Construction of a Genetic Linkage Map and QTL Mapping of Growth-Related Traits in Giant Freshwater Prawn, Macrobrachium Rosenbergii

Growth-related traits are major determinants of production performance in the giant freshwater prawn, Macrobrachium rosenbergii, but their genetic architecture remains incompletely resolved. An F1 full-sib family of 133 individuals and two parents was analyzed, with the two parents genotyped using high-depth whole-genome sequencing (WGS) and the progeny genotyped using IIB restriction-site associated DNA (2b-RAD) sequencing. A total of 858,375,066 paired-end reads were generated, and 9427 single nucleotide polymorphism markers were assigned to 59 linkage groups in the sex-averaged map. The map spanned 8591.22 cM, with a mean marker interval of 0.91 cM. Quantitative trait locus (QTL) mapping identified 22 QTLs for body weight (BW), body length (BL), carapace length (CL), carapace width (CW), carapace height (CH) and telson length (TeL) across nine linkage groups, and individual QTLs explained 9.96-28.13% of phenotypic variation. Functional annotation and enrichment analysis of genes within QTL-associated regions indicated that BW variation was mainly associated with nutrient sensing, extracellular matrix-receptor interaction, focal adhesion, actin-cytoskeleton regulation and calcium-dependent signaling, whereas BL was associated with insulin signaling, lipid metabolism, cyclic-nucleotide signaling, mitochondrial energy production and microtubule organization. To further evaluate key candidates, representative body weight- and body length-related genes were examined by real-time PCR in low-, medium- and high-growth groups. Growth-group real-time PCR analysis was performed for 32 representative body weight- and body length-related candidate genes, and the results prioritized a focused subset of expression-supported candidates, including InR, VAV, Itgβ-PS, Itgα-PS2, Col1A1, PLCD4, CaM4, PDE4C and PAK2 for body weight, and IRS2, HSL, MCD, LIP3, NDUFB7, TUBA1A, LamA, PMCA4, AC1, GC32E and Gαo for body length. These results provide a high-density linkage map, trait-associated QTLs and expression-supported candidate genes for future validation and molecular breeding of M. rosenbergii.