关于绵羊肌肉生长遗传调控机理的研究
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摘要
本研究采用候选基因法和全基因组基因芯片检测法研究绵羊肌肉生长性状的遗传调控机理,主要内容如下：
一、湖羊Dlk1、GHR、 IGF-I、 MSTN、 MyoG基因在背最长肌中的表达及其与屠宰性状、肉质性能关联分析
摘要：本实验以湖羊为研究对象,以6月龄陶赛特羊为参照群体,采用RT-PCR法检测Dlk1、GHR、IGF-I、MSTN、MyoG基因在湖羊不同生长阶段背最长肌中表达丰度,并分析其与屠宰性状、肉质性能的关联性,旨在揭示湖羊肌肉生长性状的分子遗传学基础,为湖羊肌肉生长性状的选育提供遗传学资料,丰富湖羊品种遗传资源的研究。本实验得到了以下结果：
1、Dlk1、GHR、IGF-I、MSTN、MyoG基因在湖羊背最长肌中的表达趋势分析
Dlk1、GHR、IGF-I、MSTN、MyoG基因在不同生长阶段之间、不同性别间大量存在显著或极显著差异,这表明不同生长阶段、性别对于这5个基因在绵羊肌肉组织中的表达具有重要影响。出生后,各基因表达水平并非一直随着上升或者下降,各基因表达水平出现拐点的时间点也不相同。就6月龄而言,这5个基因在湖羊中的表达均高于陶塞特羊,品种因素对于这5个基因的表达差异表达具有一定的影响,但是两个品种在其他生长阶段的表达差异水平有待进一步研究。
5个基因间大多存在显著或极显著正相关,只有GHR与MSTN、MyoG间的表达相关不显著。
2、Dlk1、GHR、IGF-I、MSTN和MyoG基因表达与湖羊屠宰性状指标的相关分析
Dlk1、GHR、IGF-I、MSTN基因与宰前活重和胴体重存在显著或极显著正相关,与净肉重相关不显著；MyoG与宰前活重、胴体重和净肉重间均未达到显著水平。
3、Dlk1、GHR、IGF-I、MSTN和MyoG基因表达与肉质性能指标的相关分析
Dlk1、GHR、IGF-I、MSTN和MyoG基因表达均与肌纤维直径和肌纤剪切力存在正相关,与肌纤维密度存在负相关。其中,Dlk1、GHR、IGF-I、MSTN基因表达与肌纤维直径和肌纤维密度存在显著或极显著相关,Dlk1、GHR、IGF-I基因表达与肌纤剪切力存在显著或极显著相关。MyoG基因表达与肌纤维直径、肌纤剪切力和肌纤维密度均不存在显著相关。
二、利用芯片表达数据构建绵羊背最长肌基因网络调控图；探讨TGF-β信号通道在美臀羊形成中的作用
摘要：[背景]在基因表达数据分析方面的最新进展可以帮助发现更为详细的导致不同处理差异的关键原因,其中包括鉴定表达不存在差异的关键基因,本文运用了这些数据分析方法到绵羊肌肉表达数据上,并重点研究美臀表型性状。绵羊的美臀基因突变以及牛上的生长抑制素基因突变都可以导致显著增加肌肉的生长。尽管两种突变类型可以增加慢肌纤维到快肌纤维的转变比率,但是表型的其他特征都是非常不同的。本文将采用新的分析算法来比较导致绵羊上美臀基因突变以及牛上的生长抑制素基因突变的通道的潜在成分的一致性。[结果]本研究构建了绵羊背最长肌的一个始终相关(Always correlated)的基因表达网络。确定了5个稳健的功能模块,包括编码肌肉蛋白、线粒体蛋白、核糖体蛋白、26S蛋白酶和参与翻译的蛋白的基因。Module-to-Regulator(模块-调控影响因子)分析方法被用于识别模块的潜在的转录调控因子,除了得到一些已知的模块调控因子,还得到了一些新的候选调控因子。采用RIF2算法来分析美臀羊和正常表型羊的基因表达数据,可以清晰地揭示导致不同处理/表型的关键的调控因子(虽然在这些调控影响因子表达上并没有显著差异性)。相关文献、数据挖掘以及前10个候选调控因子均支持TGF(转化生长因子)-β的信号通道在增加DLK1在美臀羊肌肉中表达从而导致肌肉聚集中的作用。另外,在同一坐标平面内作出美臀羊和双肌臀牛的RIF2得分图,结果进一步支持这两种表型在TGF-β信号通道上有相同之处。这两个数据集的RIF2分析的交叉之处包含有YAP1基因,该基因编码导致调节器官大小的Hippo信号通道的一个组成部分。本研究首次提供了Hippo信号通道参与草食动物肌肉生长的活体证据,这支持了最近的有关Hippo通道在大鼠肌肉生长中的作用的报道。[结论]本研究提供了解释洞角反刍科草食动物中两种肌肉增加表型的机制的新观点。特别是,揭示了美臀羊和双肌臀牛存在比预期大得多的相同之处。本研究结果丰富了洞角反刍科草食动物重要功能基因遗传资源的研究。
In this study, methods of candidate gene and whole genome microarray were applied to analyze the mechanisms of genetic control mechanism of growth traits in sheep muscle, and the main contents were as the following:
I Developmental Changes of Gene Expression of Dlk1,GHR,IGF-l,MSTN and MyoG Genes and Their Association Analysis with Carcass Traits, meat quality in Hu Sheep
