Abstract
The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.
Highlights
Milk fat and protein play a vital role in New Zealand’s milk payment scheme [1], no attention is currently given to environmental traits such as nitrogen excretion
Efficiency of protein utilization can be defined in several ways [4]; (1) efficiency of crude protein utilization (ECPU): the ratio of crude milk protein yield (CPY) to dietary crude protein intake (CPI); (2) the crude protein balance (CPB): the difference between CPI and CPY, or (3) the residual protein intake (RPI): the difference between actual CPI and predicted CPI
Beatson et al [8] analyzed cows from 540 herds located throughout New Zealand for four lactations, their milk urea (MU) predictions should be a better representative of average MU in New Zealand dairy cows than our predictions based on 634 cows on just two farms at Massey University
Summary
Milk fat and protein play a vital role in New Zealand’s milk payment scheme [1], no attention is currently given to environmental traits such as nitrogen excretion. Protein utilization efficiency, measured as the proportion of dietary protein that is converted to protein in milk or protein in muscles, is influenced by gut microbes and is highly sensitive to the ratio of protein and fermentable energy in the diet [2]. If the diet is high in protein and relatively deficient in energy, such as most fresh pasture, surplus dietary protein results in the production of ammonia in the rumen and this is converted to urea in the liver where it circulates in the blood supply. Urea in the blood is processed through the kidneys into the bladder excreted in urine or diffused into the mammary gland as a component of milk. The most widely used measure of protein efficiency is ECPU [4,5,6]
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