Genome Study Pinpoints DNA Regions Tied to Milk Quality in Indian Crossbred Cattle

Researchers have mapped stretches of DNA linked to milk yield, milk composition and fatty acid traits in Holstein Friesian crossbred cattle in India, identifying 36 SNPs across multiple chromosomes, including one statistically significant marker and 35 suggestive ones.

The genome-wide association study, published in Molecular Biology Reports, genotyped 128 crossbred animals using 53,218 SNPs, of which 44,128 passed quality control for the analysis. The work was carried out by Ashish Yadav, Richa Singh, Kashif Dawood Khan, Rani Alex, G. R. Gowane and colleagues.

Phenotypic evaluation of the herd showed moderate variation in test-day milk yield and milk composition traits. Fatty acid profiling revealed a predominance of long-chain fatty acids, particularly palmitic and oleic acids, in the milk of these animals.

Among the markers detected, one pleiotropic SNP, ARS-BFGL-NGS-96359 on Bos Taurus autosome 24, was associated with lactose, protein and solids-not-fat percentages simultaneously, suggesting a single genetic variant may influence several aspects of milk composition at once.

Several SNPs were associated with short-, medium- and long-chain saturated fatty acids, with both positive and negative allelic effects. Notable effect sizes were observed for oleic acid (C18:1cis) and for desaturase indices, particularly DI C17, an indicator related to fatty acid desaturation activity.

Positional candidate gene analysis in the associated regions identified HACL1, SGPP2, IMMP2L, MYO5B, ZNF536, GADD45A, PRDM9 and PROKR2, genes involved in lipid metabolism and cellular regulation, offering clues to the biological pathways underlying milk quality traits.

Individual SNPs explained between 0.087 and 0.194 of the phenotypic variance, with several loci contributing substantially to milk composition traits and to the fatty acids C4, C10 and C15, according to the study’s results.

The authors conclude that the findings highlight the polygenic nature of milk production and quality traits in these crossbred cattle, meaning many genes each contribute small effects rather than a few genes dominating the traits.

The team describes the results as preliminary insights into the genetic architecture of milk quality traits, which may contribute to future genomic selection efforts only after validation in larger and independent populations.

Crossbred cattle play a pivotal role in India’s milk production, and the study’s stated aim was to identify genomic regions and candidate genes associated with milk yield, milk composition, fatty acid profile and desaturase indices in Holstein Friesian crossbred cattle.

Subject of Research: Genomic regions associated with milk composition and fatty acid traits in Indian Holstein Friesian crossbred cattle

Article Title: Genome-wide association study identifies genomic regions associated with milk composition and fatty acid traits in Indian Holstein Friesian crossbred cattle

Article References: Yadav, A., Singh, R., Khan, K. D., Alex, R., & Gowane, G. R. (2026). Genome-wide association study identifies genomic regions associated with milk composition and fatty acid traits in Indian Holstein Friesian crossbred cattle. Molecular Biology Reports, 53(1), 1835. https://doi.org/10.1007/s11033-026-13071-4

Image Credits: AI Generated

DOI: 10.1007/s11033-026-13071-4

Keywords: GWAS, Holstein Friesian crossbred cattle, milk composition, fatty acids, SNPs, desaturase indices, candidate genes, lipid metabolism, genomic selection, India, Genome-wide, association