TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium.
TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-65186 Shiraz, Iran.
J Dairy Sci. 2023 May;106(5):3397-3410. doi: 10.3168/jds.2022-22351. Epub 2023 Mar 7.
The aims of this study were (1) to identify genomic regions associated with a N efficiency index (NEI) and its composition traits and (2) to analyze the functional annotation of identified genomic regions. The NEI included N intake (NINT1), milk true protein N (MTPN1), milk urea N yield (MUNY1) in primiparous cattle, and N intake (NINT2+), milk true protein N (MTPN2+), and milk urea N yield (MUNY2+) in multiparous cattle (2 to 5 parities). The edited data included 1,043,171 records on 342,847 cows distributed in 1,931 herds. The pedigree consisted of 505,125 animals (17,797 males). Data of 565,049 SNPs were available for 6,998 animals included in the pedigree (5,251 females and 1,747 males). The SNP effects were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of about 240 kb) was calculated. The top 3 genomic regions explaining the largest rate of the total additive genetic variance of the NEI and its composition traits were selected for candidate gene identification and quantitative trait loci (QTL) annotation. The selected genomic regions explained from 0.17% (MTPN2+) to 0.58% (NEI) of the total additive genetic variance. The largest explanatory genomic regions of NEI, NINT1, NINT2+, MTPN1, MTPN2+, MUNY1, and MUNY2+ were Bos taurus autosome 14 (1.52-2.09 Mb), 26 (9.24-9.66 Mb), 16 (75.41-75.51 Mb), 6 (8.73-88.92 Mb), 6 (8.73-88.92 Mb), 11 (103.26-103.41 Mb), 11 (103.26-103.41 Mb). Based on the literature, gene ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction, 16 key candidate genes were identified for NEI and its composition traits, which are mainly expressed in the milk cell, mammary, and liver tissues. The number of enriched QTL related to NEI, NINT1, NINT2+, MTPN1, and MTPN2+ were 41, 6, 4, 11, 36, 32, and 32, respectively, and most of them were related to the milk, health, and production classes. In conclusion, this study identified genomic regions associated with NEI and its composition traits, and identified key candidate genes describing the genetic mechanisms of N use efficiency-related traits. Furthermore, the NEI reflects not only its composition traits but also the interactions among them.
(1) 确定与氮效率指数 (NEI) 及其组成性状相关的基因组区域；(2) 分析鉴定基因组区域的功能注释。NEI 包括初产牛的氮摄入量 (NINT1)、乳真蛋白氮 (MTPN1)、乳尿素氮产量 (MUNY1)，以及经产牛的氮摄入量 (NINT2+)、乳真蛋白氮 (MTPN2+) 和乳尿素氮产量 (MUNY2+) (2-5 胎次)。编辑后的数据包括 342847 头奶牛的 1043171 条记录，分布在 1931 个牛群中。系谱由 505125 头动物（17797 头雄性）组成。在包含在系谱中的 6998 头动物（5251 头雌性和 1747 头雄性）中，有 565049 个 SNP 的数据可用。使用单步基因组 BLUP 方法估计 SNP 效应。计算了由 50 个连续 SNP（平均大小约为 240 kb）组成的窗口解释的总加性遗传方差的比例。选择解释 NEI 及其组成性状总加性遗传方差最大的前 3 个基因组区域，用于候选基因鉴定和数量性状位点 (QTL) 注释。所选基因组区域解释了 NEI、NINT1、NINT2+、MTPN1、MTPN2+、MUNY1 和 MUNY2+ 总加性遗传方差的 0.17%（MTPN2+）至 0.58%（NEI）。NEI、NINT1、NINT2+、MTPN1、MTPN2+、MUNY1 和 MUNY2+ 的最大解释基因组区域分别为牛 Taurus 染色体 14（1.52-2.09 Mb）、26（9.24-9.66 Mb）、16（75.41-75.51 Mb）、6（8.73-88.92 Mb）、6（8.73-88.92 Mb）、11（103.26-103.41 Mb）、11（103.26-103.41 Mb）。基于文献、基因本体论、京都基因与基因组百科全书和蛋白质-蛋白质相互作用，确定了与 NEI 和其组成性状相关的 16 个关键候选基因，这些基因主要在乳细胞、乳腺和肝脏组织中表达。与 NEI、NINT1、NINT2+、MTPN1 和 MTPN2+相关的丰富 QTL 数量分别为 41、6、4、11、36、32 和 32，其中大多数与牛奶、健康和生产类相关。总之，本研究确定了与 NEI 及其组成性状相关的基因组区域，并鉴定了描述与氮利用效率相关性状遗传机制的关键候选基因。此外，NEI 不仅反映了其组成性状，还反映了它们之间的相互作用。
