School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand.
INRA, UE Herbipôle, F-63122 Saint-Genès-Champanelle, France.
Genes (Basel). 2021 Mar 23;12(3):456. doi: 10.3390/genes12030456.
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 -values ≤ 1.11 × 10 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 (, , , , , and ) and CPP (, , , , and ) were identified as candidates. Gene ontology revealed six novel candidate genes (, , , , , and ) 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.
本研究旨在利用新西兰放牧、混合品种的奶牛，鉴定与乳脂率（FP）、粗蛋白率（CPP）、尿素浓度（MU）和粗蛋白利用效率（ECPU：乳中粗蛋白产量与日粮粗蛋白摄入量之比）相关的基因组区域。表型数据来自梅西大学的两个牛群的 634 头荷斯坦弗里生牛、泽西牛或杂交牛。其中 490 头奶牛的一部分使用 Bovine Illumina 50K SNP 芯片进行了基因分型。使用两种全基因组关联方法，一种是拟合 490 头牛数据的单基因座模型，另一种是拟合 634 头牛数据的单步贝叶斯 C 模型。单基因座分析使用 SVS 软件包中的 Efficient Mixed-Model Association eXpedited 模型进行。具有全基因组关联值≤1.11×10 的单核苷酸多态性（SNP）被认为是潜在的数量性状基因座（QTL）。贝叶斯 C 分析使用 JWAS 软件包进行，解释遗传变异>0.37%的 1-Mb 基因组窗口中的 SNP 被认为是潜在的 QTL。在单基因座 GWAS 或 1-Mb 窗口中鉴定到的与 SNP 相关的 100kb 内的候选基因，使用基因本体论（GO）进行鉴定，GO 作为 Ensembl 基因组浏览器中的一部分。与 FP（，，，，，和）和 CPP（，，，，和）相关的基因被鉴定为候选基因。GO 揭示了六个与 MU 显著相关的新候选基因（，，，，，和），其功能与蛋白质分解代谢、尿素循环、离子转运和 N 排泄有关。与 ECPU（MAP3K1）相关的一个新候选基因被鉴定出来，MAP3K1 参与蛋白质的转录后修饰。这些发现应该使用更大的新西兰放牧奶牛群体进行验证。
