多基因标记辅助选择及Lbx基因家族的分子生物学研究
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摘要
随着分子数量遗传学及其相关学科的发展,有关动物遗传标记辅助选择方面的研究也在不断深入。在过去的研究中,已发现黑素皮质素受体4 (Melanocortin-4 Receptor, MC4R),心脏型脂肪酸结合蛋白(Heart FABP, H-FABP),瘦素(Leptin, LEP),氟烷基因(Halothane, HAL),钙蛋白酶抑制蛋白(calpastatin, CAST)和肌细胞生成素(myogenin, MyoG)等基因与胴体、肉质性状相关。我们通过PCR-RFLP分析了以上基因在DIv2系(中国瘦肉猪新品系)和7个纯种猪中的多态性分布,并在DIV2系中进行了遗传效益分析,同时研究了多基因标记同时选择的可能性。在脊椎动物中,Lbx基因(Ladybird-like genes)家族对于肌肉形成和神经发育起着重要作用。本研究对猪Lbx1和Lbx2基因进行了分离和遗传效应分析。作为重要的表观遗传学现象之一,DNA甲基化对基因的表达发挥重要的调控功能。因此,我们在肌肉组织中研究了Lbx1和Lbx2基因表达和甲基化之间的关系。并通过诱导分化C2C12细胞,研究DNA甲基化对MyoD (myogenic differentiation 1), Myf5 (myogenic factor 5), Pax 7 (paired box 7)和Lbx1基因表达的影响。主要试验结果如下：
1通过PCR-RFLP分析了MC4R, H-FABP, LEP, HAL, CAST和MyoG基因多态位点在DIv2系和7个纯种猪中的分布,并在DIV2系中进行了遗传效应分析,结果表明：(1)MC4R基因中的TaqⅠ酶切位点与平均背膘厚、瘦肉率显著相关(P<0.05)；(2)LEP基因中的HinfⅠ酶切位点,BB基因个体的曰增重极显著高于AA基因型个体(P<0.01),AB基因个体的日增重显著高于AA基因型个体(P<0.05)；(3)H-FABP基因第二内含子的HaeⅢ酶切位点,DD基因型个体的瘦肉率显著高于dd基因型个体(P<0.05)；(4)在CAST基因MspⅠ位点中,EE基因型个体的日增重显著高于FF基因型个体(P<0.05),EF基因型个体的日增重极显著高于FF基因型个体(P<0.01)。
2连锁不平衡分析显示：在DIv2系、大白猪、长白猪和八眉猪中,MC4R和LEP基因位点间、LEP和H-FABP基因位点间的连锁不平衡度不显著(P>0.05)；在DIv2系、大白猪、长白猪、皮特兰猪和八眉猪中,MC4R与H-FABP基因位点间的连锁不平衡度不显著(P>0.05)。这表明两个位点间是独立的,因此对其中一个位点的选择不会影响另一个位点的等位基因频率。
3采用电子克隆方法获得了两个候选基因的编码区序列：(1) Lbx1, mRNA中的CDS全长846bp,编码281个氨基酸；(2) Lbx2, mRNA中的CDS全长591bp,编码196个氨基酸。通过比较不同物种氨基酸序列,对以上两个基因进行了系统进化树分析,发现猪Lbxl与牛、小鼠、人、犬、类人猿进化关系较近,猪Lbx2与牛、猩猩、犬进化关系较近。
4 RT-PCR分析显示：猪Lbx1基因在肌肉组织中高表达；Lbx2基因在肝、肾和脾中微弱表达,但在肌肉组织中不表达。在出生后肌肉发育过程中,Lbx1基因的表达处于动态变化中,一月龄之内,表达量相对较高,在二月龄时,表达量显著下调,该变化趋势与产后肌肉组织中肌卫星细胞分化比例的变化一致,由于Lbx1基因已被证实在肌卫星细胞分化初期表达,因此我们推测该基因可能与出生后肌肉增生机制有关。在不同肌肉组织中的分析表明：猪Lbx1基因在股二头肌中的表达量显著高于在咬肌,背最长肌和半腱肌中的表达量,推测Lbx1基因的表达量与肌纤维类型并无直接关系。
5通过亚硫酸盐测序技术,在猪背最长肌中分析Lbx1和Lbx2基因启动子和外显子l的甲基化状态。发现：(1) Lbx1基因的甲基化差异区在外显子1处的CpG岛内；(2) Lbx2基因的甲基化差异区在CpG岛外的启动子区。Lbx1基因CpG岛内的高密度甲基化可能参与下调该基因在背最长肌中的表达量。
6通过对猪Lbx1基因组SNP扫描,发现2个引起酶切位点改变的SNP: g.752A>G和g.-1559C>G。在大白╳梅山F2代资源家系中进行性状关联分析发现,Lbx1基因g.752A>G突变与眼肌面积和内脂率显著相关(P<0.05),该突变位于内含子,并不影响蛋白结构,因此该相关可能是由于g.752A>G突变与真正的功能突变处于连锁不平衡状态造成的。
7 RT-PCR分析显示：MyoD和Myf5基因在未分化及分化的C2C12细胞中均表达,MyoG基因在成肌分化后期表达,另外,在C2C12细胞分化过程中始终检测到Pax7基因微弱表达。Lbx1基因在C2C12细胞中不表达。通过亚硫酸盐测序发现,在C2C12细胞成肌分化过程中MyoD, Myf5, Pax7和Lbx1基因外显子1或启动子区的甲基化密度处于动态变化中,推测这种变化影响其mRNA表达变化。
