绿头野鸭与北京鸭杂交后代等位基因差异表达分析

发布时间：2018-04-05 22:41

本文选题：北京鸭　切入点：绿头野鸭　出处：《西北农林科技大学》2017年硕士论文

【摘要】：从野鸭到北京鸭的驯化过程中其基因组发生了海量的变异,包括单核苷酸变异(Single nucleotide polymorphism,SNP)、短片段插入缺失(indels)和拷贝数变异(Copy number variation,CNV)等。这些变异可能会导致基因表达量的改变和蛋白编码的变化。其中,基因表达量的改变由顺式调控元件、反式作用因子和环境等因素共同影响,这些因素均可能造成北京鸭和野鸭之间基因表达的差异。而杂交后代中,来自双亲的等位基因处于相同的反式作用和环境下,两个等位基因的差异表达则主要由受顺式调控造成。因此,杂交后代两个等位基因之间的表达差异可以反映北京鸭和野鸭顺式调控元件的不同,为快速定位顺式调控的变异奠定了基础。本研究选取远缘群体绿头野鸭和北京鸭构建了F2资源群体,研究中所需血液样本和组织样本均来源于该F2资源群体。本研究共对杂交后代F1的32个组织样本(来自3个家系,分3个时间点采集)进行了转录组测序,并通过生物信息学软件和Perl语言编程完成了杂交后代等位基因差异表达的分析。分析结果如下:(1)32个样本聚类分析表明不同组织的基因表达模式差异显著;相同组织内不同时期的样本表达模式虽然比较相近,但1日龄的样本单独聚在一支,19日龄和35日龄的样本之间没有明显的区分;不同性别的样本基因表达模式相近,雌性和雄性个体的基因表达数据并没有明显的区分。(2)腹脂、肝脏、皮肤、脾、法氏囊、脑、肺、胸腺、心共9个组织的混合样品中有624个基因为差异表达的等位基因,占基因总数的3.8%,其中部分基因和脂代谢、细胞连接有关。(3)在16个杂交后代胸肌样本中鉴定出577个,占基因总数的3.5%,其中2号染色体上的OBSCN、MYL3基因,7号染色体上的NEB基因,19号染色体上的MYH3,27号染色体上MYBPH等基因的产物都是肌肉组织的重要组成部分。综上,等位基因差异表达现象在鸭子中是广泛存在的,杂交后代中差异表达等位基因的顺式调控元件在驯化过程中可能发生了改变。顺式调控序列改变对基因表达的影响,可能最终导致了驯化过程中丰富的表型变异。另外,本研究揭示了顺式调控可能在鸭子的驯化过程中发挥重要作用,为鸭子驯化过程中受选择基因的鉴定和鸭子基因组的进一步解析奠定了基础。
[Abstract]:In the course of domestication from wild duck to Beijing duck, there were a lot of variations in their genomes, including single nucleotide polymorphismSNPs, short fragment insertion deletion in dels, copy number variation and so on.These variations may lead to changes in gene expression and protein coding.The changes of gene expression were affected by the cis-regulatory elements, trans-action factors and environmental factors. These factors may result in the difference of gene expression between Peking duck and wild duck.In the hybrid progeny, the alleles from both parents were in the same trans action and environment, and the differential expression of the two alleles was mainly caused by cis regulation.Therefore, the difference of expression between the two alleles can reflect the difference of cis-regulatory elements between Peking duck and wild duck, which lays a foundation for rapid localization of cis regulation variation.In this study, a F2 resource population was constructed from the distant populations of mallard duck and Beijing duck. The blood samples and tissue samples were obtained from the F2 resource population.In this study, 32 tissue samples (from 3 families, collected at 3 time points) of F1 were sequenced.The allelic differential expression of hybrid offspring was analyzed by bioinformatics software and Perl programming.The results were as follows: (1) 32 samples cluster analysis showed that there were significant differences in gene expression patterns among different tissues, while the expression patterns of different samples in the same tissues were similar at different stages.However, there was no significant difference between the samples of 19 and 35 days of age, and the gene expression patterns of the samples of different genders were similar, and the gene expression data of female and male individuals had no significant difference between them.In the liver, skin, spleen, bursa of Fabricius, brain, lung, thymus and heart, there are 624 alleles which are differentially expressed alleles, accounting for 3.8% of the total genes, some of which are genes and lipid metabolism.A total of 577 breast muscle samples from 16 hybrid progenies were identified.The products of OBSCN MYL3 gene on chromosome 2, NEB gene on chromosome 7, MYH330 gene on chromosome 19 and MYBPH gene on chromosome 27 are important components of muscle tissue.In conclusion, allelic differential expression is widespread in ducks, and the cis-regulatory elements of differentially expressed alleles may be changed during acclimation.The effect of cis regulation sequence change on gene expression may eventually lead to abundant phenotypic variation during acclimation.In addition, this study revealed that cis-regulation may play an important role in duck acclimation, which lays a foundation for the identification of selected genes and further analysis of duck genome during duck acclimation.
【学位授予单位】：西北农林科技大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S834

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