adaptability to tropical conditions. Future breeding strategies should balance production and adaptation traits while monitoring inbreeding through genomic tools. This study provides crucial insights for optimizing breeding programs and sustaining genetic progress in the tropical crossbred dairy cattle population.