Analyzing Sunn pest resistance in bread wheat genotypes using phenotypic characteristics and molecular markers.

Sunn pest is one of the most destructive insects in the western and central parts of Asia causing severe reductions of wheat yield and flour quality. Therefore, an effort was undertaken to find effective resistance by analyzing genetic variation among 25 wheat genotypes artificially infested in field-cages as well as using start codon targeted (SCoT) polymorphism and inter- retrotransposon amplified polymorphism (IRAP) markers. High variation was revealed amongst genotypes with Sunn pest resistance characteristics including Bayat, Bezostaya, Sayson, Line93, Line120, Rashagol, Golsepi and AarasGolsoor, which were classified as resistant to moderately resistant. SCoTs and IRAPs were determined as efficient markers for studying genetic diversity. The non-parametric Kruskal-Wallis test was conducted to evaluate the effect of specific SCoT and IRAP amplicons on Sunn pest resistance characteristics for wheat genotypes. The stepwise regression analysis exhibited seven informative SCoTs and IRAPs explaining the highest resistance characteristics variation ranging from 25.7-50.1 to 17.6-40.1, respectively. The relationship between resistance of genotypes and informative SCoT and IRAP amplicons was found based on canonical discriminant analysis showing the capacity of informative markers for functional marker selection method and screening the wheat germplasms for Sunn pest resistance characteristics.

Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers.

Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation.