Data from: Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China

Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China.

鳙（Bighead carp, Hypophthalmichthys nobilis）与鲢（Silver carp, Hypophthalmichthys molitrix）均为入侵物种，依据《莱西法案》被列为美国联邦有害物种。目前二者已在密西西比河流域（MRB，涵盖密西西比河、伊利诺伊河与密苏里河）的大部分区域形成自然种群，且可产生可育杂交后代并发生复杂的基因渐渗现象。要解析此类遗传混合的构成，需要大量高质量、进化保守的诊断性遗传标记，以在二者形态学鉴定存在模糊性的背景下，辅助这两种鱼类的物种识别与种群管理。研究人员对采自美国与中国的45尾经条形码标记的鳙和鲢进行限制性酶切位点相关DNA（restriction site-associated DNA, RAD）测序，将测序读段比对至鲢的转录组后，共得到261个在两个物种间存在固定等位基因差异的候选单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点。随后从中筛选出质量最优的112个SNP位点，利用194份采自密西西比河流域的推定纯种个体与F1杂交样本，以及采自中国黑龙江、珠江与长江流域的推定纯种鳙和鲢样本进行验证。因引物设计失败、扩增失败或不具备诊断效用，共剔除50个SNP位点。最终在中美两国河流的鳙鲢种群中，共鉴定得到57个物种保守的诊断性SNP位点，其中32个位点被注释至功能基因座。在181份推定纯种样本中，有27份（占比15%）经验证被鉴定为杂交回交个体，其中包括3份采自黑龙江流域的回交样本——此前该流域尚未有杂交事件的相关报道。本研究通过RAD测序获得的57个SNP位点，可为中美两国的亚洲鲤种群遗传混合检测、杂交个体与纯种个体的鉴别提供高效的诊断工具。