Abstract:In this experiment, Hu sheep was regarded as the researched object and6-month-old Dorset sheep was regarded as the referenced group. Methods of RT-PCR was applied to analyze the expression of Dlkl,GHR,IGF-I,MSTN,MyoG gene in Longissimus Dorsi at different growth stages of Hu sheep,and their association analysis with carcass traits, meat quality in Hu Sheep also been studied. The purpose is to reveal the molecular genetics basis of muscle growth, and provide genetic information for the selection of muscle growth trait, and enriched the genetic resources research of Hu sheep. The results were as follows:
1. Developmental Changes of Expression of Dlk1, GHR, IGF-I, MSTN and MyoG Genes in Hu Sheep
The expressions of Dlkl, GHR, IGF-I, MSTN and MyoG had a lot of significant differences or extreme significant differences among different growth stages and different genders, which showed that different stages and different genders had important influences on the expressions of the five genes in sheep skeletal muscle. After birth, the expressions of the five genes did not always increase or decrease, the turning points of different genes expression were not at the same time. In terms of6-month-old, the expressions of the five genes in Hu sheep were all higher than that in Dorset sheep, therefore, breed factors might also have some impacts on the different expressions of the five genes, but a further study would be needed for the expressions of the five genes in other growth stages between the two breeds.
The results showed that almost every two genes had a significant or an extreme significant positive correlation except the correlation between GHR and MSTN or MyoG.
2. The correlation analysis between the5genes expression and Carcass traits in Hu sheep
The expressions of Dlkl, GHR, IGF-I, MSTN had a significant or an extreme significant positive correlation with the Live weight and carcass weight and didn't have any correlation with the net meat weight in Hu sheep; the expression of MyoG didn't have any significant correlation with the Live weight, carcass weight and net meat weight in Hu sheep.
3. The correlation analysis between5genes expression and meat quality in Hu sheep
The expressions of the5genes all had positive correlation with diameter of muscle fibers and shear force of muscle fibers; in addition, they had a negative correlation with the density of muscle fibers. The expressions of Dlkl, GHR, IGF-I, MSTN had a significant or a extreme significant correlation with diameter of muscle fibers and shear force of muscle fibers, and the expressions of Dlkl、 GHR、IGF-I had a significant or a extreme significant correlation with shear force of muscle fibers. The expression of MyoG didn't have any correlation with the diameter of muscle fibers, shear force of muscle fibers and density of muscle fibers.
