Deletion of a 1049 bp sequence from the 5′ UTR upstream of SiHEC3 gene induces a seed non-shattering mutation in sesame

Sesame is a labor intensive crop with low mechanized harvest mainly for the seed shattering (SS) trait. In this study, we performed genetic analysis of seed-shattering resistance (SR) trait with a SR sesame mutant 12M07. Differing from the SS type, the parenchyma cells in the abscission zone of the 12M07 mutant arrange loosely but adhere to the seed coat. Inheritance analysis of six generations derived from 12M07 (SR)×Xiangcheng Dazibai (SS) showed that SR trait is recessive and controlled by single gene pair. Association mapping of F2 population with 888619 variants (SNPs and InDels) and 31884 structural variation (SV) determined that only SV12002 in the 5′ upstream region of gene Sindi0765000 (named SiHEC3) in SiChr.3 was significantly associated with SR trait. SiHEC3 encodes the HLH transcription factor. A 1049-bp deletion occurred in the 5′ UTR of Sihec3 in 12M07. SiHEC3 was mainly expressed in developing placental tissues, with the expression peak in 45 days after pollination capsules. A dual-luciferase reporter assay in tobacco confirmed that the promoter activity of Sihec3 reduced because of the deletion of 1049 bp promoter sequence. Protein-protein interaction network analysis showed that HEC3 co-expressed with nine key proteins, such as SHATTERPROOF1 (SHP1) and SEEDSTICK (STK) which participate in the secondary wall biosynthesis of the absciss layer in plants. The findings exhibit the important function of SiHEC3 corresponding with the SR trait and supply the gene information for new variety breeding with high mechanized harvest in sesame and other crops.