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

• Published in: Biology (Basel, Switzerland) Vol. 12; no. 3; p. 429
• Main Authors: Wang, Mengchao, Jin, Shubo, Liu, Shuai, Fu, Hongtuo, Zhao, Yunfeng, Jiang, Li
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 10.03.2023; MDPI
• Subjects: Aquaculture; Association analysis; binary trait; Body weight; Breeding; Chromosome 13; Chromosome 17; Chromosome 4; Chromosome 7; Chromosomes; Females; Generalized linear models; Genes; genetic selection; Genome-wide association studies; genome-wide association study; Genomes; Genomics; genotype; Genotype & phenotype; GWAS; Heritability; hybrids; linear models; Macrobrachium nipponense; males; Methods; phenotypic variation; Phenotypic variations; Puberty; Quality control; Rivers; Sex differentiation; sex trait; Single-nucleotide polymorphism; Software; China; binary trait; GWAS; Macrobrachium nipponense; sex trait; heritability
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology12030429

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.