he elevating demand for fuels has raised an interest towards culling an alternate and promising renewable source of energy i.e. biodiesel from non-edible crops which do not compete with aliment crops and agricultural lands. Jatropha (Jatropha curcas L.), a non-edible energy crop of the family euphorbiaceae, has the potential of providing biodiesel feedstock due to high seed oil content (42%). The stumbling roadblock for commercialization of Jatropha-predicated biodiesel is low seed yield per inflorescence. Low female to male flower ratio (1:25-30) is considered as a major constraining factor responsible for low seed yield in Jatropha. The molecular substructure female flower and the transition into female flower as well as the genetic factors contribute to differential female to male flower ratio in different genotypes has not been kenned in J. curcas. To increment the seed yield, an exogenous cytokinin application was performed on floral meristems which resulted in an incrementation of total flower count with a higher female to male flower ratio but the seed biomass did not increment in the same proportion. Molecular mechanisms underlying carbon capture and flux affected between the source and sink (flowers/fruits/seed) due to cytokinin application have not been studied yet. Thus, the current study, consequently, investigated: (1) the molecular cues for floral transitions and female flowering in high female flower genotype of Jatropha curcas and then validating the expression status identified genes in low (1:25-30) female to male flower ratio genotype; (3) deciphering molecular components of cytokinin on flowering and source-sink relationship of Jatropha curcas L.The expression profile of forty-two genes for floral organ development and sex tenaciousness was done at six floral developmental stages of a J. curcas genotype was investigated. Key genes identified for reproductive phase transition were CUC2, CRY2, PIN1, TFL1, AP1, SUP, CKX1 and TAA1. Further, CUC2, TAA1, CKX1 and PIN1 were identified for their role in female flowering and SUP and CRY2 for female flower transition. When the expression staus of these genese was compared with low female flower ratio genotype, genes TAA1, SUP, CKX1 and CRY2 showed paramount genes at a stage, where transition towards female flower occurs through abortion of male flower primordia. To understand the transcriptional regulation of these developmental transitions, promoter regions of key genes were analyzed for regulatory elements. GAREAT, UP2ATMSD and MYB1AT were identified uniquely for genes associated with female flowering. Furthermore, to understand, the molecular mechanisms underlying carbon capture and flux affected between the source and sink in developing flowers, fruits and seeds after cytokinin application, RNA-seq predicated comprehensive transcriptome sequencing of inflorescence meristems (treated with cytokinin) and control (untreated inflorescence meristems) at time-intervals of 15 & 30 days, respectively of J. curcas by utilizing NextSeq 500 platform of Illumina was performed. KEGG predicated functional annotation identified sundry metabolic pathways associated with carbon capture and flux. Pathways such as photosynthesis, carbon fixation, carbohydrate metabolism and nitrogen metabolism were upregulated after 15 days of cytokinin treatment however, they were downregulated after 30 days. Five genes FBP, SBP, GS, GDH and AGPase were identified to be significantly downregulated after 30 days of cytokinin application and are associated with biomass and yield.The current study provides repertoire of key genes which can be potential targets to increment the feedstock yield of Jatropha through transgenic or molecular breeding approaches. Further this study provides information on molecular mechanisms of female flower development and transitions towards female flowers. The study withal shed light on the metabolic pathways affected by cytokinin treatment thereby altering source to sink ratio, in turn the feedstock yield of Jatropha. By understanding this phenomenon felicitous gene target were identified for incrementing the yield through genetic interventions.