Identification of SSR Markers Linked to Chilli Leaf Curl Virus (ChLCV) Resistance in Chilli (Capsicum annuum L.)

This study was conducted during April to September, 2022 at ICAR-IIHR, Bengaluru, Karnataka, India to identify molecular markers linked to Chilli leaf curl virus (ChLCV) resistance in Capsicum spp. Simple sequence repeat (SSR) markers were utilised to screen the contrasting parental lines and their F2 segregating population. A total of 120 SSR primers were screened among the parents, of which 22 exhibited clear polymorphism, resulting in an 18.33% polymorphism rate. However, no polymorphism was observed in the bulks, indicating that the selected markers might not be closely linked to the resistance gene. This suggested that the resistance gene might be located in genomic regions not covered by the chosen SSR markers or that resistance involves more complex genetic interactions, such as quantitative trait loci (QTLs) or minor effect genes. The findings highlighted the need for alternative strategies, including expanding the marker set, utilizing high-throughput genotyping methods such as SNP arrays or whole-genome sequencing, and conducting QTL mapping or genome-wide association studies (GWAS).