Landscape and bioclimatic diversity of milk protein variability in tropical goats

•The relationship between geographical coordinates, climatic variables, milk composition traits and milk-protein genotypes in 17 breeds/genotypes of different agro-climatic zones was analyzed.•The lowest coefficient of inbreeding was found at the BLG locus (-0.25) and highest at CSN1S2 locus (0.74).•Haplotype A-A-A-A and B-A-A-A were observed to exhibit highest frequency in all the population indicating the evolutionary significance.•The latitude effect was significant (P < 0.05) on milk protein diversity. Bioclimatic variables Temp_seas and Temp_iso were significantly associated with diversity.•This study provides useful indication for the selection of the animals based on adaptive and functional diversity in milk protein complex.