Identification of genetic effects and potential causal polymorphisms of CPM gene impacting milk fatty acid traits in Chinese Holstein
Identification of genetic effects and potential causal polymorphisms of CPM gene impacting milk fatty acid traits in Chinese Holstein
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中国荷斯坦牛 CPM 基因影响乳脂肪酸性状的遗传效应和潜在因果多态性鉴定
DOI：
10.1111/age.12936
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发表时间：
2020
期刊：
影响因子：
2.4
通讯作者：
B.Han
中科院分区：
文献类型：
--
作者：
L.Shi;L.Liu;X.Lv;Z.Ma;C.Li;Y.Li;F.Zhao;D.Sun;B.Han
我们之前的GWAS发现了与奶牛乳脂肪酸性状相关的83个显著snp和20个有希望的候选基因。其中，羧基肽酶M （CPM）基因包含一个全基因组范围的显著SNP， Hapmap49848‐BTA‐106779，与肉豆汁酸密切相关（C14:0；P= 0.0064）。在此，我们旨在证实cpmon乳脂肪酸在中国荷斯坦奶牛中的遗传效应。通过对pmgene的整个外显子和3000 bp的上下侧翼区序列进行重测序，共检测到7个snp，其中3个位于5 ‘侧翼区，1个位于3 ’ UTR区，3个位于3 '侧翼区。使用Haploview 4.1，我们估计了识别的snp之间的LD，并找到了两个单倍型块。在动物模型中，我们进行了基于SNP和单倍型的关联分析，发现这些SNP和单倍型块主要与中链饱和脂肪酸（己酸，C6:0；辛酸，C8:0；癸酸，C10:0；月桂酸，C12:0）有很强的遗传关联（P< 0.0001-0.0257）。此外，利用Genomatix软件，我们预测cpm的5 '侧翼区域有3个snp (g。45079507A>G、G . 45080228c >A和G . 45080335c >G)改变了PREF（孕酮受体结合位点）、ZBRK1（具有8个中心锌指和一个N端KRAB结构域的转录因子）、SOX9（性别决定区Y - box 9，二聚体结合位点）、SOX6（性别决定区Y - box 6）和FOXP1 - ES （FOXP1的选择性剪接变体，在ESCs中激活）的转录因子结合位点。此外，双荧光素酶报告基因实验显示，这三个snp改变了cpmgene的转录活性（P≤0.0006）。总之，利用GWAS后策略，我们首先证实了cpm对奶牛乳脂肪酸的显著遗传效应，并确定了三种潜在的因果突变。
Our previous GWAS revealed 83 significant SNPs and 20 promising candidate genes associated with milk fatty acid traits in dairy cattle. Out of them, the carboxypeptidase M (CPM) gene contains a genome‐wide significant SNP, Hapmap49848‐BTA‐106779, which is strongly associated with myristic acid (C14:0;P= 0.0064). Herein, we aimed to confirm the genetic effects ofCPMon milk fatty acids in Chinese Holstein. Seven SNPs were detected by re‐sequencing the sequences of entire exons and 3000 bp of up‐/downstream flanking regions of theCPMgene, of which three were in 5′ flanking region, one in the 3′ UTR and three were in the 3′ flanking region. Using the Haploview 4.1, we estimated the LD among the identified SNPs and found two haplotype blocks. With the animal model, we performed the SNP‐ and haplotype‐based association analyses, and observed that these SNPs and haplotype blocks mainly had strong genetic associations with medium‐chain saturated fatty acids (caproic acid, C6:0; caprylic acid, C8:0; capric acid, C10:0; and lauric acid, C12:0) (P< 0.0001–0.0257). In addition, using the Genomatix software, we predicted that three SNPs in the 5′ flanking region ofCPM(g.45079507A>G, g.45080228C>A and g.45080335C>G) changed the transcription factor binding sites for PREF (progesterone receptor biding site), ZBRK1 (transcription factor with eight central zinc fingers and an N‐terminal KRAB domain), SOX9 (sex‐determining region Y‐box 9, dimeric binding sites), SOX6 (sex‐determining region Y‐box 6) and FOXP1‐ES (alternative splicing variant of FOXP1, activated in ESCs). Further, the dual‐luciferase reporter assay showed these three SNPs altered the transcriptional activity ofCPMgene (P≤ 0.0006). In summary, using the post‐GWAS strategy, we first confirmed the significant genetic effects ofCPMwith milk fatty acids in dairy cattle, and identified three potential causal mutations.