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

Conservation Status Evaluation of Two Luyuan Chicken Populations Based on RAD-seq Simplified Genome Sequencing Technology

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(P>0.05)。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。

This study aimed to evaluate the conservation status of Luyuan chicken breeds which were saved in the national chicken genetic resources and Zhangjiagang Luyuan chicken conservation farm, respectively. The genetic differences of Luyuan chicken populations between national chicken genetic resources and Zhangjiagang Luyuan chicken conservation farm were analyzed by identifying SNP markers and calculating genetic statistics based on RAD-seq simplified genome sequencing technology. The results showed that 395 021 and 428 314 SNP markers were identified in two populations after two steps of data quality control. The average heterozygosity of two Luyuan chicken populations were 0.211 1 and 0.206 8, respectively. The genetic differentiation coefficient of two Luyuan chicken populations was 0.005 6. Results of cluster analysis based on Structure model showed that two Luyuan chicken populations were always clustered together and no individual was separated. These results indicated that the difference between the two populations was not significant（P〉0.05）. Moreover, the inbreeding coefficient of the two populations were 0.178 8 and 0.193 5, respectively. The relative high inbreeding level could be caused by the smaller scale of the initial population （rescuing conservation）. The selection signal analysis found that there were some differentiation between two Luyuan chicken populations on 1, 2, 5, Z chromosomes （locus）. 58 selected areas and 96 candidated genes were identified through the Fst and θπ testing. GO and KEGG analysis showed that these candidate genes were mainly enriched in some biological pathways such as energy metabolism, signal transduction, stress and immunity response pathways, and so on. In conclusion, the method of genome-wide SNP marker can more comprehensively evaluate the conservation status. The results provide the basis for further optimizing the conservation solution of Luyuan chickens.