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Background  Economical cultivation of the  oilseed crop  Jatropha curcas  is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker–trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations.    Results  The mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the  Jatropha  genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes.    Conclusions  The QTL we have identified will serve as a useful starting point in the creation of new varieties of  J. curcas  with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the  Jatropha  genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0326-8) contains supplementary material, which is available to authorized users.

Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L.