家畜生殖轴和生长轴基因进化驱动力及功能研究
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摘要
本文目的是研究家畜生殖轴和生长轴相关基因的进化驱动力,并试探性解释基因与性状之间联系。以透明带蛋白(Zona Pellucida, ZP)基因和乳铁蛋白(Lactoferrin,LF)基因为例,研究家畜群体中基因与多态的进化机制,期望为家畜遗传育种提供理论参考。
研究中首先通过对已发表生长相关文献进行挖掘并结合已有数据库搜集了一些与生殖轴和生长轴相关的基因。采用CODEML软件估计了基因编码序列的非同义替换率与同义替换率比值ω(=dN/ds),以此来检测生殖轴、生长轴中正选择驱动下的基因(即ω>1)。之后利用GO和DAVID对生殖轴和生长轴中正选择基因进行功能注释与富集。研究中构建了生长轴基因网络并研究了基因进化驱动力与网络的关系。最后利用基因测序技术识别了猪ZP2和ZP4基因中的SNP位点,利用基于FST和He联合分布的聚合模型(coalescent model),结合Tajima'D、Fu和Li's D*、Fu和Li's H*和Fu's Fs等群体进化检验方法来研究大白猪、长白猪和长大二元杂猪群体中ZP基因核苷酸多态的进化。
研究结果有：
(1)搜集了311个生殖轴基因,722个生长轴基因,其中45个生殖轴,46个生长轴基因由正选择驱动,其余基因为中性进化或纯化选择。生殖轴正选择基因功能涉及调控星形细胞的分化和相关过程的激活,正调控蛋白的代谢和调控MAP蛋白激酶的活性。生长轴正选择基因功能涉及细胞死亡(cell death)、增殖(cell proliferation)、调控等和生长过程中的蛋白激酶代谢和修饰过程。
(2)生长轴基因系统发生树中不同进化枝(branch)受到选择压力不同。基因进化驱动力与基因网络之间存在弱的负相关(相关系数Φ=—0.200)。
(3)猪ZP2基因中检测到7个SNP,这7个多态位点全部处于中性进化下,与猪产仔数均无显著关联；ZP4中检测到27个SNP,其中T2950C受正选择,但该突变与猪产仔数无显著关联,其余SNP均为中性突变,但A268T与猪产仔数存在显著关联(P<0.05),研究发现T2950C与A268T在大白猪群体中紧密连锁。
(4)乳铁蛋白在进化中为正选择。正选择的蛋白位点位于乳铁蛋白与病原菌识别区域,这一区域也是LF中抗菌结构域Lfcin和Lfampin所在区域。
生殖轴和生长轴中正选择基因是家畜适应性进化的反映,筛选出的正选择基因可以作为研究家畜繁殖与生长的重要参考。对乳铁蛋白的研究说明正选择驱动下的蛋白位点或结构域意味着功能重要性,这可以为实验室开展基因功能研究提供线索。通过对ZP基因的研究说明,虽然基于统计的方法可以推测受正选择的蛋白位点或结构域,但是这些区域的功能仍需进行实验验证。
In this study, we detected positive selection with reproductive axis and growth axis genes.
Growth axis genes are extracted from literatures of which topic is about animal growth and repeoduction, some reproductive axis genes come form a pig repduction gene database, ReCGiP.
A maximum likelihood method in codeml program is used to investigate evolution pressure of coding sequences, the excess of non-synonymous to synonymous nucleodite substitution rates per site indicate positive selection. GO and DAVID tools are used to annotate and visualize posotive selection gene function that decected in animal reproductive and growth axis, and gave a comprehensive understanding the biological meaning behind these positive selection genes. We also build a gene-to-gene co-citation netwoek for growth axis genes to study the relationship between gene network and gene evolutionary pressure. In this study we identify some SNPs in ZP2and ZP4by sequencing. The coalescent model in DetSel and LOSITAN software are used to investgate the molecular adaptation in ZP2and ZP4, besides statistical test in Tajima'D, Fu and Li's D*, Fu and Li's H*and Fu's Fs.
The main results of this study are:
(1)311reprodutive axis genes are collected and45genes are subjected to positive selection, and722growth axis genes are collected and46genes are under positive selection. The positive genes function in reproductive axis are involved in (a) astrocyte different and activation;(b) positive regulation of protein metabolic process and (c) regulation of MAP kinase activity and positive selection genes in growth genes are related with (a) cell locomotion, including cell death, cycle, proliferation, communication;(b) metabolic, including phosphate metabolic process, protein modication process, triglyceride catabolic process;(c) activity, including protein kinase activity, catalytic activity, transferase activity, growth factors activity most of biological process were positive regulation.
(2) We find a weak negative correlation between gene evolutionary pressure and gene location, and this suggests that gene location may constraint gene function.
(3) We identify7SNPs in ZP2, and these mutation sites are under neutrual evolution and none of them are significantly affectet the litter size in pigs. There are27SNPs dectected in ZP4, T2950C is subjected positive selection but not is associat with litter size in swine, A268T is significantly associated with litter size but under neutral evolution.
(4) LF is subjected to positive selection, Further study find that the positive selection sites are either located in the LF-bacteria binding region or the peptides of LFcin and LFampin, indicating that the selection pressure is related to LF-bacteria interaction.