With the development of molecular and quantitative genetics and its related subjects, it made a great progress on the research about animal genetic marker assisted selection (MAS). We have known that polymorphism of MC4R (Melanocortin-4 Receptor), H-FABP (Heart FABP), LEP (Leptin), HAL (Halothane), CAST (calpastatin) and MyoG (myogenin) genes associated relation with meat quality in recent research. PCR-RFLP was used to analyze these polymorphisms in a swine breed composite (DIV2) and 7 swine breeds. The implications of the allelic distribution of these genes for meat production, and applicability of molecular markers in pig breeding were discussed. In all animals investigated so far, both the protostome genes and the vertebrate Lbx genes (Ladybird-like genes) were found to play crucial roles in muscle and neural development. As candidate genes of animal growth and meat quality, the porcine Lbx1 and Lbx2 were cloned and identified and genetics effect were analyzed. DNA methylation is an important epigenetic system. It plays many crucial roles in the gene regulation. In this study we investigated whether DNA methylation regulates the expression of the Lbx1 and Lbx2 genes in porcine skeletal muscle. In addition, we analyzed the DNA methylation pattern of four genes (MyoD, Myf5, Pax7 and Lbx1) in myogenic differentiation in C2C12 cells. The results are summarized as follows:
1 PCR-RFLP was used to analyze the polymorphisms of MC4R, LEP, H-FABP, HAL, CAST, MyoG genes in a swine breed composite (DIV2) and 7 swine breeds. The association study of these polymorphisms with several economic traits was carried out on a DIV2 population. The results obtained showed that MC4R/TaqI genotype had an effect for average backfat thickness (P<0.05) and lean meat percentage (P<0.05); At locus LEP/HinfI animals of AA genotype had lower test daily gain than that of BB (P<0.01) or AB genotype (P<0.05); At the H-FABP/HaeⅢlocus lean meat percentage of the individuals with genotype DD were higher than that with genotype dd (P<0.05); At locus CAST/MspI animals of FF genotype had lower test daily gain than that of EF(P<0.01) or EE genotype (P<0.05).
2 Linkage disequilibrium analysis among MC4R, LEP and H-FABP revealed that these genes were independent. Therefore, exerting selection pressure on one locus should not influence the allelic frequencies of the other locus. This represented two or more genes that could be combined together within one genotype in order to facilitate breeding for objective traits.