Ⅱ Deciphering the regulatory circuitry of ovine skeletal muscle genes from expression data; signaling pathway in Callipyge sheep evidence for the involvement of the TGF-β
Abstract:[Background] Recent advances in the analysis of gene expression data enables a detailed picture of the drivers of differences between treatments to be identified, including the identification of key genes that are not differentially expressed. Here we apply these approaches to gene expression data from sheep muscle with a particular focus on the callipyge phenotype. The callipyge mutation in sheep and mutations in the myostatin gene in cattle both lead to significantly increased muscle growth. Although both types of mutations increase the ratio of fast to slow twitch muscle fibers, many other aspects of the phenotypes are very different. Here we have applied new analysis methodologies to compare the identities of putative components of the path from the mutations to the phenotypic outcomes in callipyge sheep and a myostatin mutation in cattle.[Results] The reversed engineering of an Always Correlated gene expression landscape of sheep Longissimus dorsi (LD) muscle is described. Five robust modules including genes encoding muscle, mitochondrial, ribosomal, translation proteins and components of the26S proteosome were identified. We analyzed the callipyge versus normal sheep muscle gene expression data using the Regulatory Impact Factor (RIF2) methodology, which can identify key regulators not differentially expressed between two conditions, but which may be drivers of the phenotypic response. Literature and data-mining of the functions and signaling pathway in relationships of the top candidates supported a role for the TGF-β the processes by which increased DLKl expression in the affected muscles of callipyge sheep leads to increased muscle mass. In addition, plotting the RIF2scores for the callipyge sheep muscle dataset against the RIF2scores for a muscle gene expression data set from cattle with a mutation in the myostatin signaling pathway in both genes further supported a common role for the TGF-β phenotypes. The genes at the intersection of the RIF2analyses of the two datasets included YAP1, which encodes a component Hippo signaling pathway which regulates organ size. This provides the first in vivo evidence for a role for the Hippo signaling pathway in muscle growth in ruminants, supporting recent in vitro evidence for a role in muscle differentiation in the mouse.[Conclusions]The analyses provide new insights into the mechanisms underlying two increased muscle growth phenotypes in ruminants. In particular, they suggest a greater overlap between the mechanisms in callipyge sheep and myostatin cattle, than has previously been anticipated. The results of this study largely enriched the genetic resources research about important functional genes in herbivore of hollow horn ruminant families.
一、湖羊Dlk1、GHR、 IGF-I、 MSTN、 MyoG基因在背最长肌中的表达及其与屠宰性状、肉质性能关联分析
摘要：本实验以湖羊为研究对象,以6月龄陶赛特羊为参照群体,采用RT-PCR法检测Dlk1、GHR、IGF-I、MSTN、MyoG基因在湖羊不同生长阶段背最长肌中表达丰度,并分析其与屠宰性状、肉质性能的关联性,旨在揭示湖羊肌肉生长性状的分子遗传学基础,为湖羊肌肉生长性状的选育提供遗传学资料,丰富湖羊品种遗传资源的研究。本实验得到了以下结果：
1、Dlk1、GHR、IGF-I、MSTN、MyoG基因在湖羊背最长肌中的表达趋势分析
