Genome-Wide Association Study of Body Weight and Body Length in the Giant Freshwater Prawn (Macrobrachium rosenbergii)

The giant freshwater prawn (Macrobrachium rosenbergii) is an economically important aquaculture species; however, few growth-associated polymorphisms have been reported. Whole-genome resequencing (WGS) was performed on 104 farmed prawns from Vietnam, Thailand, and China, and 51,883,592 SNPs were identified for genome-wide association analyses of body weight and body length. At p < 5 × 10−8, six candidate association loci for body weight and one for body length were identified, with the strongest signal on chromosome 33 (p = 3.02 × 10−9); in a parallel mixed-linear model, none of the seven loci reached p < 5 × 10−8, although they remained at least suggestive for their respective traits. Conditional analyses suggested that the two traits share only partially overlapping signals. Lead SNPs from six loci were located within annotated genes (e.g., cell adhesion molecule 3-like); some loci also harbored cuticle-protein, resilin, and P4HA2-like genes as positional clues within the ±200 kb window. These findings provide candidate association loci and candidate genes for validation in larger, independent populations.