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.

鳙鱼（Hypophthalmichthys nobilis）与鲢鱼（Hypophthalmichthys molitrix，简称H. molitrix）均为外来入侵物种，依据《莱西法案》被列入美国联邦有害物种名录。它们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）的大部分区域建立稳定野生种群，且可产生可育杂交后代并发生复杂的基因渐渗。解析这类遗传混合种群的组成，亟需一套高质量、进化保守的诊断性遗传标记组合，以在形态学鉴定存在歧义的场景下，辅助这两种鱼类的物种识别与种群管理。本研究对采自美国与中国的45个带条形码标记的鳙鱼和鲢鱼样本开展限制性酶切位点相关DNA（RAD）测序，将所得测序读段比对至鲢鱼转录组后，共筛选得到261个在两物种间存在固定等位基因差异的候选单核苷酸多态性（SNPs）位点。我们从中选取质量最优的112个SNP位点，利用来自密西西比河流域的194个疑似纯种及F1杂交个体，以及采自中国黑龙江、珠江与长江流域的疑似纯种鳙鱼和鲢鱼样本进行验证。因引物设计失败、扩增无产物或不具备诊断效用，共剔除50个位点。最终成功鉴定出57个在中美两国河流的鲤科鱼类间保守的物种诊断性SNP位点，其中32个位点被注释至功能基因座。在181个疑似纯种个体中，有27个（占比15%）经验证被确认为杂交回交个体，其中包括3个采自黑龙江流域的回交个体——此前该流域尚未有杂交事件的文献报道。本研究通过RAD测序鉴定得到的57个SNP位点，可为检测中美两国的亚洲鲤种群遗传混合、区分纯种与杂交个体提供高效的诊断工具。