Lates_calcarifer_linkage_maps_2026

Here are the linkage maps (male, female, sex averaged and sex additive) for Lates calcaifer (Australian barramundi). A total of 49,885 SNP markers were used to construct this linkage map using Lep-MAP3. Code for the construction of this map can be found https://github.com/DigitalFins/Lates_calcarifer_Linkage_map_2025. These maps are a result of 7 males and 3 females and their 1,952 progeny. What was found was that there are male- and female- only regions of recombination across each of the chromosomes, with no overlap. This map therefore creates a consensus map using two methods, sex-avg and sex-additive.

The Linkage Map is a tab separated tect file with the following columns. Please refer to the paper for more information on how columns were calculated.

SNPID = Name of the unique SNP
Chromosome = the chromosome where the SNP is found based on the 2016 reference genome (GCF_001640805.2) (Note, errors in the assembly are corrected here. See paper for more information.)
Physical_pos_bp = the phyisical position of each of the SNPs on the 2016 reference genome (GCF_001640805.2)
Male_cM = the centimorgan position of each SNP in the male-only maps
Female_cM = the centimorgan position of each SNP in the female-only maps
Sex_avg_mean = the mean position of the SNP between the male and female maps (use with caution)
Sex_avg_additive = the male cM + female cM position (calculated due to no overlap in recombination regions between males and females)