Low water temperature is a prevailing abiotic stress which adversely impacts global shrimp growth and production. In this study, a high-density genetic linkage map of L. vannamei was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with an F1 full-sib family mapping panel comprising 148 progenies and 2 parents. A total of 2528 single-nucleotide polymorphisms (SNPs) were assigned to 48 linkage groups (LGs), with a total genetic map length of 3227.383 centimorgans (cM) and an inter-locus density of 0.783 cM/locus. The number of markers per LG ranged from 12 to 190, with a mean of 56. The length of LGs varied from 15.07 to 158.314 cM, with a mean length of 67.237 cM. Five quantitative trait loci (QTLs) for low-temperature tolerance with a logarithm of odds (LOD) threshold≥2.5 were detected, of which only one was identified based on a linkage group-wide significant LOD threshold. Notably, two growth-trait (body weight) related QTLs were located on LG36 with a genome-wide significant LOD threshold. According to the genome and relevant annotations of L. vannamei, a major growth-related candidate gene, tRNA methyltransferase 10 homolog A (TRMT10A), was identified from genomic scaffolds. Further analysis demonstrated that four linked missense mutation SNPs within TRMT10A were closely related to the body weight. Taken together, the constructed genetic linkage map under low-temperature stress provides a valuable reference for QTL mapping and future genomic studies. Its application can facilitate comparative mapping with other populations, as well as marker-assisted selection (MAS) breeding of L. vannamei.

低水温是一种普遍存在的非生物胁迫，对全球虾的生长和生产产生不利影响。在本研究中，南美白对虾的高密度遗传连锁图谱使用双酶切限制性位点相关 DNA 测序 (ddRAD-seq) 构建了 F1 全同胞家族作图面板，包括 148 个后代和 2 个亲本。共有 2528 个单核苷酸多态性 (SNP) 被分配到 48 个连锁群 (LG)，总遗传图谱长度为 3227.383 厘摩 (cM)，基因座间密度为 0.783 cM/基因座。每个 LG 的标记数范围为 12 至 190，平均为 56。LG 的长度为 15.07 至 158.314 cM，平均长度为 67.237 cM。检测到 5 个耐低温的数量性状位点 (QTL)，其对数 (LOD) 阈值≥2.5，其中仅一个基于连锁组范围内的显着 LOD 阈值确定。尤其，两个生长性状（体重）相关的 QTL 位于 LG36 上，具有全基因组显着的 LOD 阈值。根据基因组和相关注释从基因组支架中鉴定出南美白对虾，一种主要的生长相关候选基因，tRNA 甲基转移酶 10 同源物 A (TRMT10A)。进一步分析表明，TRMT10A 中的四个连锁错义突变 SNP 与体重密切相关。综上所述，构建的低温胁迫遗传连锁图谱为QTL定位和未来基因组研究提供了有价值的参考。它的应用可以促进与其他种群的比较作图，以及南美白对虾的标记辅助选择（MAS）育种。