This study suggest that:Positive selection genes in reproduction axis and growth axis may be candidate gene in animal reproduction and growth study. Statical test could be used to identify sites or domains under positive selection express that function important (like study in chapter5), but it should be carfully investaged (T2950C was under potive selection but not associated with litter size in swine) in lab.
研究中首先通过对已发表生长相关文献进行挖掘并结合已有数据库搜集了一些与生殖轴和生长轴相关的基因。采用CODEML软件估计了基因编码序列的非同义替换率与同义替换率比值ω(=dN/ds),以此来检测生殖轴、生长轴中正选择驱动下的基因(即ω>1)。之后利用GO和DAVID对生殖轴和生长轴中正选择基因进行功能注释与富集。研究中构建了生长轴基因网络并研究了基因进化驱动力与网络的关系。最后利用基因测序技术识别了猪ZP2和ZP4基因中的SNP位点,利用基于FST和He联合分布的聚合模型(coalescent model),结合Tajima'D、Fu和Li's D*、Fu和Li's H*和Fu's Fs等群体进化检验方法来研究大白猪、长白猪和长大二元杂猪群体中ZP基因核苷酸多态的进化。
研究结果有：
(1)搜集了311个生殖轴基因,722个生长轴基因,其中45个生殖轴,46个生长轴基因由正选择驱动,其余基因为中性进化或纯化选择。生殖轴正选择基因功能涉及调控星形细胞的分化和相关过程的激活,正调控蛋白的代谢和调控MAP蛋白激酶的活性。生长轴正选择基因功能涉及细胞死亡(cell death)、增殖(cell proliferation)、调控等和生长过程中的蛋白激酶代谢和修饰过程。
(2)生长轴基因系统发生树中不同进化枝(branch)受到选择压力不同。基因进化驱动力与基因网络之间存在弱的负相关(相关系数Φ=—0.200)。
(3)猪ZP2基因中检测到7个SNP,这7个多态位点全部处于中性进化下,与猪产仔数均无显著关联；ZP4中检测到27个SNP,其中T2950C受正选择,但该突变与猪产仔数无显著关联,其余SNP均为中性突变,但A268T与猪产仔数存在显著关联(P<0.05),研究发现T2950C与A268T在大白猪群体中紧密连锁。
(4)乳铁蛋白在进化中为正选择。正选择的蛋白位点位于乳铁蛋白与病原菌识别区域,这一区域也是LF中抗菌结构域Lfcin和Lfampin所在区域。
生殖轴和生长轴中正选择基因是家畜适应性进化的反映,筛选出的正选择基因可以作为研究家畜繁殖与生长的重要参考。对乳铁蛋白的研究说明正选择驱动下的蛋白位点或结构域意味着功能重要性,这可以为实验室开展基因功能研究提供线索。通过对ZP基因的研究说明,虽然基于统计的方法可以推测受正选择的蛋白位点或结构域,但是这些区域的功能仍需进行实验验证。
In this study, we detected positive selection with reproductive axis and growth axis genes.
Growth axis genes are extracted from literatures of which topic is about animal growth and repeoduction, some reproductive axis genes come form a pig repduction gene database, ReCGiP.
A maximum likelihood method in codeml program is used to investigate evolution pressure of coding sequences, the excess of non-synonymous to synonymous nucleodite substitution rates per site indicate positive selection. GO and DAVID tools are used to annotate and visualize posotive selection gene function that decected in animal reproductive and growth axis, and gave a comprehensive understanding the biological meaning behind these positive selection genes. We also build a gene-to-gene co-citation netwoek for growth axis genes to study the relationship between gene network and gene evolutionary pressure. In this study we identify some SNPs in ZP2and ZP4by sequencing. The coalescent model in DetSel and LOSITAN software are used to investgate the molecular adaptation in ZP2and ZP4, besides statistical test in Tajima'D, Fu and Li's D*, Fu and Li's H*and Fu's Fs.
The main results of this study are:
(1)311reprodutive axis genes are collected and45genes are subjected to positive selection, and722growth axis genes are collected and46genes are under positive selection. The positive genes function in reproductive axis are involved in (a) astrocyte different and activation;(b) positive regulation of protein metabolic process and (c) regulation of MAP kinase activity and positive selection genes in growth genes are related with (a) cell locomotion, including cell death, cycle, proliferation, communication;(b) metabolic, including phosphate metabolic process, protein modication process, triglyceride catabolic process;(c) activity, including protein kinase activity, catalytic activity, transferase activity, growth factors activity most of biological process were positive regulation.
(2) We find a weak negative correlation between gene evolutionary pressure and gene location, and this suggests that gene location may constraint gene function.
(3) We identify7SNPs in ZP2, and these mutation sites are under neutrual evolution and none of them are significantly affectet the litter size in pigs. There are27SNPs dectected in ZP4, T2950C is subjected positive selection but not is associat with litter size in swine, A268T is significantly associated with litter size but under neutral evolution.
(4) LF is subjected to positive selection, Further study find that the positive selection sites are either located in the LF-bacteria binding region or the peptides of LFcin and LFampin, indicating that the selection pressure is related to LF-bacteria interaction.
This study suggest that:Positive selection genes in reproduction axis and growth axis may be candidate gene in animal reproduction and growth study. Statical test could be used to identify sites or domains under positive selection express that function important (like study in chapter5), but it should be carfully investaged (T2950C was under potive selection but not associated with litter size in swine) in lab.
引文
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