Identification of genetic variation in innate immune response genes associated with resistance to chicken viral infections

英国家禽业在21世纪面临着越来越多的挑战。许多用于控制家禽疾病的药物正在停止使用。与此同时，福利标准的提高意味着该行业正变得更加自由。但缺点是，自由放养的鸡面临着更高的疾病挑战，例如通过与野生鸟类接触。解决这个问题的一个办法是饲养鸟类，因为它们对疾病有更高的天然抵抗力。要做到这一点，我们需要了解鸟类对疾病的免疫力，这样我们就能找到控制这种反应的方法。我们已经知道，在鸟类和哺乳动物中，免疫反应可以分为两部分——先天反应和适应性反应。后者是一种非常特殊的反应，有望导致免疫“记忆”，换句话说，能够对同一病原体的后续感染做出快速反应。这就是疫苗的工作原理，然而，它对鸟类遇到的每种病原体都是特定的，因此不会对疾病产生普遍的抵抗力。我们的目标是先天免疫反应。这是一种广义的反应，可以识别各种病原体的成分，例如，细菌外壳中的特定类型的分子。它有两个作用——在适应性免疫反应启动之前限制感染，并提供控制适应性免疫反应的信号。对于许多感染，强大的先天免疫反应是控制病原体和预防疾病发作所需要的全部。在这个项目中，我们的最初目标是尽可能多地识别鸡体内与先天免疫反应有关的基因。这现在是可能的，因为去年对鸡的基因组进行了测序，已经预测了近1.8万个基因。我们的初始基因集将通过与哺乳动物的相似基因集的比较来确定，我们可以从鸡的基因组序列中识别出什么。下一步将是确定这组预测的基因中的哪些成员实际上参与了对病毒感染的先天免疫反应。我们将用不同的病毒感染鸟类，并在全球范围内使用全基因组微阵列来观察感染后的基因表达。这些玻璃载玻片包含与鸡基因组中每个已知基因对应的短独特序列，可用于检测基因是否打开或关闭。经过复杂的数学分析，人们可以使用这些微阵列检查全局基因表达，并确定哪些鸡基因对特定的病毒感染有反应。我们有鸡系，我们知道它们对病毒感染的抵抗力不同。我们怀疑，至少有一部分差异是在先天免疫反应的水平上。一旦我们知道哪些基因参与了对病毒感染的先天反应，我们就会在这些鸡系之间寻找序列差异或多态性。我们将寻找这些基因DNA序列中单核苷酸的变化，即单核苷酸多态性（SNPs）。然后，我们将预测并稍后测试这些snp是否可能对基因编码的蛋白质产生功能差异，无论是在其结构（例如通过改变氨基酸序列）还是在其表达水平上。最后，我们将利用抗性和易感品系之间的杂交来评估单个SNP是否与病毒感染的抗性相关，简单来说，就是观察SNP是否总是在抗性鸟类中被发现。然后，这些snp可以用作正常育种计划中的可选择标记，以选择自然对病毒感染更有抵抗力的鸟类。此外，耐药家禽将成为我们防御人类传染病的新工具。

The UK poultry industry faces increasing challenges in the 21st century. Many of the drugs used to control diseases in poultry are being withdrawn from use. At the same time, improving welfare standards mean that the industry is becoming more free-range. But the downside is that free-range chickens face higher rates of disease challenge, for example through contact with wild birds. One answer to this problem is to breed birds, which have a higher natural resistance to disease. To do this, we need to understand the bird's immunity to disease, so that we can identify ways to control that response. We already know that in birds and mammals, the immune response can be divided into two arms - the innate response and the adaptive response. The latter is a very specific response, which hopefully leads to immune 'memory', in other words the ability to respond rapidly to subsequent infections with the same pathogen. This is how vaccination works, however, it is specific to each pathogen the bird encounters, and thus would not give general resistance to disease. Our target is the innate immune response. This is a generalised response that recognises components of a wide range of pathogens, for example, specific types of molecules in a bacterial coat. It serves two roles - it limits infection until the adaptive immune response can kick in, and also provides signals that control the adaptive immune response. For many infections, a strong innate immune response is all that is needed to control the pathogen and prevent the onset of disease. Our initial aim in this project is to identify as many of the genes in the chicken as possible that are involved in the innate immune response. This is now possible since the chicken genome was sequenced last year and already almost 18,000 genes have been predicted. Our initial gene set will be determined by comparisons with similar gene sets in mammals, and what we can identify from the chicken genome sequence. The next step will be to identify which members of this predicted set of genes are actually involved in the innate immune response to infection with viruses. We will do this by infecting birds with different viruses and looking at the expression of genes following infection, on a global level using whole genome microarrays. These are glass slides containing short unique sequences corresponding to each known gene in the chicken genome that can be used to detect whether a gene is turned on or off. After complex mathematical analysis, one can examine global gene expression using these microarrays and identify which chicken genes respond to a particular viral infection. We have chickens lines, which we know differ in their resistance to viral infections. We suspect that at least some of that difference will be at the level of the innate immune response. Once we know which genes are involved in the innate response to viral infection, we will then look for sequence differences or polymorphisms between these chicken lines. We will be looking for changes at single nucleotides within the DNA sequence of these genes, known as SNPs (single nucleotide polymorphisms). We will then predict, and later test, if these SNPs are likely to make a functional difference to the protein encoded by the gene, either in its structure (for example by changing the amino acid sequence) or the level of its expression. Finally, we will then assess if individual SNPs track with resistance to viral infection using crosses between resistant and susceptible lines, in simplest terms by seeing if the SNP is always found in a resistant bird. These SNPs can then be used as selectable markers in normal breeding programmes to select birds that are naturally more resistant to viral infection. In addition, resistant poultry will represent a new tool in our defense against infectious disease in humans.