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Genome-wide association studies (GWAS) offer potential for discovering genomic regions that can be exploited to increase milk production. However, available GWAS and single nucleotide polymorphism (SNP) datasets are heavily skewed towards taurine breeds, which restricts their utility for genomic research in indicine cattle breeds. This study conducts a GWAS on the Badri breed of Indicine cattle to estimate variance components and identify significant variants associated with milk composition traits, utilizing double digest restriction-site associated DNA (ddRAD) sequencing data. A total of 65,483 high-confidence SNPs were identified and utilized to conduct GWAS on various milk composition traits, including fat percent (FP), protein percent (PP), casein percent (CP), lactose percent (LP), glucose percent (GP), galactose percent (GLP), total solids percent (TS), and solids-not-fat percent (SNF), each analysed separately. The heritability estimates for the studied milk composition traits were 0.386 for fat percent (FP), 0.427 for protein percent (PP), 0.469 for casein percent (CP), 0.567 for lactose percent (LP), 0.547 for glucose percent (GP), 0.590 for galactose percent (GLP), 0.437 for total solids percent (TS), and 0.476 for solids-not-fat percent (SNF). Several genomic regions and candidate genes, including SLC9A9, LPP, C2H2orf76, LGSN, HMGCS2, Bv1, SCYL2, PLAC8, SRGAP2, CR2, ZNF787, OTUB2, DSC2, SYNPO2, and CTNNA3 which may have a potential role in regulating milk production in indicine cattle were identified. The high confidence SNPs and candidate genes will be an important inclusion into commercial genotyping arrays for the early and best selection of breeding animals for desired milk composition and improved production.
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