Genetic diversity of Greek Aegilops species using different types of nuclear genome markers

Association analysis and evaluation of genetic diversity in wheat genotypes using SSR markers

A population of 105 wheat genotypes (including 94 hexaploid and 11 tetraploid genotypes) was used to determine genetic diversity. Samples were grown based on the randomized complete block design with three replications under salinity stress (120 mM NaCl (and control (10 mM NaCl (conditions. Morpho-physiological traits associated with tolerance of salinity at the seedling stage were recorded. The results of the analysis of variance showed that there were significant differences between genotypes in all studied traits, except K⁺/Na⁺ ratio. The amount of potassium content of leaves and roots in control was higher than salt stress conditions. Salinity significantly decreased all traits measured except Na⁺ concentration in root and shoot and leaf stomata conduction. A total of 12 SSR (simple sequence repeats) markers were assessed for the existence of polymorphism between genotypes. The highest Nei (Nei 1973) gene diversity was observed for gwm410 (0.72) and gpw2181 (0.71) markers, and PIC (polymorphic information content index) values ranged from 0.2 to 0.67. According to PIC, only six markers were informative during this study. These markers could be more efficient in displaying the genotypic differentiation of the near-wheat species as they showed the highest genetic diversity. Simple regression analysis showed that barc212 marker had the most significant relationship with root dry weight, leaf moisture and stomatal conductance (at 0.01 significant level). The gpw2181 marker showed a significant correlation with different traits under stress conditions. It was suggested that this marker could be used for marker-assisted selection to improve salt stress tolerance of wheat.

Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

BACKGROUND

Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) markers.

RESULTS

Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei's gene diversity (He), and Shannon's information index (I) were estimated for Ae. cylindrica species.

CONCLUSION

The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping

Fluorescence in situ hybridization karyotypes have been widely used for evolutionary analysis on chromosome organization and genetic/genomic diversity in the wheat alliance (tribe Triticeae of Poaceae). The karyotpic diversity of Aegilops umbellulata, Ae. markgrafii, Ae. comosa subsp. comosa and subsp. subventricosa, and Ae. uniaristata was evaluated by the fluorescence in situ hybridization (FISH) probes oligo-pSc119.2 and pTa71 in combination with (AAC)5, (ACT)7, and (CTT)12, respectively. Abundant intra- and interspecific genetic variation was discovered in Ae. umbellulata, Ae. markgrafii, and Ae. comosa, but not Ae. uniaristata. Chromosome 7 of Ae. umbellulata had more variants (six variants) than the other six U chromosomes (2-3 variants) as revealed by probes oligo-pSc119.2 and (AAC)5. Intraspecific variation in Ae. markgrafii and Ae. comosa was revealed by oligo-pSc119.2 in combination with (ACT)7 and (CTT)12, respectively. At least five variants were found in every chromosome of Ae. markgrafii and Ae. comosa, and up to 18, 10, and 15 variants were identified for chromosomes 2 of Ae. markgrafii, 4 of Ae. comosa subsp. comosa, and 6 of Ae. comosa subsp. subventricosa. The six Ae. uniaristata accessions showed identical FISH signal patterns. A large number of intra-specific polymorphic FISH signals were observed between the homologous chromosomes of Ae. markgrafii and Ae. comosa, especially chromosomes 1, 2, 4, and 7 of Ae. markgrafii, chromosome 4 of Ae. comosa subsp. comosa, and chromosome 6 of Ae. comosa subsp. subventricosa. Twelve Ae. comosa and 24 Ae. markgrafii accessions showed heteromorphism between homologous chromosomes. Additionally, a translocation between the short arms of chromosomes 1 and 7 of Ae. comosa PI 551038 was identified. The FISH karyotypes can be used to clearly identify the chromosome variations of each chromosome in these Aegilops species and also provide valuable information for understanding the evolutionary relationships and structural genomic variation among Aegilops species.

Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time

Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.

Comparison of old and new wheat cultivars in Iran by measuring germination related traits, osmotic tolerance and ISSR diversity

A primary concern of modern plant breeding is that genetic diversity has decreased during the past century. This study set out to explore changes in genetic variation during 84 years of breeding by investigating the germination-related traits, inter-simple sequence repeat (ISSR) fingerprinting and osmotic stress tolerance of 30 Iranian wheat (Triticum aestivum L.) cultivars. Seeds were planted under control and osmotic stress (-2, -4 and -6 bar) in three replications. The ISSR experiment was carried out using 32 different primers. Genotypes were divided into two groups (old and new) each containing 15 members. The results of ANOVA showed that highly significant differences existed among genotypes and among growth conditions. The results showed that during breeding in some traits such as coleoptile length and seedling vigor index, a significant decrease has been occurred. New cultivars had a mean coleoptile length of 33 mm, shorter than that of old cultivars (42 mm) under osmotic stress of -6 bar. Genetic variance of root length, shoot length and seedling vigor index for old cultivars were 1.59, 1.93 and 45,763, respectively, significantly higher than those for new cultivars (0.55, 1.08 and 27,996, respectively). This difference was also verified by ISSR results as the polymorphism information content was 0.28 in old cultivars, higher than that of new cultivars (0.26). These results prove this claim that during breeding, genetic diversity has decreased for many germination-related traits and breeders are better to pay more attention to genetic diversity.

