Description of DNA analysis techniques and their application in oat (Avena L.) genome research

DNA markers are used not only to estimate genetic similarity and distance but also to select and identify desirable forms, to assess the adjustment of breeding material, to confirm crossbreeding efficiency, to determine seed purity, and to identify the genes which determine important functional traits. In the case of oat, DNA markers were used to construct and increase the density of genetic maps both in hexaploid and diploid species. The development of markers for some important traits provides a fast selection of genotypes containing dwarf genes as well as the resistance genes to crown rust and powdery mildew. Numerous analyses of genetic similarity between different species belonging to the genus Avena which are currently carried out may contribute to explaining the process of evolution within this genus and may also explain the development of particular species of oat

Phylogenetic Characterization of Botryosphaeria Strains Associated with Asphondylia Galls on Species of Lamiaceae

In the last decade, Botryosphaeria dothidea has been steadily reported as an associate of gall midges (Diptera, Cecidomyiidae) in a variety of host plants and ecological settings. This cosmopolitan fungus is well-known for its ability to colonize many plant species, as both a pathogen and an endophyte. Thus, the shift from this general habit to a lifestyle involving a strict symbiotic relationship with an insect introduces expectancy for possible strain specialization which could reflect separated phylogenetic lineages. Considering the recent taxonomic revision concerning species of Botryosphaeria, we evaluated the phylogenetic relationships among strains recovered from Asphondylia galls collected on several species of Lamiaceae in Poland and in Italy, and all the currently accepted species in this genus. A number of strains previously characterized from gall samples from Australia and South Africa, whose genetic marker sequences are deposited in GenBank, were also included in the analysis. As a result, full identity as B. dothidea is confirmed for our isolates, while strains from the southern hemisphere grouped separately, indicating the existence of genetic variation related to the geographic origin in the association with gall midges

Molecular identification and chromosomal localization of new powdery mildew resistance gene Pm11 in oat

The appropriate selection of various traits in valuable plants is very important for modern plant breeding. Effective resistance to fungal diseases, such as powdery mildew, is an example of such a trait in oats. Marker-assisted selection is an important tool that reduces the time and cost of selection. The aims of the present study were the identification of dominant DArTseq markers associated with a new resistance gene, annotated as Pm11 and derived from Avena sterilis genotype CN113536, and the subsequent conversion of these markers into a PCR-based assay. Among the obtained 30,620 silicoDArT markers, 202 markers were highly associated with resistance in the analysed population. Of these, 71 were selected for potential conversion: 42 specific to resistant and 29 to susceptible individuals. Finally, 40 silicoDArT markers were suitable for primer design. From this pool, five markers, 3 for resistant and 2 for susceptible plants, were selected for product amplification in the expected groups. The developed method, based on 2 selection markers, provides certain identification of resistant and susceptible homozygotes. Also, the use of these markers allowed the determination of heterozygotes in the analysed population. Selected silicoDArT markers were also used for chromosomal localization of new resistance genes. Five out of 71 segregating silicoDArT markers for the Pm11 gene were found on the available consensus genetic map of oat. Five markers were placed on linkage groups corresponding to Mrg12 on the Avena sativa consensus map

Reticular basement membrane thickness is associated with growth : and fibrosis-promoting airway transcriptome profile-study in asthma patients

Airway remodeling in asthma is characterized by reticular basement membrane (RBM) thickening, likely related to epithelial structural and functional changes. Gene expression profiling of the airway epithelium might identify genes involved in bronchial structural alterations. We analyzed bronchial wall geometry (computed tomography (CT)), RBM thickness (histology), and the bronchial epithelium transcriptome profile (gene expression array) in moderate to severe persistent (n = 21) vs. no persistent (n = 19) airflow limitation asthmatics. RBM thickness was similar in the two studied subgroups. Among the genes associated with increased RBM thickness, the most essential were those engaged in cell activation, proliferation, and growth (e.g., CDK20, TACC2, ORC5, and NEK5) and inhibiting apoptosis (e.g., higher mRNA expression of RFN34, BIRC3, NAA16, and lower of RNF13, MRPL37, CACNA1G). Additionally, RBM thickness correlated with the expression of genes encoding extracellular matrix (ECM) components (LAMA3, USH2A), involved in ECM remodeling (LTBP1), neovascularization (FGD5, HPRT1), nerve functioning (TPH1, PCDHGC4), oxidative stress adaptation (RIT1, HSP90AB1), epigenetic modifications (OLMALINC, DNMT3A), and the innate immune response (STAP1, OAS2). Cluster analysis revealed that genes linked with RBM thickness were also related to thicker bronchial walls in CT. Our study suggests that the pro-fibrotic profile in the airway epithelial cell transcriptome is associated with a thicker RBM, and thus, may contribute to asthma airway remodeling

