Genome-wide scan for SNPs and selective sweeps reveals candidate genes and QTLs for milk production and reproduction traits in Indian Kankrej cattle.

Genome-wide identification and annotation of SNPs and selective sweeps was done in Kankrej cattle using the ddRAD sequencing method. Identified 1,983,581 SNPs and nearly half (48.81%) of the effects were found in intron region. Around 624 SNPs annotated in 215 candidate genes were associated with various milk production and reproduction traits. The degree of heterozygosity as 0.2907 against expected heterozygosity of 0.3216. Identified 300 candidate selective sweeps and functional profiling of genes in selective sweep regions resulted with 20 significant (adj p < 0.05) functions. Functional annotation revealed 53.2% of QTLs for milk association while 15.33% for production association, 10.68% for reproduction association, and 8.4% for exterior association. The functional enrichment analysis revealed the presence of significant QTLs in 14 chromosomes. The QTL for milk protein percentage was identified as the top most significant milk type along with the milk potassium content, milk casein percentage, milk yield, milk fat yield, etc. The interval to first estrus after calving, age at puberty, calving interval, conception rate, and birth index were some of the significant QTLs identified for reproduction traits. Genes related to keratinization indicated the selection signature in relation to environmental stressors contributing to adaptation of animals to tropical climatic condition.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04263-z.