基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状

发布时间：2018-12-31 08:07

【摘要】：本研究旨在评价基因库与保种场两个鹿苑鸡保种群的保种现状。利用RAD-seq简化基因组测序鉴定基因库与保种场两个鹿苑鸡群体的SNP标记,通过计算遗传统计量,比较分析两个群体的遗传差异。结果,经过两步数据质控,在基因库与保种场两个鹿苑鸡群体中分别鉴定出SNPs标记395 021个和428 314个,两个群体的平均杂合度Ho分别为0.211 1和0.206 8,群体间的遗传分化系数Fst为0.005 6;在Structure模型聚类分析中两个群体始终聚为一类,没有个体分离出来,表明两个鹿苑鸡群体未发生显著遗传分化(P0.05)。两个群体的近交系数Fis分别为0.178 8和0.193 5,相对较高的近交水平可能是由于起始基础群规模较小(抢救性保护)所导致的。进一步的选择信号分析发现,两个鹿苑鸡群体在1、2、5、Z等染色体区域(位点)上存在一定分化,通过F_(st)和θ_π检验鉴定出58个受选择区域,筛选到96个受选择候选基因。GO和KEGG分析表明,这些差异基因主要富集在能量代谢、信号传递、应激免疫反应等调控通路。利用全基因组SNP标记信息可以更全面地评价保种现状,研究结果为进一步优化鹿苑鸡保种技术方案提供了依据。
[Abstract]:The purpose of this study was to evaluate the current status of conservation of chicken populations in gene pool and seed conservation farm. The SNP markers of two populations of Luyuan chicken were identified by RAD-seq simplified genome sequencing. The genetic differences between the two populations were compared and analyzed by calculating the genetic statistics. The results showed that after two step data quality control, 395,021 SNPs markers and 428,314 SNPs markers were identified in two populations of Luyuan chicken in gene pool and seed preservation farm, respectively. The average heterozygosity Ho of the two populations were 0.211 1 and 0.206 8, respectively. The genetic differentiation coefficient (Fst) was 0.005; In the cluster analysis of Structure model, the two populations were always clustered into one group and no individuals were isolated, which indicated that there was no significant genetic differentiation between the two populations of Luyuan chicken (P0.05). The number of inbred lines of the two populations was 0.178 8 and 0.193 5, respectively. The relatively high inbreeding level may be due to the small size of the initial basic group (rescue protection). Further selection signal analysis showed that the two populations of Luyuan chicken had some differentiation on chromosomal regions (loci), such as the chromosome region (loci), and 58 selected regions were identified by F- (st) and 胃 _ 蟺 test. GO and KEGG analysis showed that these differentially expressed genes were mainly concentrated in energy metabolism, signal transduction, stress immune response and other regulatory pathways. The whole genome SNP markers can be used to evaluate the status quo of species conservation more comprehensively. The results provide a basis for further optimization of breeding conservation techniques of Luyuan chicken.
【作者单位】：江苏省家禽科学研究所国家级地方鸡种基因库;张家港市畜禽有限公司;
【基金】：扬州市自然科学基金项目(YZ2016134) 扬州市高效农业项目(YZ2016051)
【分类号】：S831.2

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