Relationships between Genetic Diversity and Fusarium Toxin Profiles of Winter Wheat Cultivars

Fusarium head blight is one of the most important and most common diseases of winter wheat. In order to better understanding this disease and to assess the correlations between different factors, 30 cultivars of this cereal were evaluated in a two-year period. Fusarium head blight resistance was evaluated and the concentration of trichothecene mycotoxins was analysed. Grain samples originated from plants inoculated with Fusarium culmorum and naturally infected with Fusarium species. The genetic distance between the tested cultivars was determined and data were analysed using multivariate data analysis methods. Genetic dissimilarity of wheat cultivars ranged between 0.06 and 0.78. They were grouped into three distinct groups after cluster analysis of genetic distance. Wheat cultivars differed in resistance to spike and kernel infection and in resistance to spread of Fusarium within a spike (type II). Only B trichothecenes (deoxynivalenol, 3-acetyldeoxynivalenol and nivalenol) produced by F. culmorum in grain samples from inoculated plots were present. In control samples trichothecenes of groups A (H-2 toxin, T-2 toxin, T-2 tetraol, T-2 triol, scirpentriol, diacetoxyscirpenol) and B were detected. On the basis of Fusarium head blight assessment and analysis of trichothecene concentration in the grain relationships between morphological characters, Fusarium head blight resistance and mycotoxins in grain of wheat cultivars were examined. The results were used to create of matrices of distance between cultivars - for trichothecene concentration in inoculated and naturally infected grain as well as for FHB resistance Correlations between genetic distance versus resistance/mycotoxin profiles were calculated using the Mantel test. A highly significant correlation between genetic distance and mycotoxin distance was found for the samples inoculated with Fusarium culmorum. Significant but weak relationships were found between genetic distance matrix and FHB resistance or trichothecene concentration in naturally infected grain matrices.

Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae)

Phylogenetic inferences of the polyploid Aegilops taxa were drawn based upon the analysis of 909 nuclear 5S rDNA sequences obtained from 15 Aegilops polyploid taxa (531 sequences new to this paper) and 378 sequences from our previous study on the diploid taxa. The 531 sequences can be split into two orthologous groups (unit classes), the long AE1 and short AE1 previously identified in the diploid set. An examination of the relationships between unit classes and their associated haplomes suggests that U haplome sequences found in Ae. umbellulata are the closest to the T sequences found in Amblyopyrum muticum and that sequences of the polyploid species expected to be the M type found in Ae. comos are more similar to the T haplome sequences, except in the three hexaploids Ae. glumiaristata, Ae. juvenalis, and Ae. vavilovii and the tetraploid Ae. crassa where they are found to be similar to the M haplome sequences. These three hexaploid taxa likely originated from the tetraploid Ae. crassa (DM), while the closest taxon to the fourth hexaploid, Ae. recta, is the tetraploid Ae. neglecta (UM). Based upon the distribution of the unit classes, several reticulate phylogenies depicting evolutionary relationships among diploid, tetraploid, and hexaploid taxa were constructed; however, none of these widely used methods could depict the expected reticulate relationship as previously drawn from cytogenetic analyses in this group of allopolyploid species. These results suggest that evolutionary relationships derived from models based upon the assumption of bifurcating species require careful interpretation when these same models are applied to species with reticulate evolution.

ISSR: a reliable and cost-effective technique for detection of DNA polymorphism

With the emergence of more and more molecular markers as useful tools in plethora of population genetic and phylogenetic studies, choice of marker system for a particular study has become mind boggling. These marker systems differ in their advantages and disadvantages, so it is imperative to keep in mind all the pros and cons of the technique while selecting one for the problem to be addressed.Here, we have shed light on the ISSR (intersimple sequence repeat) technique, as a marker of choice if one wants to go for properties such as reliability, simplicity, cost effectiveness, and speed, in addition to assessing genetic diversity between closely related individuals. We have outlined here the whole methodology of this technique with an example of Tribulus terrestris as case study.