Milk Nitrogen Genes Shift Across Lactation in Holstein Cows

Milk nitrogen traits in Holstein cows carry a genetic signature that changes shape as lactation progresses, according to a large-scale analysis of more than three-quarters of a million test-day records. The study, published in BMC Genomics, examined three traits that serve as proxy phenotypes for nitrogen metabolism and partitioning in dairy cattle: milk urea nitrogen, known as MUN; milk urea nitrogen yield, or MUNY; and an estimated milk true protein nitrogen measure corrected for urea, abbreviated MTPN. Researchers led by Hao Zhu, Yu Zhou, Jianing Diao, Xubin Lu and Zhangping Yang analyzed 759,955 test-day records from 59,122 cows, of which 6,461 animals had genotype data available for genomic analyses.

The first key finding concerns how parity shapes the phenotypic picture. After adjustment in linear mixed models, primiparous cows showed higher adjusted MUN levels, whereas multiparous cows recorded higher MUNY and MTPN values. The adjusted phenotypic differences between parity groups indicate that milk nitrogen trait levels differ systematically between first-lactation animals and older, repeatedly lactating cows. Because milk nitrogen traits are useful proxy phenotypes for characterizing nitrogen metabolism and partitioning in dairy cows, these parity-linked phenotypic differences are relevant to studies of nitrogen metabolism in animals of different ages.

Heritability, the fraction of phenotypic variation attributable to genetics, proved to be anything but static. MUN heritability ranged from approximately 0.06 to 0.13. MUNY heritability spanned 0.08 to 0.15 in primiparous cows and 0.09 to 0.13 in multiparous cows. MTPN showed a distinctive trajectory: its heritability generally increased during mid-to-late lactation, reaching maxima of roughly 0.16 in primiparous animals and 0.22 in multiparous ones. The daily heritability estimates varied across lactation stages and between parity groups.

Genetic and permanent environmental correlations followed a consistent spatial pattern along the lactation timeline. Both types of correlation were generally highest between adjacent test days and declined as the test-day interval increased. The genetic and permanent environmental correlations were generally highest between adjacent test days and declined as the test-day interval increased. These correlation patterns show that the estimated genetic relationships among test days changed with the test-day interval across lactation.

The genomic search then moved to the DNA level. Both GWAS approaches identified bovine chromosome 14, BTA14, as a major associated region for MUN and MTPN in the two parity-group analyses. Notably, no genome-wide significant SNPs were detected for MUNY. Candidate genes located within 200 kilobases of significant SNPs were then subjected to functional enrichment analysis, which highlighted different biological categories in the two parity groups, a further sign that the genetic underpinnings of milk nitrogen traits are not identical across parities.

The TWAS identified associations involving DGAT1, EXOSC4, FBXL6, CCDC166, and LYNX1 in multiple tissues, traits, or parity-group analyses.

The TWAS results named a short list of candidate genes with associations spanning multiple tissues, traits or parity-group analyses: DGAT1, EXOSC4, FBXL6, CCDC166 and LYNX1. DGAT1 was among the genes identified in the TWAS associations. The TWAS associations involving these genes spanned multiple tissues, traits, or parity-group analyses.

The study’s authors conclude that milk nitrogen traits exhibit phenotypic differences between parity groups and show lactation stage-dependent genetic architectures. They position these results as a basis for further validation of the genomic regions and candidate genes associated with milk nitrogen traits. The authors state that these results provide a basis for further validation of the genomic regions and candidate genes associated with milk nitrogen traits.

The scale of the dataset lends weight to these conclusions. The analysis included 759,955 test-day records from 59,122 cows, of which 6,461 had genotype data, and used imputed sequence-level variants in the GWAS. The study is published as an open-access article in BMC Genomics. The authors conclude that milk nitrogen traits exhibit phenotypic differences between parity groups and show lactation stage-dependent genetic architectures.

Subject of Research: Genetic architecture and genome-wide association analysis of milk urea nitrogen and protein nitrogen traits in primiparous and multiparous Holstein cows

Article Title: Dynamic genetic architecture and integrative association analysis of milk nitrogen traits in primiparous and multiparous Holstein cows

Article References: Zhu, H., Zhou, Y., Diao, J., Lu, X., & Yang, Z. (2026). Dynamic genetic architecture and integrative association analysis of milk nitrogen traits in primiparous and multiparous Holstein cows. BMC Genomics. https://doi.org/10.1186/s12864-026-13515-y

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13515-y

Keywords: Holstein cows, milk urea nitrogen, MUNY, MTPN, GWAS, TWAS, heritability, lactation, parity, BTA14, DGAT1, dairy genomics