3 We obtained the full coding region of the 2 genes with electronic cloning technology. (1) The cDNA sequence of porcine Lbx1 contains an ORF of 846 bp encoding a protein of 281 residues. (2) The cDNA sequence of porcine Lbx2 contains an ORF of 591 bp encoding a protein of 196 residues. Phylogenetic trees were constructed by aligning the amino acid sequences of different species. The porcine protein sequence of Lbx1 has high sequence similarity with Bos taurus, Mus musculus, Homo sapiens, Canis familiaris, Pan troglodytes than with other species, and the porcine protein sequence of Lbx2 has high sequence similarity with Bos taurus, Pongo abelii, Canis familiaris than with other species.
4 RT-PCR analyses showed that Lbx1 was highly expressed in porcine skeletal muscle tissues, Lbx2 was lowly expressed in liver, kidney and spleen. And we provide the first evidence that Lbx1 has a certain regulated expression pattern during the postnatal period of the porcine skeletal muscle development. The percentage of differentiating satellite cells was highest in 1-week-old pigs and significantly decreased in 7-week-old pigs. It is very interesting that the expression of the porcine Lbx1 gene in skeletal muscle shows the same trend of a higher expression in early postnatal porcine growth. Therefore, we deduce that Lbx1 gene may have a relationship with postnatal hyperplastic mechanisms. Lbx1 gene expressed at higher levels in bicepsfemoris muscles compared with masseter, semitendinosus and longissimus dorsi muscles in Meishan pigs. Thus, our study indicates that there is no direct relationship between the Lbx1 transcription level and type of muscle fiber.
5 Bisulfite sequencing (BS) technique was used to analyze the specific methylation on promoter and exon 1 regions of Lbx1 and Lbx1 genes in longissimus dorsi muscle. (1) Lbx1, the differentially methylated region was found in a CpG island of the exon 1. (2) Lbx2, the differentially methylated region was outside of the CpG island. These results suggested that the high DNA methylation in CpG island might be involved in the down regulation of Lbx1 in longissimus dorsi muscle.
6 Single nucleotide polymorphism (SNP) scanning in the Lbx1 genomic fragment identified two mutations, g.752A>G and g.-1559C>G. Association analysis in our experimental pig populations showed that the mutation of g.752A>G was significantly associated with loin muscle area (P<0.05) and internal fat rate (P<0.05). The g.752A>G does not affect the encoded protein structure. It means that a direct effect of this polymorphism is unlikely. Our results suggest that the associations are caused by linkage disequilibrium with QTLs for these traits.
7 RT-PCR analyses showed MyoD and Myf5 were expressed in activated and quiescent C2C12 cells. MyoG was expressed in a later stage of myogenesis. Pax7 was weakly expressed in differentiated C2C12 cells. In addition, the C2C12 cells do not express endogeneous Lbxl. In myogenic differentiation in C2C12 cells, the changes of promoter and exon 1 methylation of MyoD, Myf5, Pax7 and Lbxl genes were observed. These results suggested the methylation of these genes is a dymamic process, which play a dominant role in regulating gene expression for development of muscle.
1通过PCR-RFLP分析了MC4R, H-FABP, LEP, HAL, CAST和MyoG基因多态位点在DIv2系和7个纯种猪中的分布,并在DIV2系中进行了遗传效应分析,结果表明：(1)MC4R基因中的TaqⅠ酶切位点与平均背膘厚、瘦肉率显著相关(P<0.05)；(2)LEP基因中的HinfⅠ酶切位点,BB基因个体的曰增重极显著高于AA基因型个体(P<0.01),AB基因个体的日增重显著高于AA基因型个体(P<0.05)；(3)H-FABP基因第二内含子的HaeⅢ酶切位点,DD基因型个体的瘦肉率显著高于dd基因型个体(P<0.05)；(4)在CAST基因MspⅠ位点中,EE基因型个体的日增重显著高于FF基因型个体(P<0.05),EF基因型个体的日增重极显著高于FF基因型个体(P<0.01)。
