High-density genetic linkage map based on arbitrary and microsatellite markers using inter-specific recombinant inbred lines in eggplant ( Solanum melongena L.)

Eggplant is an important Solanaceous vegetable crop with distinct morphological forms, colours, and shape of the fruits. Limited genomic coverage of the crop is a major constraint to unfold the cause of morphological variations underlying the contrasting traits. Therefore, with the aim to initiate targeted breeding efforts and to render ready-to-use markers for application in mapping quantitative trait loci (QTLs)/genes and to facilitate MAS, arbitrary and microsatellite molecular markers were used to map an inter-specific mapping population of 114 F 8 -recombinant inbred lines (RILs) developed using two contrasting lines, Ramnagar Giant ( Solanum melongena L.) and W-4 ( S. incanum L.). The arbitrary and microsatellite markers were screened for polymorphism with aim to cover the whole genome of eggplant. Of the total 1443 number of markers investigated, 6.07% RAPDs, 25% ISSR, 46.25% SCoT, and 22.46% SSRs revealed polymorphism between the parental lines, and were used for genotyping the RILs population. The results exhibit robust and sturdy nature of SCoT and microsatellite markers in unwrapping variations between both genotypes. Further, a high-density genetic linkage map was constructed with LOD threshold ≥ 4 clustered into 12 tentative linkage groups and spanning 1165 cM of the eggplant genome with an average marker density of 4.13 cM. The results shall further be used in mapping QTLs of agri-horticultural traits in eggplant.