Once polymorphism was detected using the small test panel, markers were then used for genotyping with the entire IRMF panel following standard laboratory protocols.
Approximately 150 polymorphic markers were developed and subsequently used for genotyping with the entire IRMF panel.
Out of the 100 markers genotyped with the entire IRMF panel, 67 were placed on to 14 linkage groups of ShrimpMap and 34 remained unlinked using CRIMAP with LOD score of 3.
Considering the variability observed with our CRIMAP analysis, due perhaps to variability in segregation of alleles within the mapping family, segregation distortion in a large number of markers, the composition/structure of the IRMF family itself, a large number of codominant markers (such as EST-SSRs and single nucleotide polymorphism [SNP]), as well as other mapping families, will be used to increase the density and accuracy of ShrimpMap and other published linkage maps for shrimp.
However, considering the high number of sequences homologous to reverse transcriptase-like and other transposable elements, caution should be taken about using genomic libraries for marker development with this IRMF family.
Five of the seven polymorphic markers were tested with the entire IRMF panel and 2 of these (D28118 U26403) were used for CRIMAP analysis (Table 2) and remain unlinked.
The sex of the IRMF progeny was treated as a marker and analyzed using CRIMAP with LOD scores of 3.