2连锁不平衡分析显示：在DIv2系、大白猪、长白猪和八眉猪中,MC4R和LEP基因位点间、LEP和H-FABP基因位点间的连锁不平衡度不显著(P>0.05)；在DIv2系、大白猪、长白猪、皮特兰猪和八眉猪中,MC4R与H-FABP基因位点间的连锁不平衡度不显著(P>0.05)。这表明两个位点间是独立的,因此对其中一个位点的选择不会影响另一个位点的等位基因频率。
3采用电子克隆方法获得了两个候选基因的编码区序列：(1) Lbx1, mRNA中的CDS全长846bp,编码281个氨基酸；(2) Lbx2, mRNA中的CDS全长591bp,编码196个氨基酸。通过比较不同物种氨基酸序列,对以上两个基因进行了系统进化树分析,发现猪Lbxl与牛、小鼠、人、犬、类人猿进化关系较近,猪Lbx2与牛、猩猩、犬进化关系较近。
4 RT-PCR分析显示：猪Lbx1基因在肌肉组织中高表达；Lbx2基因在肝、肾和脾中微弱表达,但在肌肉组织中不表达。在出生后肌肉发育过程中,Lbx1基因的表达处于动态变化中,一月龄之内,表达量相对较高,在二月龄时,表达量显著下调,该变化趋势与产后肌肉组织中肌卫星细胞分化比例的变化一致,由于Lbx1基因已被证实在肌卫星细胞分化初期表达,因此我们推测该基因可能与出生后肌肉增生机制有关。在不同肌肉组织中的分析表明：猪Lbx1基因在股二头肌中的表达量显著高于在咬肌,背最长肌和半腱肌中的表达量,推测Lbx1基因的表达量与肌纤维类型并无直接关系。
5通过亚硫酸盐测序技术,在猪背最长肌中分析Lbx1和Lbx2基因启动子和外显子l的甲基化状态。发现：(1) Lbx1基因的甲基化差异区在外显子1处的CpG岛内；(2) Lbx2基因的甲基化差异区在CpG岛外的启动子区。Lbx1基因CpG岛内的高密度甲基化可能参与下调该基因在背最长肌中的表达量。
6通过对猪Lbx1基因组SNP扫描,发现2个引起酶切位点改变的SNP: g.752A>G和g.-1559C>G。在大白╳梅山F2代资源家系中进行性状关联分析发现,Lbx1基因g.752A>G突变与眼肌面积和内脂率显著相关(P<0.05),该突变位于内含子,并不影响蛋白结构,因此该相关可能是由于g.752A>G突变与真正的功能突变处于连锁不平衡状态造成的。
7 RT-PCR分析显示：MyoD和Myf5基因在未分化及分化的C2C12细胞中均表达,MyoG基因在成肌分化后期表达,另外,在C2C12细胞分化过程中始终检测到Pax7基因微弱表达。Lbx1基因在C2C12细胞中不表达。通过亚硫酸盐测序发现,在C2C12细胞成肌分化过程中MyoD, Myf5, Pax7和Lbx1基因外显子1或启动子区的甲基化密度处于动态变化中,推测这种变化影响其mRNA表达变化。
With the development of molecular and quantitative genetics and its related subjects, it made a great progress on the research about animal genetic marker assisted selection (MAS). We have known that polymorphism of MC4R (Melanocortin-4 Receptor), H-FABP (Heart FABP), LEP (Leptin), HAL (Halothane), CAST (calpastatin) and MyoG (myogenin) genes associated relation with meat quality in recent research. PCR-RFLP was used to analyze these polymorphisms in a swine breed composite (DIV2) and 7 swine breeds. The implications of the allelic distribution of these genes for meat production, and applicability of molecular markers in pig breeding were discussed. In all animals investigated so far, both the protostome genes and the vertebrate Lbx genes (Ladybird-like genes) were found to play crucial roles in muscle and neural development. As candidate genes of animal growth and meat quality, the porcine Lbx1 and Lbx2 were cloned and identified and genetics effect were analyzed. DNA methylation is an important epigenetic system. It plays many crucial roles in the gene regulation. In this study we investigated whether DNA methylation regulates the expression of the Lbx1 and Lbx2 genes in porcine skeletal muscle. In addition, we analyzed the DNA methylation pattern of four genes (MyoD, Myf5, Pax7 and Lbx1) in myogenic differentiation in C2C12 cells. The results are summarized as follows:
1 PCR-RFLP was used to analyze the polymorphisms of MC4R, LEP, H-FABP, HAL, CAST, MyoG genes in a swine breed composite (DIV2) and 7 swine breeds. The association study of these polymorphisms with several economic traits was carried out on a DIV2 population. The results obtained showed that MC4R/TaqI genotype had an effect for average backfat thickness (P<0.05) and lean meat percentage (P<0.05); At locus LEP/HinfI animals of AA genotype had lower test daily gain than that of BB (P<0.01) or AB genotype (P<0.05); At the H-FABP/HaeⅢlocus lean meat percentage of the individuals with genotype DD were higher than that with genotype dd (P<0.05); At locus CAST/MspI animals of FF genotype had lower test daily gain than that of EF(P<0.01) or EE genotype (P<0.05).
