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Basal stem rot caused by Sclerotinia sclerotiorum (Lib.) de Bary is one of the most important diseases of sunflower. Quantitative trait loci (QTL) implicated in partial resistance to two isolates of S. sclerotiorum (SSU107 and SSKH41) were investigated using F₉ recombinant inbred lines (RILs) from the cross between sunflower parental lines PAC2 and RHA266. Experiments were conducted in completely randomized design with 3-6 replications under controlled conditions. The reaction of genotypes to basal stem rot disease was evaluated by measuring the percentage of necrosis area three days after inoculation. Combined analysis of experiments showed significant interactions between sunflower genotypes and S. sclerotiorum isolates suggesting that partial resistance to S. sclerotiorum should be isolate-specific in sunflower. QTLs were mapped using an updated high-density SSR and SNP linkage map. The map consisted of 210 SSRs and 11 gene-derived markers placed in 17 linkage groups (LGs). The total map length was 1,653.1 cM with a mean density of 1 marker per 7.44 cM. A total of 14 QTLs were detected for partial resistance to two isolates. The phenotypic variance explained by QTLs (R²) ranged from 0.10 to 9.85. The sign of additive gene effects showed that favorable alleles for partial resistance to isolates came from both parents. Six QTLs were common between two isolates on LGs 1, 8 and 17, whereas the others were specific for each isolate. Co-localized QTLs on LG 1 were linked to the glutathione S-transferase gene (GST). The co-localized QTLs for partial resistance to basal stem rot isolates could be good candidates for marker assisted selection (MAS).

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The effectiveness of IRAP, REMAP, SSR, and ISSR markers were investigated to assess genetic diversity among and within eight Medicago sativa L. populations. A total of 101, 119, 117 loci and 31 alleles were amplified using 10 IRAP, 14 REMAP, 16 ISSR and eight SSR primers, respectively. IRAP markers generated the maximum proportion of polymorphic loci per primer (PPLP) while the maximum value of percentage of polymorphic loci (PPL) was observed for SSR markers. ISSR markers showed the highest value of marker index (MI). The maximum amount of expected heterozygosity (He), effective number of alleles (Ne), and Shannon’s information index was produced by SSR markers. UPGMA cluster using Nei’s genetic distance coefficients and combined data of four markers separated the populations into three major groups. Correlation coefficients among pairwise genetic and geographic distance matrices, made on the basis of all studied markers, were calculated using Mantel's test. Regression and correlation analysis between genetic distance and geographic distance showed no significant correlations (p>0.05).

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Retrotransposons (RTNs) constitute informative molecular markers for plant species because of their ability to integrate into a multitude of loci throughout the genome and thereby generate insertional polymorphisms between individuals. In the present study, RTN-based molecular markers, IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), were applied to study RTN integration events and genetic diversity in 100 melon genotypes (88 genotypes from 11 populations, three inbred lines, and 9 hybrids). A total of 94 and 262 loci were amplified using 5 IRAP and 15 REMAP primers, respectively. The percentage of polymorphic loci (PPL) in populations ranged from 39% (Zivari Shahrood) to 48% (Shadegani E). The Mantel test between IRAP and REMAP cophenetic matrices evidenced no significant correlation (r= 0.29). IRAP+REMAP-based cluster analysis using UPGMA algorithm and Dice similarity coefficient depicted 6 groups among 100 melon genotypes. AMOVA revealed the higher level of genetic variation within populations (67%) compared to among populations (33%). The mean Fst values of all groups, except for group VI, were more than 0.20, demonstrating differentiation among the populations and genetic structure of the studied melon collection. 

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Understanding of genetic diversity is essential in breeding programs and plant genetic resources management. In this study, the genetic diversity of 77 individuals of Teucrium from different regions of Iran was investigated using 18 ISSR markers. A total number of 198 bands were detected by ISSR primers, of which 184 (92.9%) bands with an average of 10.2 bands per primer were polymorphic. The Percentage of Polymorphic bands (PPL) ranged from 80 (UBC834) to 100% (UBC811, 812, 818, 820, 825, 826, and UBC855). The average Polymorphic Information Content (PIC), Shannon’s Information index (I), and Number of effective alleles (Ne) were 0.39, 0.526, and 1.6, respectively. The Analysis of Molecular Variance (AMOVA) revealed the higher level of genetic variation within populations (77%) compared to among populations (23%). Cluster analysis separated the individuals into three major groups using WPGMA based on Nei’s genetic distance coefficients. In addition, a model-based Bayesian approach subdivided the individuals into three major subgroups. The results of this study revealed that estimation of population genetics parameters using ISSR markers can be applied for assessing the differences between Teucrium populations and management of the genetic resources.

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Retrotransposons (RTNs) are a major source of genomic changes in plant genomes and, therefore, are extensively used as ideal molecular markers for genetic variability, DNA fingerprinting, and genetic mapping studies in plant species. In the present study, two RTN-based marker systems, inter-retrotransposon amplified polymorphisms (IRAPs), and the retrotransposon-microsatellite amplified polymorphisms (REMAPs) were used to assess genetic variability and structure in a collection of 94 durum wheat genotypes. In general, 63 and 141 loci were amplified using 6 IRAP and 15 REMAP primers, respectively. Percentage of polymorphic loci (PPL) in the studied collection for IRAP and REMAP markers were 47.15% and 47.81%, respectively. The average of expected heterozygosity (He), number of effective alleles (Ne), and Shannon's information index (I), separately estimated based on IRAP and REMAP data, were not considerably different. A model-based Bayesian method and cluster analysis using Neighbor joining (NJ) algorithm depicted five clusters. A moderate level of inter-group genetic variability was detected among the clusters (11%) obtained from STRUCTUR software (PhiPT =0.111; P=0.001) with the vast majority of variation (89%) still uncaptured within groups. Most of the accessions and landraces from Iran aggregated together in clusters I and III with the cultivars from Turkey. Also, Iranian and foreign durum wheat landraces were assigned to different clusters or subpopulations in both clustering methods. In conclusion, the results showed that the genetic diversity of Iranian durum wheat is low and it is necessary to extend the genetic base of durum wheat germplasm in Iran.
 

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To extend the genetic base of Iranian tomato germplasm, 93 landraces were collected from the northwest of Iran and East Anatolian of Turkey, along with three commercial cultivars, and their genetic structure were studied using 39 SSR primers. Thirty-five polymorphic SSR loci generated a total of 118 alleles in the studied germplasm. Number of alleles per locus and effective number of alleles averaged 3.37 and 2.47, respectively. Expected heterozygosity of SSRs varied from 0.227 (TMS24) to 0.773 (LEta016), averaged 0.558. The mean number of alleles per genomic-SSRs (3.61) was more than that of EST-SSRs (2.66). Cluster analysis using Neighbour Joining (NJ) method placed 96 tomato genotypes in eight groups. Little congruence was found between NJ dendrogram and geographical distances. Genetic structure analysis of the germplasm using Bayesian method revealed two sub-populations and separated cherry tomatoes from the other landraces and commercial cultivars. Out of the 21 morphological characters, significant (P≤ 0.05) marker-trait associations were found for 18 characters. Each of SSR loci TC11, TC948, and Tom236-237 was associated with three characters. The genetic variability, structure, and markers associated with the studied traits in the current study can be used for planning tomato breeding programs and future studies.