A genetic linkage map based on Genotyping-By-Sequencing SNPs for giant freshwater prawn Macrobrachium rosenbergii (De...

The giant freshwater prawn Macrobrachium rosenbergii, a commercially important aquaculture species undergoing selective breeding for improved growth performance, lacks a dense SNP-based linkage map despite recent availability of a chromosome-level reference genome. Here we report for the first time a single nucleotide polymorphism (SNP) marker-based linkage map in M. rosenbergii adopting Genotyping-By-Sequencing (GBS) technology. In-silico restriction enzyme evaluation showed that, EcoRI-MseI combination was optimal for Illumina sequencing and effective genome complexity reduction. The GBS sequencing generated approximately 3.6 Gb of sequence data per sample across 147 individuals, including both parents, yielding 61,417 high-quality SNP markers. which were further filtered for missing genotypes (≤30%), HWE (p ≤ 0.05), minor allele frequency (MAF ≥ 0.05), segregation distortion, identical genotype and redundant markers, resulting in 5,317 informative SNP markers for downstream analysis. Linkage analysis using OneMap at LOD 6 successfully mapped 2,723 markers into 59 linkage groups (LGs) corresponding to the haploid chromosome number spanning 5,576.48 cM with an average marker interval of 2.18 cM. The average length of LGs was 94.52 cM. Synteny analysis of linkage groups with the chromosome-level assembled genome exhibited one-to-one correspondence while comparative genome analysis between M. rosenbergii and M. nipponense revealed both chromosomal synteny and extensive structural rearrangements highlighting shared genomic features alongside lineage-specific rearrangements. The present SNP-based linkage map of M. rosenbergii, represents a remarkable advancement in crustacean genomics and provides a valuable genomic resource to facilitate future genetic improvement and breeding programs in this commercially important species.