A high density genetic map by whole-genome resequencing for QTL fine-mapping and dissecting candidate genes for growth or sex traits in the pearl oyster (Pinctada fucata martensii)

Pinctada fucata martensii is an economically important shellfish in pearl production. Marker-assisted breeding can be accelerated by whole-genome resequencing (WGR), which is faster and more precise for detecting recombination breakpoints and constructing genetic maps than marker-based genotyping methods. To obtain more genetic information and dissect the loci associated with growth- or sex-related traits, we have constructed a high density genetic linkage map consisting of 4469 recombination bin markers (91,448 SNPs) covering 2232.14 cM, with an average distance of 0.50 cM based on WGR. Thirty-two quantitative trait loci (QTL) related to seven growth traits and one sex trait were mapped in 10 linkage groups (LGs) with 695 candidate genes annotated, and QTLs related to growth traits were mainly mapped on LG4. The combination analysis of QTL mapping and bulked segregant analysis (BSA) revealed that many receptor genes, such as PfNPYR, PfTRHR, PfGABAR(B), PfSSTR-2, and PfDD2R, were involved in neuroendocrine regulation, which is important in growth and reproduction. Moreover, transcriptome analysis of pearl oyster exhibiting extreme opposite traits for shell length revealed that four differentially expressed genes (DEGs) were located on the regions of QTLs related to growth traits, and three genes were consistent with the transcriptome after validation by real-time quantitative PCR (RT-qPCR). This study provided new insight into the molecular mechanism of candidate genes determining traits and provided an ideal platform for MAS by dissecting QTL and candidate genes related to economical traits in P. f. martensii.