Yang Huiping, Grouzdev Denis, Wang Zhenwei, Yee Jayme C, Zeng Yangqing, Sturmer Leslie, Allam Bassem
School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32653, USA.
School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
BMC Genomics. 2025 May 30;26(1):547. doi: 10.1186/s12864-025-11689-5.
The northern quahog Mercenaria mercenaria is a major aquaculture species on the US East Coast, and heat resistance is the most sought trait for aquaculture. This study aimed to establish a genome-wide association for heat tolerance using a 66K SNP array for M. mercenaria. Quahogs from three farms were combined for a heat challenge at 1 °C per day from 24 °C to 35 °C and stay for two days (Phase I), decreasing to 27 °C in 24 h, to 24 °C in another 24 h, and maintaining at 24 °C (Phase II) until no one dead within 48 h at 24 °C (Phase III). Dead and live quahogs were sampled for genotyping using the SNP array.
During the heat challenge, different mortalities among the quahogs from the three farms were identified at 38, 46, and 55% at Phase I, and 36, 30, and 29% at Phase II. For the survivors (Phase III), no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with quahog survival under heat stress across the different farms. The heritability of the heat tolerance was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait on chromosome 7 (p = 1.98 × 10). More significant SNPs (p < 10) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50 K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs).
The fastStructure analysis revealed the proportions of different ancestral components within the quahogs from different farming stocks, highlighting that the genetic factors may contribute to their varying survival rates under heat stress. The associated genes have potential roles in immune response, cellular stress, and tissue repair. The findings highlighted the power of high-throughput approaches for the identification of superior quahog genotypes for further breeding.
北方圆蛤（Mercenaria mercenaria）是美国东海岸的主要养殖贝类，耐热性是水产养殖中最受关注的性状。本研究旨在利用66K单核苷酸多态性（SNP）芯片对北方圆蛤进行全基因组关联分析以研究耐热性。将来自三个养殖场的圆蛤合并，在24℃至35℃的条件下每天升温1℃并持续两天（第一阶段），然后在24小时内降至27℃，再在接下来的24小时内降至24℃，并在24℃维持（第二阶段），直至在24℃条件下48小时内无死亡个体（第三阶段）。对死亡和存活的圆蛤进行采样，使用SNP芯片进行基因分型。
在热应激试验期间，三个养殖场的圆蛤在第一阶段的死亡率分别为38%、46%和55%，在第二阶段分别为36%、30%和29%。对于存活个体（第三阶段），热应激前后体重无变化（p < 0.265）。SNP频率的主成分分析（PCA）表明，不同养殖场的圆蛤在热应激下的存活情况存在显著的遗传差异。耐热性的遗传力为0.680 ± 0.063。全基因组关联研究（GWAS）分析表明，一个SNP与7号染色体上的死亡时间性状显著相关（p = 1.98 × 10）。更多显著的SNP（p < 10）位于已报道在耐热性中起作用的基因内，如丝氨酸/苏氨酸蛋白激酶31和碳水化合物硫酸转移酶11，并且在距离SNP位点50K bp范围内发现的一些基因与耐热性有关，如Toll样受体4和6（TLRs 4和TLRs 6）、尿嘧啶-DNA糖基化酶以及具有血小板反应蛋白基序的解聚素和金属蛋白酶gon-1（ADAMTs）。
fastStructure分析揭示了不同养殖群体中北方圆蛤内不同祖先成分的比例，突出了遗传因素可能导致它们在热应激下存活率不同。相关基因在免疫反应、细胞应激和组织修复中具有潜在作用。这些发现突出了高通量方法在鉴定优良圆蛤基因型以用于进一步育种方面的作用。
