Genome-Wide Association Study of Growth and Sex Traits Provides Insight into Heritable Mechanisms Underlying Growth Development of Macrobrachium nipponense (Oriental River Prawn)

SIMPLE SUMMARY: Macrobrachium nipponense is an important economic aquaculture animal, and due to its delicious taste, it is a popular food in South China. The growth of male and female Macrobrachium nipponense is significantly different. The female grows slowly due to precocious puberty, whereas males have a clear growth advantage. Therefore, due to their fast growth, males are often the subject of genetic breeding by scientists. For this study, we obtained single-nucleotide polymorphisms (SNPs) that could affect growth and sex differentiation to assist artificial selection in genetic breeding. This study entailed a genetic evaluation of 10 growth traits and one sexual trait using genome-wide association analysis (GWAS), while some significant SNPs associated with growth and sexual traits were detected. Moreover, genetic correlations were also found between traits, especially between growth and sexual traits, which greatly simplified genetic selection or made multiple joint selection convenient for more than one trait. At the same time, multiple SNPs were found to be located in two chromosomes and greatly contributed to a high heritability. These results illustrate the genetic nature of growth and sex traits in Macrobrachium nipponense. ABSTRACT: Male hybrid oriental river prawns grow significantly faster than hybrid females. In this study, the growth and sex traits of 181 individuals of Macrobrachium nipponense were recorded, and each individual genotype was evaluated using the 2b-RAD sequencing method. The genetic parameters for growth and sex traits were estimated. A genome-wide association analysis (GWAS) of these traits was performed. In total, 18 growth-related SNPs were detected from 12 chromosomes using a mixed linear model. The most significant loci of weight are located on the position of the SNP (102638935, chromosome 13), which can explain 11.87% of the phenotypic variation. A total of 11 significant SNPs were detected on four chromosomes associated with sex trait (three on chromosome 4, one on chromosome 7 and seven on chromosome 17). The heritability of this trait is 0.8998 and belongs to the range of ultra-high heritability. Genetic correlations were prevalent among the 11 traits examined, the genetic coefficient between sex and body weight reached a significant level of −0.23. This study is the first GWAS for sex of binary and growth traits in oriental river prawn. Our results provide a set of markers for the genetic selection of growth traits and help us to further understand the genetic mechanisms of growth in Macrobrachium nipponense.