QTL mapping and candidate gene identification for lower temperature tolerance and growth traits using whole genome re-sequencing in Argopecten scallops

• Published in: Aquaculture 2025-01, Vol.595, p.741513, Article 741513
• Main Authors: Wang, Fu-Kai, Zhu, Pei-Can, Zhang, Xiao-Tong, Yu, Kai, Wang, Chun-De, Liu, Bo
• Format: Article
• Language: English
• Subjects: aquaculture; Argopecten irradians; Argopecten irradians irradians; Bohai red; China; chromosome mapping; genes; Genetic linkage map; hybrids; overwintering; phenotypic variation; Quantitative trait locus; quantitative traits; scallops; sequence analysis; species; temperature; Whole-genome resequencing
• ISSN: 0044-8486
• DOI: 10.1016/j.aquaculture.2024.741513

Lower temperature tolerance (LTT) and growth traits are vital to the success of overwintering scallop farming in the North China Sea. Bohai Red, a novel selected scallop strain is the main aquaculture species in this region. However, its poor LTT hinders its growth. To improve these traits, the larger Bohai Red scallop was crossed with the smaller bay scallop (A. irradians irradians) which tolerates low temperatures. The full-sib F1 hybrids and the whole-genome resequencing (WGR) method were used to construct a high-density genetic linkage map comprising 5925 single nucleotide polymorphisms (SNPs). The consensus linkage map consisted of 16 linkage groups spanning 1343.46 cM with an average distance of 0.23 cM. Based on this genetic linkage map, 42 potentially significant quantitative trait loci (QTLs) for LTT and growth were detected in eight different linkage groups (LGs) explaining 9.2–18.6% of the phenotypic variation. LG11 may regulate both LTT and growth as 20 QTLs were localized there. Eighteen candidate genes were identified, including 2 (SCARF1, SLC28A3) for LTT and 16 for the growth-related traits. To the best of our knowledge, the present work is one of the first to fine-map the LTT and growth-related QTLs in a genetic linkage map for hybrid Argopecten spp. scallops. •The first high-density genetic linkage map to be constructed for hybrid Argopecten spp. scallops using the WGR technique.•The lower temperature tolerance (LTT) and growth-related QTLs have been mapped in the genetic linkage map.•The SNP markers associated with relevant traits and candidate genes will facilitate breeding of novel Argopecten scallops.