Abstract
In this study, genome-wide association study (GWAS) was conducted for identifying significantly associated genomic regions/SNPs with milk protein and minerals in the 96 taurine-indicine crossbred (Vrindavani) cows using 50K SNP Chip. After quality control, a total of 41,427 SNPs were retained and were further analyzed using a single-SNP additive linear model. Lactation stage, parity, test day milk yield and proportion of exotic inheritance were included as fixed effects in GWAS model. Across all traits, 13 genome-wide significant (p < 1.20 x 10−06) and 49 suggestive significant (p < 2.41 x 10−05) SNPs were identified which were located on 18 different autosomes. The strongest association for protein percentage, calcium (Ca), phosphorus (P), copper (Cu), zinc (Zn), and iron (Fe) were found on BTA 18, 7, 2, 3, 14, and 2, respectively. No significant SNP was detected for manganese (Mn). Several significant SNPs identified were within or close proximity to CDH13, BHLHE40, EDIL3, HAPLN1, INHBB, USP24, ZFAT, and IKZF2 gene, respectively. Enrichment analysis of the identified candidate genes elucidated biological processes, cellular components, and molecular functions involved in metal ion binding, ion transportation, transmembrane protein, and signaling pathways. This study provided a groundwork to characterize the molecular mechanism for the phenotypic variation in milk protein percentage and minerals in crossbred cattle. Further work is required on a larger sample size with fine mapping of identified QTL to validate potential candidate regions.
Highlights
Calcium has been reported to play an important role in reducing cholesterol absorption, and in regulating blood pressure in humans [5]
The aim of this study was to identify genomic regions associated with milk protein percentage (%) and milk minerals including Ca, P, Cu, Zn, Fe, and Mn in Vrindavani cattle, a tropically adapted composite crossbred breed of dairy cattle of India
Four significant SNPs found on BTA18 (7.6399.15Mb) includes Beta-carotene oxygenase 1(BCO1), C-Maf inducing protein (CMIP), N-terminal EF-hand calcium binding protein 2 (NECAB2), Cadherin 13 (CDH13), oxidative stress induced growth inhibitor 1 (OSGIN1) and Solute carrier family 38 member 8 (SLC38A8) genes
Summary
Milk and dairy products are considered a nutrient-rich diet, consisting of fat, protein, lactose along with several essential micronutrients including vitamins and minerals. The minerals in milk are present either as an inorganic ion (soluble phase) or form colloidal complexes with organic matter such as proteins, carbohydrates, and ligands including amino acids and citrates [2, 3]. Calcium has been reported to play an important role in reducing cholesterol absorption, and in regulating blood pressure in humans [5]. The zinc, manganese, iron, and copper are important components of several enzymes and play role in the immune system [6]. These elements serve as catalysts for many biochemical processes such as muscle contraction, nervous transmission, and nutrient absorption [7]
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