Association Mapping of Fatty Acid Composition in Pepper Recombinant Inbred Lines

This study aimed to identify molecular markers associated with fatty acid composition in the fruit tissues of recombinant inbred lines (RILs) derived from an interspecific cross between Capsicum annuum and Capsicum frutescens . A total of 94 genotypes were phenotyped for 12 fatty acids (C12:0, C14:0, C16:0, C16:1, C17:0, C17:1, C18:0, C18:1, C18:2, C20:0, C18:3, and C22:0), as well as for monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA), and genotyped using 164 SRAP, ISSR, RAPD, and SSR markers. Only statistically significant ( p < 0.05) and highly explanatory ( R 2 > 0.15) associations were considered in the final analysis. In total, 35 markers were found to be significantly associated with 10 different fatty acids. Notably, markers linked to key saturated fatty acids such as palmitic, stearic, and behenic acids suggest the presence of genomic regions involved in their biosynthetic pathways. Conversely, no significant markers were identified for PUFA, possibly due to their complex inheritance patterns and low heritability. These findings may serve as a useful genetic basis for future marker‐assisted selection (MAS) efforts aiming to improve fatty acid composition in pepper and represent a promising step toward enhancing Capsicum breeding programs.