The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce “South Sea” pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result genetic tools that can be readily implemented into breeding programs have been developed. However, to date there is no routine single nucleotide polymorphism (SNP) pedigree reconstruction tool publicly available.

In this study, we isolated and assessed a panel of 934 genome-wide DArTcap™ SNPs for their utility and discriminatory power in resolving pedigree relationships in P. maxima. The panel was assessed for its power to assign parentage through in silico simulations of 1,000 progeny in a mass-spawning scenario, based on genotypes of 100 broodstock (1:1 sex ratio) and allowing for random missing genotypes in individuals (0–40%). Assignment success was then assessed across various pedigree panel sizes (25–934 SNPs ranked from the highest minor allele frequency). Simulations showed that a SNP panel comprising 50 or more SNPs had high pedigree resolution and the power to correctly assign progeny to a parent-progeny trio with 95 % confidence. In the simulation examining the effect of missing genotypes on assignment success, even where 40 % of alleles were missing in individuals only 150 SNPs were required in the panel to accurately assign parentage. Progeny from a commercial hatchery mass spawn involving 184 candidate parents were also assigned to their parents using the SNP panel and identified 79 full-sib families and genetic contributions from 33 sires and 11 dams. A highly skewed representation of family distributions in the cohort was observed which highlights the challenge of using a mass-spawning approach to the capture and identification of genetic diversity in P. maxima breeding programs.

唇唇银牡蛎牡蛎Pinctada maxima是重要的水产养殖品种，广泛种植在澳大利亚热带地区和东南亚，生产“南海”珍珠。澳大利亚的珍珠业正在实施针对提高抗病性，生长和珍珠品质的育种计划，因此，已经开发出可以容易地应用于育种计划的遗传工具。但是，迄今为止，尚无公开的常规单核苷酸多态性（SNP）谱系重建工具。

在这项研究中，我们分离和评估了一组934个全基因组DArTcap™SNP，以解决其在最大体育家谱关系中的效用和歧视性。评估小组通过计算机进行分配父母身分的权力基于100种亲鱼的基因型（性别比例为1：1）并允许个体随机缺失的基因型（0–40％），对大规模产卵方案中的1000个后代进行了模拟。然后，评估跨谱系小组大小的分配成功（25-934个SNP从最高的次要等位基因频率中排名）。模拟表明，包含50个或更多SNP的SNP面板具有较高的谱系分辨率，并且能够以95％的置信度正确地将后代分配给亲子后代三重奏。在模拟中，研究了缺失基因型对分配成功的影响，即使个体中缺少40％的等位基因，小组中也只需要150个SNP即可准确分配亲子关系。还使用SNP小组将来自商业孵化场大规模产卵的后代（涉及184个候选亲本）分配给其亲本，并确定了79个同胞家族，并从33个父系和11个大坝中获得了遗传贡献。观察到该队列中家庭分布的高度偏斜表示，这凸显了使用大规模产卵方法来捕获和鉴定遗传多样性的挑战。P. maxima繁殖计划。