A linkage map was constructed consisting of 105 SSR (simple sequence repeat) markers converged into
11 linkage groups. With this map, we identified a total of 28 QTLs for 11 growth and seed traits using a population
of 296 backcrossing jatropha trees. Two QTLs qTSW-5 and qTSW-7 controlling seed yield were mapped on LGs 5
and 7 respectively, where two QTL clusters controlling yield related traits were detected harboring five and four
QTLs respectively. These two QTL clusters were critical with pleiotropic roles in regulating plant growth and seed
yield. Positive additive effects of the two QTLs indicated higher values for the traits conferred by the alleles from
J. curcas, while negative additive effects of the five QTLs on LG6, controlling plant height, branch number (in the
4th and 10th months post seed germination), female flower number and fruit number respectively, indicated
higher values conferred by the alleles from J. integerrima. Therefore favored alleles from both the parents could be
expected to be integrated into elite jatropha plant by further backcrossing and marker assisted selection. Efficient
ways to improve the seed yield by applying the two QTL clusters are discussed.