Dlk1、GHR、IGF-I、MSTN、MyoG基因在不同生长阶段之间、不同性别间大量存在显著或极显著差异,这表明不同生长阶段、性别对于这5个基因在绵羊肌肉组织中的表达具有重要影响。出生后,各基因表达水平并非一直随着上升或者下降,各基因表达水平出现拐点的时间点也不相同。就6月龄而言,这5个基因在湖羊中的表达均高于陶塞特羊,品种因素对于这5个基因的表达差异表达具有一定的影响,但是两个品种在其他生长阶段的表达差异水平有待进一步研究。
5个基因间大多存在显著或极显著正相关,只有GHR与MSTN、MyoG间的表达相关不显著。
2、Dlk1、GHR、IGF-I、MSTN和MyoG基因表达与湖羊屠宰性状指标的相关分析
Dlk1、GHR、IGF-I、MSTN基因与宰前活重和胴体重存在显著或极显著正相关,与净肉重相关不显著；MyoG与宰前活重、胴体重和净肉重间均未达到显著水平。
3、Dlk1、GHR、IGF-I、MSTN和MyoG基因表达与肉质性能指标的相关分析
Dlk1、GHR、IGF-I、MSTN和MyoG基因表达均与肌纤维直径和肌纤剪切力存在正相关,与肌纤维密度存在负相关。其中,Dlk1、GHR、IGF-I、MSTN基因表达与肌纤维直径和肌纤维密度存在显著或极显著相关,Dlk1、GHR、IGF-I基因表达与肌纤剪切力存在显著或极显著相关。MyoG基因表达与肌纤维直径、肌纤剪切力和肌纤维密度均不存在显著相关。
二、利用芯片表达数据构建绵羊背最长肌基因网络调控图；探讨TGF-β信号通道在美臀羊形成中的作用
摘要：[背景]在基因表达数据分析方面的最新进展可以帮助发现更为详细的导致不同处理差异的关键原因,其中包括鉴定表达不存在差异的关键基因,本文运用了这些数据分析方法到绵羊肌肉表达数据上,并重点研究美臀表型性状。绵羊的美臀基因突变以及牛上的生长抑制素基因突变都可以导致显著增加肌肉的生长。尽管两种突变类型可以增加慢肌纤维到快肌纤维的转变比率,但是表型的其他特征都是非常不同的。本文将采用新的分析算法来比较导致绵羊上美臀基因突变以及牛上的生长抑制素基因突变的通道的潜在成分的一致性。[结果]本研究构建了绵羊背最长肌的一个始终相关(Always correlated)的基因表达网络。确定了5个稳健的功能模块,包括编码肌肉蛋白、线粒体蛋白、核糖体蛋白、26S蛋白酶和参与翻译的蛋白的基因。Module-to-Regulator(模块-调控影响因子)分析方法被用于识别模块的潜在的转录调控因子,除了得到一些已知的模块调控因子,还得到了一些新的候选调控因子。采用RIF2算法来分析美臀羊和正常表型羊的基因表达数据,可以清晰地揭示导致不同处理/表型的关键的调控因子(虽然在这些调控影响因子表达上并没有显著差异性)。相关文献、数据挖掘以及前10个候选调控因子均支持TGF(转化生长因子)-β的信号通道在增加DLK1在美臀羊肌肉中表达从而导致肌肉聚集中的作用。另外,在同一坐标平面内作出美臀羊和双肌臀牛的RIF2得分图,结果进一步支持这两种表型在TGF-β信号通道上有相同之处。这两个数据集的RIF2分析的交叉之处包含有YAP1基因,该基因编码导致调节器官大小的Hippo信号通道的一个组成部分。本研究首次提供了Hippo信号通道参与草食动物肌肉生长的活体证据,这支持了最近的有关Hippo通道在大鼠肌肉生长中的作用的报道。[结论]本研究提供了解释洞角反刍科草食动物中两种肌肉增加表型的机制的新观点。特别是,揭示了美臀羊和双肌臀牛存在比预期大得多的相同之处。本研究结果丰富了洞角反刍科草食动物重要功能基因遗传资源的研究。
In this study, methods of candidate gene and whole genome microarray were applied to analyze the mechanisms of genetic control mechanism of growth traits in sheep muscle, and the main contents were as the following:
I Developmental Changes of Gene Expression of Dlk1,GHR,IGF-l,MSTN and MyoG Genes and Their Association Analysis with Carcass Traits, meat quality in Hu Sheep
Abstract:In this experiment, Hu sheep was regarded as the researched object and6-month-old Dorset sheep was regarded as the referenced group. Methods of RT-PCR was applied to analyze the expression of Dlkl,GHR,IGF-I,MSTN,MyoG gene in Longissimus Dorsi at different growth stages of Hu sheep,and their association analysis with carcass traits, meat quality in Hu Sheep also been studied. The purpose is to reveal the molecular genetics basis of muscle growth, and provide genetic information for the selection of muscle growth trait, and enriched the genetic resources research of Hu sheep. The results were as follows:
1. Developmental Changes of Expression of Dlk1, GHR, IGF-I, MSTN and MyoG Genes in Hu Sheep
The expressions of Dlkl, GHR, IGF-I, MSTN and MyoG had a lot of significant differences or extreme significant differences among different growth stages and different genders, which showed that different stages and different genders had important influences on the expressions of the five genes in sheep skeletal muscle. After birth, the expressions of the five genes did not always increase or decrease, the turning points of different genes expression were not at the same time. In terms of6-month-old, the expressions of the five genes in Hu sheep were all higher than that in Dorset sheep, therefore, breed factors might also have some impacts on the different expressions of the five genes, but a further study would be needed for the expressions of the five genes in other growth stages between the two breeds.
