Genetic Diversity, Population Structure, and Association Analysis of Female and Male Fig Genotypes (Ficus carica L.)

The genotypic classification of the genetic resources and development of molecular markers for important traits could be very informative for breeding programs. The aim of the study was to analyze the genetic relationship within and between the male and female fig (Ficus carica L.) population and perform association analysis for developing molecular markers linked to sex expression in natural populations of figs. In total, 47 male and 49 female fig genotypes originating from different geographic regions of Turkey (two genotypes from the USA) were used as plant material and sequence-related amplified polymorphism (SRAP), male-specific marker-SRAP (MS-SRAP), and inter-simple sequence repeat (ISSR) primers were employed for polymerase chain reaction (PCR) amplification. A total of 62 primers produced in total 353 markers, 149 of which were polymorphic. The average number of polymorphic markers for SRAP, MS-SRAP, and ISSR were 2.14, 2.75, and 2.3, respectively. The unweighted pair group method with arithmetic mean (UPGMA) and principal component analyses (PCA) successfully distinguished the genotypes but did not group them strictly based on gender or their geographic origins. The average genetic similarity among the fig genotypes based on combined data of ISSR, SRAP, and MS-SRAP was 0.65, with a range of 0.57-0.92. STRUCTURE analysis grouped the genotypes under four subpopulations and the genotypes were partially grouped according to their genders based on combined data. As a result of association analysis, the marker MS2FEM10 derived by combining the previously developed male-specific amplified fragment-length polymorphism (AFLP) marker (Parrish et al. 2004) with an SRAP marker explained the 66% of the total variation alone. The MS2FEM10 marker together with MS1RM12, M10E11, M3E14, and M5E10 explained 77% of the total variation for male/female characters. The genetic relationship between fig genotypes was revealed, and association mapping was successfully employed in natural populations of F. carica with three different PCR-based marker systems. Increasing the number of markers may result in the identification of tightly linked or gene-specific markers in natural populations of F. carica.