Development and validation of L allele-specific markers in Capsicum

Tobamovirus is one of most destructive viruses in Capsicum. Accordingly, the L locus, a resistance gene against tobamoviruses, has been used for pepper breeding programs. Previously, the L ³ gene, one of the L alleles, was isolated through map-based cloning, and a L ⁴ gene candidate was isolated by homology-based PCR methods. Here, the L4segF&R marker was developed based on the leucine-rich repeat (LRR) region of the L ⁴ candidate, and co-segregation analysis was performed using two L ⁴ -segregating F2 populations derived from the commercial cultivars Special and Myoung-sung. The L4segF&R marker was located within 0.3?cM of the L ⁴ gene but did not completely co-segregate with the L ⁴ gene, indicating that the candidate is not actually L ⁴ . To confirm the mapping result, L4segF&R genotypes of L ⁴ -containing breeding lines from three different seed companies were analyzed, resulting in the identification of several recombinants in the breeding lines. Based on these results, we postulate several genetic models that show different introgression histories and genetic structures for the L ⁴ -containing segment in different breeding lines. All of the models demonstrate that resistance conferred by the L ⁴ segment could not be explained by the L ⁴ gene candidate alone. Although the presence of the L ⁴ gene candidate could not fully explain the L ⁴ resistance, we were able to develop allele-specific markers for the L locus using the candidate sequence. To develop allele-specific markers for the L locus, HRM analysis was performed using primer pairs based on the LRR sequence of the L ⁴ gene candidate. When commercial breeding lines homozygous for L ⁰ , L ¹ , L ² , L ³ or L ⁴ were analyzed, L4RP-3F/L4RP-3R correctly detected the L allele in 90 out of 91 lines. We believe that the L allele-specific marker developed in the study provides a solution for pepper breeders developing improved resistance lines against tobamoviruses.