基于RAD-seq技术的俄罗斯鲟SNP分子标记开发

Development of SNP molecular markers for Russian sturgeon(Acipenser gueldenstaedti) based on RAD-seq technology

  • 摘要: 【目的】 基于限制性位点相关DNA测序(RAD-seq)开发出俄罗斯鲟(Acipenser gueldenstaedti)的潜在单核苷酸多态性(SNP)分子标记,掌握俄罗斯鲟人工养殖群体的遗传多样性,为深入研究鲟形目鱼类的保护遗传学提供技术支撑。【方法】 通过CTAB法提取俄罗斯鲟鳍条DNA,构建DNA文库后利用Illumina NovaSeq 6000测序平台完成RAD-seq,经质控过滤、聚类组装及比对分析等筛选出潜在的SNP位点,并以SNaPshot和Sanger测序对SNP位点进行验证。【结果】 5个俄罗斯鲟样本RAD-seq共获得14.24 Gb原始数据(Raw base),平均每个样本的有效数据(Clean base)为2.84 Gb,平均有效数据率为99.54%,Q20均在96.00%以上,GC含量在40.52%~41.36%。数据组装总长度为53211245 bp,组装Contig的平均长度为343 bp,N50为404 bp;各样本测序得到Reads与组装基因组的比对率在59.89%~62.43%,平均测序深度为15.75~23.84倍。5个俄罗斯鲟样本RAD-seq获得的SNPs位点总数在299416~367709个,SNP转换位点数在183070~224458个,SNP颠换位点数在116346~143251个,转换/颠换比(Ts/Tv)平均为1.57;SNP位点的杂合率在82.81%~97.43%,其突变类型可分为6种(T/C、T/A、T/G、C/G、C/A和A/G),以T/C或A/G的出现频率最高。基于Sanger测序从随机挑选的100个潜在SNPs位点中筛选出36个多态性SNPs位点,其突变类型中以A/G的出现频率最高(44.4%),其次是T/C(出现频率为36.1%),A/C、C/G和G/T的出现频率相对较低,分别为8.3%、8.3%和2.7%。36个SNPs位点共检测到72个等位基因,最小等位基因频率(MAF)的范围在0.0147~0.5000,观察杂合度(HO)为0.029~0.971,期望杂合度(HE)为0.029~0.523;除Ag18、Ag33、Ag35和Ag36等4个SNPs位点呈低度多态性(PIC≤0.25)外,其他32个SNPs位点均为中度多态性位点(0.25HWE>0.05)。【结论】 基于RAD-seq开发俄罗斯鲟SNP分子标记是一种切实可行的方法,开发出的SNP分子标记通用性高、数量多、覆盖率广,为俄罗斯鲟群体遗传学研究、遗传连锁图谱构建及分子辅助育种提供了技术支撑。

     

    Abstract: 【Objective】 To develop potential single nucleotide polymorphism(SNP) molecular markers for the Russian sturgeon(Acipenser gueldenstaedti) using restriction site-associated DNA sequencing(RAD-seq) and evaluate the genetic diversity of artificially farmed populations, which could provide technical support for in-depth research on the conservation genetics of sturgeon species. 【Method】 DNA was extracted from fins of Acipenser gueldenstaedti using the CTAB method. DNA libraries were constructed, and RAD-seq was performed on the Illumina NovaSeq 6000 platform. Potential SNP loci were identified through a series of steps, including quality control, filter, cluster assembly and mapping analysis. The identified SNPs were validated using SNaPshot and Sanger sequencing. 【Result】 From 5 Acipenser gueldenstaedti samples, a total of 14.24 Gb of raw base was generated via RAD-seq. Each sample had an average clean base of 2.84 Gb, with a clean base rate of 99.54% and Q20 values exceeding 96.00%. The GC content ranged from 40.52% to 41.36%. The total length of assembled data was 53211245 bp, with an average contig length of 343 bp and N50 of 404 bp. The alignment rate of reads to the assembled genome ranged from 59.89% to 62.43%, with an average sequencing depth of 15.75 to 23.84 times. RAD-seq identified 299416-367709 SNP loci across the 5 samples, with SNP transition loci number of 183070-224458 and SNP transversion loci of 116346-143251. The average transition/transversion ratio(Ts/Tv) was 1.57. The heterozygosity rate of SNP loci ranged from 82.81% to 97.43%, with mutation types classified into 6 categories(T/C, T/A, T/G, C/G, C/A, A/G), among which T/C or A/G occurred most frequently. Based on Sanger sequencing, 36 polymorphic SNPs loci were screened from 100 randomly selected potential SNPs loci. Among the mutation types, A/G had the highest frequency(44.4%), followed by T/C(36.1%). The frequencies of A/C, C/G and G/T were relatively low, at 8.3%, 8.3% and 2.7% respectively. A total of 72 alleles were detected at the 36 SNPs loci, with the minimum allele frequency(MAF) ranging from 0.0147 to 0.5000, observed heterozygosity(HO) ranged from 0.029 to 0.971, and expected heterozygosity(HE) ranged from 0.029 to 0.523. Except for 4 SNPs loci(Ag18, Ag33, Ag35 and Ag36), which exhibited low polymorphism(PIC≤0.25), the remaining 32 SNPs loci were moderately polymorphic(0.25<PIC≤0.50), indicating that the genetic diversity of artificially farmed Acipenser gueldenstaedti in southwestern China was relatively low. Hardy-Weinberg equilibrium testing revealed that 19 SNPs loci were in equilibrium(PHWE>0.05). 【Conclusion】 Developing SNP molecular markers for Acipenser gueldenstaedti using RAD-seq is a practical and feasible approach. These markers exhibit high universality, large quantity, and wide coverage, providing valuable technical support for population genetics studies, genetic linkage map construction and molecular-assisted breeding programs for Acipenser gueldenstaedti.

     

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