Chromosomal Location of Pm12—A Novel Powdery Mildew Resistance Gene from Avena sterilis

Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F2 individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F3. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8–111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection

Ocena zróżnicowania genetycznego materiałów kolekcyjnych pszenżyta ozimego stabilnych pod względem cech plonotwórczych

Celem pracy była ocena zróżnicowania genetycznego materiałów kolekcyjnych pszenżyta ozimego za pomocą marke- rów RAPD. Do badań wybrano 24 genotypy (rody hodowlane i odmiany) pochodzące z różnych rejonów świata, u których na podstawie wieloletnich badań i analiz statystycznych stwierdzo- no stabilność cech plonotwórczych. Spośród wstępnie przeanalizowanych 50 starterów RAPD do oceny polimorfizmu wybrano 9. Startery te amplifikowały łącz- nie 81 fragmentów DNA, z czego 56 (69,13%) stanowiły frag- menty polimorficzne. Średnia wartość indeksów podobieństwa genetycznego badanych genotypów wynosiła 0,81 i wahała się od 0,76 (pomiędzy odmianą Pinokio i pozostałymi obiektami) do 0,91 (pomiędzy rodem LAD 671 i mieszańcem Alzo × LAD 122/90). Odmiana Pinokio charakteryzowała się największym dystansem genetycznym do wszystkich badanych genotypów, zaś rody hodowlane: LAD 671, DED 1556/90 i mieszaniec Alzo × LAD 122/90 oraz odmiana Bolero wykazały się największym podobieństwem w porównaniu do pozostałych genotypów. Otrzymane wyniki wskazują, że mimo zróżnicowanego po- chodzenia geograficznego stabilne pod względem cech plono- twórczych materiały kolekcyjne pszenżyta ozimego charaktery- zują się niewielkim zróżnicowaniem genetyczny

The use of RAPD markers for detecting genetic similarity and molecular identification of chamomile (Chamomilla recutita (L.) Rausch.) genotypes

S u m m a r y The objectives of this study was to assess the of genetic similarity and identification of 13 wild species and 7 cultivars of chamomile using RAPD markers. 53 RAPD primers were screened, only 12 produced polymorphic and repeatable fragments. in total, all primers used produced 157 fragments out of which 149 were polymorphic. The RAPDbased genetic similarity was estimated. genetic similarity matrix was applied for cluster analysis through uPgmA method. On the dendrogram, only genotypes from Austria, czech Republic as weel as genotypes collected in area of Lublin were grouped together. The remaining genotypes from the same area were located in different groups. Present study demonstrated that RAPD markers provided a practical and effective method not only to evaluate the genetic similarity and relationships but also to identify chamomile genotypes

Molecular diversity analysis of genotypes from four Aegilops species based on retrotransposon–microsatellite amplified polymorphism (REMAP) markers

Genetic diversity analysis is an important tool in crop improvement. Species with high genetic diversity are a valuable source of variation used in breeding programs. The aim of this study was to assess the genetic diversity of four species belonging to the genus Aegilops, which are often used to expand the genetic variability of wheat and triticale. Forty-fve genotypes belonging to the genus Aegilops were investigated. Within- and among-species genetic diversity was calculated based on REMAP (retrotransposon–microsatellite amplifed polymorphism) molecular markers. Obtained results showed that REMAP markers are a powerful method for genetic diversity analysis, which produces a high number of polymorphic bands (96.09% of total bands were polymorphic). Among tested genotypes, Ae. crassa and Ae. vavilovii showed the highest genetic diversity and should be chosen as a valuable source of genetic variation