澜沧江中上游光唇裂腹鱼四个地理群体遗传多样性分析

GENETIC DIVERSITY ANALYSIS OF FOUR SCHIZOTHORAX LISSOLABIATUS TSAO POPULATIONS IN THE MIDDLE AND UPPER REACHES OF THE LANCANG RIVER

  • 摘要: 利用简化基因组测序对澜沧江中上游的苗尾-功果桥库区、黄登-大华桥库区、里底江段和乌弄龙江段4个地理群体60个光唇裂腹鱼(Schizothorax lissolabiatus Tsao)样本进行了简化基因组测序, 平均测序深度255.26X, Q30为94.96%, 平均GC含量为39.80%; 测序获得多态性SLAF标签252623个, SNP标记1151083个, 其中, SNP平均完整度为36.66%, SNP平均杂合率为9.5%; 通过测序结果进行遗传多样性分析, 结果表明, 观测等位基因数均为2, 平均期望等位基因数为1.4211—1.5029, 平均观测杂合度为0.2381—0.3131, 平均期望杂合度为0.2690—0.3115, 平均多样性指数为0.2868—03248, 平均香浓指数为0.4269—0.481, 平均次要基因频率(MAF)为0.1854—0.2216, 平均多态信息含量(PIC)为0.2237—0.2553; AMOVA分析结果显示, 在总的变异中, 89.73%的遗传变异来自群体内部, 10.27%的遗传变异来自于群体间, 群体间遗传分化指数在–0.0150—0.1299(P<0.05), 表明群体间存在不同程度的分化。4个群体间遗传距离为0.05—0.15, UPGMA聚类表明, 苗尾-功果桥库区、黄登-大华桥库区和里底3个地理群体相互交叉聚类, 乌弄龙地理群体单独聚为一类。综上, 4个群体的遗传多样性处于中等水平, 遗传距离及聚类结果与试验群体地理距离基本相符, 研究结果将为光唇裂腹鱼种质资源评价与保护提供参考依据。

     

    Abstract: Four wild Schizothorax lissolabiatus Tsao populations of 60 individuals were collected from Miaowei-Gongguoqiao Reservoir area, Huangdeng-Dahuaqiao Reservoir area, Lidi section, and Wunonglong section to analyze the genetic diversities using simplified genome sequencing. The results showed that the RsaⅠ-HaeⅢ enzyme digestion efficiency was 87.19%. A total of 240.29 Mreads were obtained. Through bioinformatics analysis, 474390 SLAF tags were obtained with an average sequencing depth of 255.26X. There are 252623 polymorphic SLAF labels. A total of 1151083 SNP markers were obtained. The average SNP integrity was 36.66%, the average heterozygosity of SNP was 9.5%, the average sequencing Q30 was 94.96%, and the average GC content was 39.80%. The observed allele number in the four wild populations was 2, and the average expected allele number was 1.4211—1.5029. The average observed heterozygosity was 0.2381—0.3131 and the average expected heterozygosity was 0.2690—0.3115. The average Nei diversity index was 0.2868—03248 and the average Shnnon Wiener index was 0.4269—0.4811. The average MAF was 0.1854—0.2216 and the average polymorphic information content was 0.2237—0.2553. AMOVA analysis showed that the genetic variation was 89.73% within populations while it was 10.27% among populations. Genetic differentiation indexes (Fst) were –0.0253150—0.1299 (P<0.05), indicating various degrees of differentiation among populations. The genetic distance between the four geographic groups was 0.05—0.15. UPGMA clustering showed that Miaowei-Gongguoqiao Reservoir, Huangdeng-Dahuaqiao Reservoir and Lidi populations were clustered into one glade due to relatively close genetic distances, while Wunonglong population was separated into another class. To sum up, the genetic diversity of the four groups was at the medium level. The genetic distance and clustering results were consistent with the geographical distance of the test population. These results can provide a reference for molecular genetic breeding and germplasm protection of Schizothorax lissolabiatus Tsao.

     

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