Dynamics of Vulmar/VulMITE group of transposable elements in Chenopodiaceae subfamily Betoideae

Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism (ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets of TE insertions specific to Beta and Patellifolia

Characterization of active miniature inverted-repeat transposable elements in the peanut genome

Miniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), AhMITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four AhMITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

<p>Abstract</p> <p>Background</p> <p>The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels.</p> <p>Results</p> <p>Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F₂mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F₂populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F₂, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 <it>D. carota </it>accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity.</p> <p>Conclusions</p> <p>The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.</p

The use of DNA markers for evaluation of genetic diversity in the Polish germplasm collection of carrot (Daucus carota L.)

Ocenę zróżnicowania genetycznego prowadzono dla 27 obiektów należących do rodzajów Daucus, Caucalis, Orlaya i Torilis w oparciu o 144 markery różnicujące badane obiekty, spośród których 67 otrzymano techniką RAPD, a 77 techniką AFLP. Macierze dystansu genetycznego były podobne, niezależnie od wybranego rodzaju markerów. Analiza pozwoliła na wyróżnienie trzech głównych grup obiektów obejmujących odpowiednio obiekty należące do rodzaju Torilis, Orlaya /Caucalis oraz Daucus. Porównanie macierzy podobieństw genetycznych dla siedmiu obiektów powtórzonych w trzech latach badań wskazało na bardzo dużą zgodność otrzymanych wyników, co zostało potwierdzone bardzo zbliżonym układem obiektów na dendrogramach. Uzyskane wyniki są wykorzystywane przez kuratora kolekcji do racjonalizacji zarządzania polskimi zasobami genowymi marchwi.Genetic diversity was evaluated for 27 accessions belonging to genera Daucus, Caucalis, Orlaya and Torilis on the basis of 144 molecular markers differentiating them, out of which 67 were obtained using RAPD, and 77 using AFLP techniques. Genetic distance matrices were similar regardless the kind of marker. Analysis allowed for the identification of three clusters grouping accessions belonging to genera Torilis, Orlaya/Caucalis and Daucus. Comparison of similarity matrices for seven accessions evaluated in all three years showed that the results were highly reproducible, which was confirmed by a similar tree topology. The results are utilized by the curator as a tool for more rational management of the collection

Search for sources of resistance to Cercospora beticola SACC. in Beta germplasm

W doświadczeniu polowym oceniono 65 obiektów z gatunku Beta vulgaris L. pod względem ich wrażliwości na Cercospora beticola. Ocenę prowadzono w trzech terminach: 19 sierpnia, 10 września i 4 października 2002. Zarówno różnice między terminami, jak i różnice stopnia porażenia poszczególnych obiektów okazały się statystycznie istotne. W kolejnych terminach oceny stwierdzono stopniowe nasilanie się objawów od 3,7 w terminie pierwszym, poprzez 5,6 w terminie drugim, do 7,5 w terminie trzecim. Wszystkie badane formy buraka ćwikłowego znalazły się w grupie odmian średnio lub bardzo wrażliwych, ze średnim porażeniem od 5,0 do 7,7. Wyodrębniono grupę obiektów o obniżonej wrażliwości na C. beticola (dwie formy buraka cukrowego oraz pięć form dzikich), dla których średnie porażenie nie było wyższe niż 4,3, nie stwierdzono natomiast występowania obiektów całkowicie odpornych. W świetle informacji o dziedziczeniu odporności na C. beticola, wykorzystanie dzikich materiałów z rodzaju Beta w hodowli byłoby procesem znacznie bardziej skomplikowanym i długotrwałym, stąd w kolejnych latach prace związane z identyfikacją form o obniżonej wrażliwości na chwościk obejmą w pierwszej kolejności większą liczbę obiektów z grupy buraków ćwikłowych.Sixty-six Beta accessions were evaluated in the field experiment for their level of susceptibility to Cercospora beticola. Observations were performed three times, on Aug. 19, Sep. 10 and Oct. 4, 2002. Differences between the subsequent observations and between accessions were statistically significant. A gradual increase in the severity of infestation was noted, mean scores being 3.7, 5.6, and 7.5, for the first, the second and the third term of observation, respectively. All garden beet accessions were classified as susceptible or very susceptible, with a mean score ranging from 5.0 to 7.7. A group of two sugar beet and five wild accessions showing a reduced susceptibility to Cercospora was differentiated. Their means infestation score did not exceed 4.3, however, no immune forms were noticed. In the light of reports on inheritance of resistance to C. beticola, the use of other Beta species as a source of resistance would be a very complicated and long-term process, hence in the following years we will focus on the identification of red beet accessions showing reduced susceptibility to Cercospora