2 Linkage disequilibrium analysis among MC4R, LEP and H-FABP revealed that these genes were independent. Therefore, exerting selection pressure on one locus should not influence the allelic frequencies of the other locus. This represented two or more genes that could be combined together within one genotype in order to facilitate breeding for objective traits.
3 We obtained the full coding region of the 2 genes with electronic cloning technology. (1) The cDNA sequence of porcine Lbx1 contains an ORF of 846 bp encoding a protein of 281 residues. (2) The cDNA sequence of porcine Lbx2 contains an ORF of 591 bp encoding a protein of 196 residues. Phylogenetic trees were constructed by aligning the amino acid sequences of different species. The porcine protein sequence of Lbx1 has high sequence similarity with Bos taurus, Mus musculus, Homo sapiens, Canis familiaris, Pan troglodytes than with other species, and the porcine protein sequence of Lbx2 has high sequence similarity with Bos taurus, Pongo abelii, Canis familiaris than with other species.
4 RT-PCR analyses showed that Lbx1 was highly expressed in porcine skeletal muscle tissues, Lbx2 was lowly expressed in liver, kidney and spleen. And we provide the first evidence that Lbx1 has a certain regulated expression pattern during the postnatal period of the porcine skeletal muscle development. The percentage of differentiating satellite cells was highest in 1-week-old pigs and significantly decreased in 7-week-old pigs. It is very interesting that the expression of the porcine Lbx1 gene in skeletal muscle shows the same trend of a higher expression in early postnatal porcine growth. Therefore, we deduce that Lbx1 gene may have a relationship with postnatal hyperplastic mechanisms. Lbx1 gene expressed at higher levels in bicepsfemoris muscles compared with masseter, semitendinosus and longissimus dorsi muscles in Meishan pigs. Thus, our study indicates that there is no direct relationship between the Lbx1 transcription level and type of muscle fiber.
5 Bisulfite sequencing (BS) technique was used to analyze the specific methylation on promoter and exon 1 regions of Lbx1 and Lbx1 genes in longissimus dorsi muscle. (1) Lbx1, the differentially methylated region was found in a CpG island of the exon 1. (2) Lbx2, the differentially methylated region was outside of the CpG island. These results suggested that the high DNA methylation in CpG island might be involved in the down regulation of Lbx1 in longissimus dorsi muscle.
6 Single nucleotide polymorphism (SNP) scanning in the Lbx1 genomic fragment identified two mutations, g.752A>G and g.-1559C>G. Association analysis in our experimental pig populations showed that the mutation of g.752A>G was significantly associated with loin muscle area (P<0.05) and internal fat rate (P<0.05). The g.752A>G does not affect the encoded protein structure. It means that a direct effect of this polymorphism is unlikely. Our results suggest that the associations are caused by linkage disequilibrium with QTLs for these traits.
7 RT-PCR analyses showed MyoD and Myf5 were expressed in activated and quiescent C2C12 cells. MyoG was expressed in a later stage of myogenesis. Pax7 was weakly expressed in differentiated C2C12 cells. In addition, the C2C12 cells do not express endogeneous Lbxl. In myogenic differentiation in C2C12 cells, the changes of promoter and exon 1 methylation of MyoD, Myf5, Pax7 and Lbxl genes were observed. These results suggested the methylation of these genes is a dymamic process, which play a dominant role in regulating gene expression for development of muscle.
引文
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