The results showed that almost every two genes had a significant or an extreme significant positive correlation except the correlation between GHR and MSTN or MyoG.
2. The correlation analysis between the5genes expression and Carcass traits in Hu sheep
The expressions of Dlkl, GHR, IGF-I, MSTN had a significant or an extreme significant positive correlation with the Live weight and carcass weight and didn't have any correlation with the net meat weight in Hu sheep; the expression of MyoG didn't have any significant correlation with the Live weight, carcass weight and net meat weight in Hu sheep.
3. The correlation analysis between5genes expression and meat quality in Hu sheep
The expressions of the5genes all had positive correlation with diameter of muscle fibers and shear force of muscle fibers; in addition, they had a negative correlation with the density of muscle fibers. The expressions of Dlkl, GHR, IGF-I, MSTN had a significant or a extreme significant correlation with diameter of muscle fibers and shear force of muscle fibers, and the expressions of Dlkl、 GHR、IGF-I had a significant or a extreme significant correlation with shear force of muscle fibers. The expression of MyoG didn't have any correlation with the diameter of muscle fibers, shear force of muscle fibers and density of muscle fibers.
Ⅱ Deciphering the regulatory circuitry of ovine skeletal muscle genes from expression data; signaling pathway in Callipyge sheep evidence for the involvement of the TGF-β
Abstract:[Background] Recent advances in the analysis of gene expression data enables a detailed picture of the drivers of differences between treatments to be identified, including the identification of key genes that are not differentially expressed. Here we apply these approaches to gene expression data from sheep muscle with a particular focus on the callipyge phenotype. The callipyge mutation in sheep and mutations in the myostatin gene in cattle both lead to significantly increased muscle growth. Although both types of mutations increase the ratio of fast to slow twitch muscle fibers, many other aspects of the phenotypes are very different. Here we have applied new analysis methodologies to compare the identities of putative components of the path from the mutations to the phenotypic outcomes in callipyge sheep and a myostatin mutation in cattle.[Results] The reversed engineering of an Always Correlated gene expression landscape of sheep Longissimus dorsi (LD) muscle is described. Five robust modules including genes encoding muscle, mitochondrial, ribosomal, translation proteins and components of the26S proteosome were identified. We analyzed the callipyge versus normal sheep muscle gene expression data using the Regulatory Impact Factor (RIF2) methodology, which can identify key regulators not differentially expressed between two conditions, but which may be drivers of the phenotypic response. Literature and data-mining of the functions and signaling pathway in relationships of the top candidates supported a role for the TGF-β the processes by which increased DLKl expression in the affected muscles of callipyge sheep leads to increased muscle mass. In addition, plotting the RIF2scores for the callipyge sheep muscle dataset against the RIF2scores for a muscle gene expression data set from cattle with a mutation in the myostatin signaling pathway in both genes further supported a common role for the TGF-β phenotypes. The genes at the intersection of the RIF2analyses of the two datasets included YAP1, which encodes a component Hippo signaling pathway which regulates organ size. This provides the first in vivo evidence for a role for the Hippo signaling pathway in muscle growth in ruminants, supporting recent in vitro evidence for a role in muscle differentiation in the mouse.[Conclusions]The analyses provide new insights into the mechanisms underlying two increased muscle growth phenotypes in ruminants. In particular, they suggest a greater overlap between the mechanisms in callipyge sheep and myostatin cattle, than has previously been anticipated. The results of this study largely enriched the genetic resources research about important functional genes in herbivore of hollow horn ruminant families.
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