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Background  Leaf shape can affect plantlet development and seed yield in sesame. The morphological, histological and genetic analyses of a sesame mutant  cl1  ( cl ) with curly leaf and indehiscent capsule traits were performed in this study. In order to clone the  cl1  gene for breeding selection, genome re-sequencing of the 130 individuals of  cl1  × USA (0)-26 F 2  population and a bulked segregation analysis (BSA) pool was carried out. The genome re-sequencing data of the 822 germplasm with normal leaf shape were applied.    Results  For  cl1  mutant, the adaxial/abaxial character of the parenchyma cells in the leaf blades is reduced. Results proved that the leaf curling trait is controlled by a recessive gene ( Sicl1 ). Cross- population association of the F 2  population of  cl1  × USA (0)-26 indicated that the target  cl  locus was located on the interval C29 between C29_6522236 and C29_6918901 of  Si Chr. 1. Further regional genome variants screening determined the 6 candidate variants using genomic variants data of 822 natural germplasm and a BSA pool data. Of which, 5 markers C29_6717525, C29_6721553, C29_6721558, C29_6721563, and C29_6721565 existed in the same gene (C29.460). With the aid of the validation in the test F 2  population of  cl1  × Yuzhi 11 and natural germplasm, the integrated marker  SiCLInDel1  (C29: 6721553–6721572) was determined as the target marker, and C29.460 was the target gene  SiCL1  in sesame.  SiCL1  is a KAN1 homolog with the full length of 6835 bp. In  cl1 , the 20 nucleic acids ( CAGGTAG CT A TG TATATGCA)  of  SiCLInDel1  marker were mutagenized into 6 nucleic acids ( T CT T TG). The deletion led to a frameshift mutation and resulted in the earlier translation termination of the CL gene. The  Sicl1  allele was shortened to 1829 bp.  SiCL1  gene was expressed mainly in the tissues of stem, leaf, bud, capsule and seed.    Conclusions   SiCL1  encodes a transcription repressor KAN1 protein and controls leaf curling and capsule indehiscence in sesame. The findings provided an example of high-efficient gene cloning in sesame. The  SiCL1  gene and the  cl1  mutant supply the opportunity to explore the development regulation of leaf and capsule, and would improve the new variety breeding with high harvest mechanization adaption in sesame.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1503-2) contains supplementary material, which is available to authorized users.

bmc plant biology

Identification of a SiCL1 gene controlling leaf curling and capsule indehiscence in sesame via cross-population association mapping and genomic variants screening