These 790 markers were located in 501 unique locations on the linkage map of the Asian seabass, with an average inter-location space of 4.8 cM (Table 1).
This may be explained that ILP markers were located in gene coding regions whereas SSRs were distributed genome-wide.
About four-fifths of these markers were located more than 5,000 base pairs from the genes that they regulated; many were even on other chromosomes.
Some SNP markers were located in or near regions where QTLs have been previously mapped by linkage analysis.
Markers were located on the scaffolds using BLAST and ePCR (electronic PCR) with high similarity parameters (taking the top hits only, with placement by BLAST (e value < 1 × 10−10) given preference over ePCR where both were available).
None of the significant markers were located in similar zones in the indica and japonica panels.
Among them, twenty two markers were located on nine starch biosynthesizing genes or very close to these genes (less than 2 Mb in physical map) (Additional file 2: Figure S1).
These markers were located in the genome by either physical or genetic mapping, or both, as described in Results.
Two other such markers were located on P. c. chabaudi unassigned linkage groups 2 and 12 (Table 2).
Five additional markers were located to a region on P. falciparum chromosome 12 which is syntenic with one on chromosome 14 of P. c. chabaudi.
Three markers were located to a region on P. falciparum chromosome 11 which is syntenic with one on P. c. chabaudi chromosome 9.
