A genetic linkage map of the Pacific white shrimp (Litopenaeus vannamei): QTL mapping for low-temperature tolerance and growth-related traits and identification of the candidate genes

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.