Determination of population structure of the qualified spinach gene pool and obtaining of F1 spinach varieties candidates resistant to peronospora effusa (PE)

The study was aimed to characterize 64 spinach genotypes, four S6 and 60 S7, obtained from local and commercial spinach genotypes. The study also aimed to evaluate the resulting phenotypic variations using principal component and cluster analyses. It was also aimed to determine resistance to spinach downy mildew, a disease known to be a major factor affecting yield and quality in spinach cultivation, using molecular markers. SLAF-seq technology, a sequencing method used to identify underrepresented spinach gene pools, was used to simultaneously genotype all individuals, aiming to determine genetic diversity and population structure. The study also selected potential parental lines to establish hybridization programs. F1 cultivars were then used to determine the agro-morphological performance and resistance levels of hybrid plants to downy mildew. This aimed to reduce foreign dependency on spinach seed and strengthen hybrid variety development programs. In this context, morphological observations were made on the genotypes according to UPOV parameters. Based on the observations, the spinach genotypes were also examined using principal component analysis (PCA) to examine multiple traits simultaneously. As a result of this analysis, six independent principal components were explained, and these components represented 69.09% of the total variation. Observations on the genotypes were subjected to cluster analysis, and it was determined that the genotypes were divided into 7 main branches. The resistance status of 65 genotypes belonging to the S7-S8 stages was also determined in the study. For the RPF3-5 marker (locus 3), 3 homozygous (RR) tolerant, 20 heterozygous (Rr) tolerant, and 42 susceptible (rr) genotypes were identified. For the RPF1-3 marker (locus 1), 34 homozygous (RR) tolerant, and 31 susceptible (rr) genotypes were identified. For the RPF1-8 marker (locus 1), 2 homozygous (RR) tolerant, 31 susceptible (rr), and 32 heterozygous (Rr) tolerant genotypes were identified. For the RPF2-2 marker (locus 2), 58 homozygous (RR) tolerant, and 9 susceptible (rr) genotypes were identified. 14 of the 65 genotypes were found to carry resistance alleles at the RPF1, RPF2, and RPF3 loci against Peronospora effusaL. To characterize the spinach gene pool at the S7-S8 stage, all individuals were simultaneously genotyped using the SLAF-seq method, a low-representation sequencing method. This allowed the determination of the genetic diversity and population structure of the genotypes. The Q30 value, which indicates sequencing quality, varied between 97.19% and 96.51%, while the GC content ranged from 46.53% to 38.2%. In our study, an average of 280,029 SLAF tags were obtained from each sample, with a sequencing depth of 24.07x for each SLAF tag, resulting in a total of 1,037,603,228 reads. A total of 36,012 SNP were obtained across genotypes. The high-quality SNP data obtained were used to assess genetic diversity. In our study, the genotypes were divided into three main groups based on the NJ dendrogram generated from the diversity analysis, and the r value was determined to be 0.89 using the Mantel test. Determining population structure is an important step in revealing genetic diversity and understanding the relationships between individuals. In our study, based on SNP data obtained from SLAF-seq, the population structure of spinach (Spinacia oleracea L.) genotypes was analyzed using structure software, and probabilistic membership coefficients (Q values) for K (three values for K = 3) were calculated for each individual. Potential parental lines were selected for the genotypes, and hybridization programs were developed. Six male and 59 female plants were crossbred, resulting in 323 F1 cultivar candidates. To determine the spring and autumn performance of the hybrid plants, agro-morphological traits such as plant weight, leaf weight, stem length, root length, root weight, and leaf area were determined in both periods. In this thesis, the resistance of 239 spinach hybrids found to be promising to spinach mildew was determined and 39 hybrid plants tolerant to locus 3, 40 tolerant to locus 1, and 238 tolerant to locus 2 were determined.