基于全基因组重测序分析酃县白鹅保种效果

Assessment of Conservation Effects of Lingxian White Goose Based on Whole Genome Resequencing

【目的】酃县白鹅是湖南地区优秀的地方鹅种,为了解酃县白鹅的保种效果,对保种场各家系进行保种工作的评估。【方法】从酃县白鹅保种场的42个家系中各选取1只公鹅,翅静脉采血,提取DNA,进行全基因组重测序。基于保种场42只酃县白鹅公鹅的重测序数据,对其群体遗传结构和遗传多样性进行分析与评价。【结果】检测到采样群体的SNPs位点14270647个,经数据质控和过滤筛选出13696453个SNPs位点。主成分分析(PCA)结果发现,42只公鹅个体可以明显聚为3个亚群;通过群体渗透分析发现,3个亚群之间未发生明显的杂化现象(K=3)。亚群1和亚群3的群体分化指数(Fst值)为0.0842。42只酃县白鹅共检测到832条连续性纯合片段(ROH),ROH片段长度都集中在0~2 Mb区间;基于ROH得到的近交系数F ROH值为0.0130。群体的期望杂合度为0.2918,观测杂合度为0.2968,群体近亲系数(Fis)为0.036,多态信息含量(PIC)为0.266,基因多样性指数(Nei)为0.336。【结论】酃县白鹅保种场的鹅遗传多样性比较丰富,群体近交程度比较低,观测杂合度略高于期望杂合度,并无显著性差异,说明群体处于平衡状态,但部分亚群出现了中度遗传分化,后续保种过程中要使这些亚群进行杂交,以减少酃县白鹅遗传分化的程度。

【Objective】Lingxian White goose is a great indigenous goose breed in Hunan province.To further understand the conservation effect of Lingxian White goose,an evaluation of the conservation work was conducted among various families in the conservation farm.【Method】One male goose was selected from each of the 42 families in the Lingxian White goose conservation farm,and blood was collected from the wing vein to extract DNA for whole genome resequencing.Based on the resequencing data of 42 Lingxian White goose male geese in the conservation farm,the population genetic structure and genetic diversity were analyzed and evaluated.【Result】A total of 14270647 SNPs were detected in the sampled population,and 13696453 SNPs were selected through data quality control and filtering.The results of principal component analysis(PCA)showed that 42 male geese were significantly clustered into three subgroups.Population admixture study revealed that there was no substantial hybridization taking place among the three subgroups(K=3).The fixation index(Fst)between subgroup 1 and subgroup 3 was 0.0842.A total of 832 runs of homozygosity(ROH)were identified among Lingxian White geese,all of ROH lengths concentrated in the range of 0 to 2 Mb.F ROH which resulting inbreeding coefficient based on ROHs was 0.0130.The expected heterozygosity for the group was 0.2918,the observed heterozygosity was 0.2968,inbreeding coefficient(Fis)was 0.036.The polymorphism information content(PIC)was 0.266,and the gene diversity index(Nei)was 0.336.【Conclusion】The conserved population of Lingxian White goose was found to have a low degree of inbreeding and a comparatively high genetic diversity.The observed heterozygosity was slightly higher than the expected heterozygosity,but without a significant difference,suggesting that the Lingxian White goose population was in a balanced state.Although some degree of moderate genetic differentiation had emerged among certain subgroups.In subsequent conservation plan,it was necessary to promote interbreeding among these subgroups to reduce the genetic differentiation of Lingxian White goose.