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Background  As an important biofuel plant, the demand for higher yield  Jatropha curcas  L. is rapidly increasing. However, genetic analysis of  Jatropha  and molecular breeding for higher yield have been hampered by the limited number of molecular markers available.    Results  An ultrahigh-density linkage map for a  Jatropha  mapping population of 153 individuals was constructed and covered 1380.58 cM of the  Jatropha  genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs,  qNF - 1 ,  qNF - 2a ,  qNF - 2b ,  qNF - 2c ,  qNF - 3 ,  qNF - 4 ,  qNF - 6 ,  qNF - 7a ,  qNF - 7b  and  qNF - 8,  that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs,  qTWF - 1 ,  qTWF - 2  and  qTWF - 3,  that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate  Jatropha  fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits.    Conclusion  This study is the first to report an ultrahigh-density  Jatropha  genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for  Jatropha .    Electronic supplementary material  The online version of this article (10.1186/s13068-017-1004-9) contains supplementary material, which is available to authorized users.

Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield