Adoption of Genomic Tools for Genetic Improvement in Smallholder Dairy Cattle and Buffalo

The adoption of genomic selection has immense potential to transform genetic improvement in smallholder dairy systems, which are often challenged by the absence of pedigree records, small herd sizes, and high environmental variability. This case study outlines how BAIF developed and implemented a comprehensive genetics program tailored for such systems. A robust digital data collection platform was established, reducing data loss and improving phenotypic and genotypic accuracy. Standardised protocols guided data recording and biological sampling, supported by a strong monitoring system for quality control. To overcome limitations of commercial SNP arrays, BAIF collaborated with national institutes to develop customised SNP chips for cattle (“Gau”) and buffalo (“Mahish”), enabling genomic evaluation across diverse populations. Along with production traits, farmer-relevant traits such as milk temperament and panting score were recorded at scale, with panting score emerging as an indicator of heat stress resilience. Genomic evaluations incorporated breed composition and genotype-by-environment interactions, offering accurate selection criteria. Multi-trait genomic selection integrating production and adaptive traits supports sustainable breeding goals. Genomic breeding values (GBVs) are gradually replacing dam-yield records for early selection and culling, accelerating genetic progress. The outcomes include a valuable reference population for cattle and buffalo, which is now part of India’s national genomic consortia for climate-resilient, farmer-focused breeding.