Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

Background

The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).

Results

Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7,542 high-quality SNPs were retained. From these, 4,236 high-quality genome-wide loci were selected for bates-probe development and 4,194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.

Conclusion

Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

背景
全基因组基因分型资源的发展，为陆生畜牧与作物产业带来了独特的技术能力：可精准评估个体间的基因组亲缘关系、解析经济性状的遗传架构，并基于个体特定的遗传特征筛选优良选育个体。借助最新的从头（de novo）全基因组基因分型技术进展，即便尚无现成的基因组组装序列，如今也可为水产养殖业提供这类同等重要的基因分型资源。本研究借助简化基因组全基因分型技术（DArTseq），开发了针对斑节对虾（Penaeus monodon，俗称黑虎虾）的全基因组单核苷酸多态性（SNP）分型检测体系。
结果
本研究基于单个简化基因组文库，从澳大利亚野生种群及商业化养殖群体的650个个体中，共鉴定出31262个多态性SNP位点。经过滤去除低测序深度、低最小等位基因频率（MAF）、低分型成功率、偏离哈迪-温伯格平衡（HWE）以及非孟德尔遗传的SNP位点后，最终保留7542个高质量SNP位点。基于上述位点，研究人员筛选出4236个全基因组优质位点用于诱饵探针开发，并最终将4194个SNP位点纳入标准化的靶向捕获测序分型检测体系（DArTcap）。该检测体系专为大规模育种计划中的常规化、低成本商业化应用而设计，其分型结果置信度更高：分型成功率从80.2%±14.7%提升至93.0%±3.5%，测序深度从20.4±15.6提升至80.0±88.7，同时相较于传统测序分型方法，该体系可将成本降低至原有水平的1/3。
结论
尤为重要的是，该检测体系可为斑节对虾产业提供多项核心技术能力：可同时对混养个体进行亲权鉴定、开展基因组亲缘关系分析、管理隐秘家系间的配对组合，还可用于开展基因组与性状架构的深入研究。至关重要的是，当斑节对虾育种计划逐步转向基因组选择育种时，该检测体系可实现低成本高效应用。