School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, 75005, Paris, France.
BMC Genomics. 2024 Sep 9;25(1):847. doi: 10.1186/s12864-024-10756-7.
The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability.
Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7% pass rate with stringent quality control. Concordance testing affirmed the array's repeatability, with an average agreement of allele calls of 99.64% across multiple tissue types, highlighting its reliability. The tissue-specific analysis demonstrated that some tissue types yield better genotyping results than others. Importantly, the array, including its embedded mitochondrial markers, effectively elucidated complex genetic relationships across different clam groups, both wild populations and aquacultured stocks, showcasing its utility for detailed population genetics studies.
The 66K SNP array is a powerful and robust genotyping tool that offers unprecedented insights into the species' genomic architecture and population dynamics and that can greatly facilitate hard clam selective breeding. It represents an important resource that has the potential to transform clam aquaculture, thereby promoting industry sustainability and ecological and economic resilience.
硬壳蛤（Mercenaria mercenaria）是一种分布在美国东海岸的海洋双壳贝类，支撑着重要的贝类产业。20 世纪 70 年代和 80 年代的过度捕捞导致了产量的减少。虽然自那时以来，该行业从野生捕捞向水产养殖的转型提高了产量，但也加剧了疾病爆发等挑战。在这项研究中，我们开发并验证了一种 66K SNP 芯片，旨在推进硬壳蛤的遗传研究和改良育种计划，特别是开发有助于了解疾病抗性和环境适应性的标记。
对 84 个蛤样本和 277 个蛤混合文库进行全基因组重测序，产生了超过 3.05 亿个 SNPs，经过筛选，得到了 370,456 个 SNPs，用于设计 66K SNP 芯片。这种中密度芯片包含 66,543 个针对编码和非编码区域的探针，包括 70 个线粒体 SNPs，以捕捉该物种内广泛的遗传多样性。SNP 在蛤基因组中均匀分布，SNP 之间的平均间隔为 25,641bp。该芯片包含用于检测蛤病原体穆氏黏球菌（以前称为 QPX）的标记，增强了其在疾病管理中的实用性。对 1,904 个样本的性能评估显示，严格质量控制下的通过率为 72.7%。一致性测试证实了该芯片的可重复性，不同组织类型的等位基因调用平均一致性为 99.64%，突出了其可靠性。组织特异性分析表明，一些组织类型的基因分型结果优于其他组织类型。重要的是，该芯片包括其嵌入式线粒体标记，有效地阐明了不同蛤群体（野生种群和水产养殖种群）之间的复杂遗传关系，展示了其用于详细种群遗传学研究的实用性。
66K SNP 芯片是一种强大而稳健的基因分型工具，提供了对该物种基因组结构和种群动态的前所未有的深入了解，并极大地促进了硬壳蛤的选择性育种。它代表了一种重要的资源，有可能改变贝类养殖，从而促进产业可持续性和生态及经济弹性。
