TMV 2, a LLS susceptible genotype and the COG 0437, a LLS resistant genotype were crossed and their F2 population was used for marker analysis in the present investigation. The phenotypic mean data on F2: 3 progenies were used as phenotype. Seventy seven SSR markers were used for the parental polymorphism. Among SSR markers, nine markers were found polymorphic between the parents TMV 2 and COG 0437. Eight markers formed a linkage group and covered a distance of 37.2 cM with an average 4.65 cM at LOD 3.0. The composite interval mapping analysis resulted in two QTLs viz., each one for hundred kernel weight and LLS severity score with 6.1 and 37.9 R2 respectively. The nearest marker for QTLs of hundred kernel weight and LLS severity score were Ah 4–26 and PM 384 respectively. The markers PMc 588 (3.9 cM) and Ah 4–26 (4.3cM) are the flanking markers for PM 384 and hence these flanking markers can be used for marker assisted breeding for LLS resistance. The parent COG 0437 is the major contributor for both of these QTLs. Considering the phenotypic variation explained by these QTLs, identification of more effective QTLs for hundred kernel weight is required to utilise in the marker assisted breeding programme. However the LLS QTL has 37.9 per cent of phenotypic variation explained and hence can be effectively utilised in marker assisted breeding programme. By using these QTLs, plant breeders can effectively monitor the flow of inheritance of the resistance characters along with desirable phenotypic traits
