通过全基因组深度测序开展鸡体重性状重要基因的克隆与突变分析

Huiyang Beard Chicken is one of the most famous indigenous breed in China，which is famous for its characteristic meat quaity while has poor performances in productive and reprodective traits. In order to combine the valuable market properties of Chinese indigeous breed with economically effecient commercial stock,we have established an F2 intercross between the slow-growing Huiyang Beard Chicken and the fast-growing commercial broiler breed Lingnan Huang chicken. Using one- and two- dimensional genome scan, multiple additive and epistatic QTL for body weight trait have been mapped on GGA1 and GGA27. The aim of this project is to thoroughly explore the genetic basis underlying body weight trait and then find out the molecular mechanism that can explain the huge growth difference between the two lines in this F2 cross.Therefore, we plan to perform the whole genome resequencing with a high coverage on these two different Chinese breeds. With the combined tools of the knowledge from functional genomics, comparative genomics, bioinformatics as well as molecular phylogenetics, and based on previouly identified QTL, we intend to determine the functional mutations underlying body weight trait and further dissect the complex genetic architecture, so as to establish breeding platform of high quality and eficiency for Huiyang Beard Chicken. Since body weight trait is one of the most economically important phenotype in broiler, the results of this research will not only help us to increase the performance of Huiyang Beard Chicken, but also could be used as a guide for other breeds.

惠阳胡须鸡是原产广东并收入《中国家禽品种志》的我国著名地方鸡种。胡须鸡风味肉质好，但体重生长和繁殖性能较差，岭南黄鸡是我国自主培育的商业化优质鸡品种，生长速度是胡须鸡的两倍，本项目利用前期建立的惠阳胡须鸡和岭南黄鸡快长型父系（A系）商业肉鸡为亲本的F2设计资源群，着重对已经定位在1号和27号染色体的影响体重性状的QTL展开分析，利用第二代测序技术，开展深度测序获得两个品种的全基因组的序列信息，检测二个品种基因组水平的变异模式，定位影响性状的功能基因，利用功能基因组学，比较基因组 ，生物信息学以及分子进化学等学科知识，了解选择选择对不同鸡品种的影响，综合阐述其生长差异的遗传机制。项目研究将有可能开发出具有自主知识产权、可直接应用于胡须鸡商业育种的分子标记或基因诊断试剂盒，对于提升我国胡须鸡育种技术水平，通过项目执行，有可能为胡须鸡的开发利用提供依据和指导，为其他地方鸡种的保护和利用提供借鉴

惠阳胡须鸡是原产广东并收入《中国家禽品种志》的我国著名地方鸡种。胡须鸡风味肉质好，但体重生长和繁殖性能较差，岭南黄鸡是我国自主培育的商业化优质鸡品种，生长速度是胡须鸡的两倍，本项目利用前期建立的惠阳胡须鸡和岭南黄鸡快长型父系（A 系）商业肉鸡为亲本的 F2 设计资源群，着重对已经定位在 1 号和 27 号染色体的影响生长性状的 QTL 展开分析。为了进一步精细定位QTL区间，基于F2代资源群，本项目构建了深度杂交系（Advanced intercross lines，AIL）来缩小重组区间，目前该家系已传至F9代。同时，本研究完善了基于测序的分型技术（Genotyping by Sequencing，GBS）和Fluidigm高通量基因分型平台，并应用于深度杂交系的F8-F9代，开发出了经济高效挖掘鸡全基因组高密度标记的方法。F9代的关联分析结果与F2代的定位结果一致，在1号染色体候选QTL区间内部进行了同源相同（Identity by desent，IBD）定位，确定了九代杂交过程中的所有历史重组事件，并以此将1号染色体的候选QTL区间缩小至660 Kb。另外，F0代的重测序数据结合比较基因组杂交芯片（Array comparative genomic hybridization，CGH）、表达分析等手段，解析了鸡胡须形状是由27号染色体上复杂的三个拷贝数变异（Structure Variation，SV）导致的。. 本项目将影响鸡生长性状的QTL进一步缩小区间，并找到导致鸡胡须形状的致因突变，为我国胡须鸡的分子育种及其他地方鸡种的保护和利用提供了很好的指导和借鉴作用。

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