Single-nucleotide polymorphisms linked to body weight revealed in growth selected Macrobrachium rosenbergii

Abstract

Association of type I single nucleotide polymorphic (SNP) markers with quantitative traits can provide an effective method for detecting genes and functions that are responsible for performance variation in domesticated species. In order to discover novel polymorphisms in candidate genes that could be associated with growth, fragments (175 to 668 bp) from 11 housekeeping, regulatory, and immune response genes of Macrobrachium rosenbergii previously reported to contain 83 SNPs were amplified from genomic DNA of 23 growth selected (cumulative genetic gain of 18%) and 23 unselected individuals and sequenced by Sanger’s method. A total of 45 SNPs were identified from eight genes, of which 20 were novel and 18 were found to be growth associated with allele frequencies > 0.65 in the selected group. Eleven of these were located in exonic regions of which 3 present in crustacean lipocalin (LIPC) and heat shock protein 21 (HSP21) were nonsynonymous. In silico prediction indicates that 2 of the non-synonymous alleles may result in higher stability of the proteins. Of the 5 synonymous growth-associated SNPs, 3 present in phosphoenol pyruvate carboxykinase (PEPCK), cytochrome oxidase 1 (COX1), and HSP70 were a switch to the preferred codon. Seven SNPs were located in the 3′UTRs of lectin 3 and 4 (LEC3, LEC4) and anti-lipopolysaccharide factor 1 (ALF1). Only one altered allele was observed at every locus. No SNPs were found in NaK-ATPase, mitochondrial manganese superoxide dismutase, and tachylectin genes. This is the first such marker association study being reported for M. rosenbergii from India and will be of use in selecting future generations.