Development of SNP-based markers associated with restorer-of-fertility in chilli (Capsicum annuum L.)

The cytoplasmic-genic male sterility (CGMS) system enhances the economic efficiency of F₁ hybrid seed production by exploiting the interaction between sterile cytoplasm and nuclear restorer-of-fertility (Rf) genes. Molecular markers linked to the Rf gene facilitate the development of stable CMS lines by enabling fixation of the recessive rf allele in male-sterile (A) and maintainer (B) lines, identification of restorer lines, and assessment of genetic purity. In the present study, phenotyping of an F₂ population derived from IIHR4392A (rfrf) × IIHR4597R (RfRf) showed a 3:1 segregation ratio, confirming monogenic dominant inheritance of fertility restoration. Genotyping-by-sequencing (GBS) of this segregating F₂ population yielded 10,443 single-nucleotide polymorphisms (SNPs) with 481 to 1,074 SNPs per chromosome. Bulk segregant analysis identified three SNPs co-segregating with the Rf gene on chromosome 6. One candidate SNP, mapped at 2,343,509 bp on chromosome 6, was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker and validated in the F₂ population. Three putative candidate genes, i.e., two fertility restorer-like proteins (CA06g01070, CA06g01090) and a pentatricopeptide repeat protein (CA06g01100), were predicted as potential Rf candidates. The developed dCAPS marker associated with the Rf gene for fertility restoration provides a valuable tool for marker-assisted breeding in chilli.