Abstract The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released strigolactones (SLs) for seed germination. Herein, we identified four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10), but absent in the resistant 29Aw (Aw). We generated chromosome-scale genome assemblies including four gapless chromosomes for each line. We found the Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYL TRANSFERASE1 ( CLAMT1 ) genes. Upon transient expression, P10CLAMT1b produced methyl carlactonoate (MeCLA), an intermediate in SL biosynthesis. Feeding Aw with MeCLA resulted in the production of two P10-specific SLs. Screening a diverse pearl millet panel confirmed the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

Chromosome-scale pearl millet genomes reveal a<i>CARLACTONOIC ACID METHYL TRANSFERASE</i>as key determinant of strigolactone pattern and Striga susceptibility

Chromosome-scale pearl millet genomes reveal aCARLACTONOIC ACID METHYL TRANSFERASEas key determinant of strigolactone pattern and Striga susceptibility