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Molecular markers in allium: Range of application, reliability and taxonomic implications: Marqueurs moleculaires chez les allium: Domaines d'utilisation, fiabilite et implications taxonomiques
Abstract
DNA polymorphisms are the markers of choice for the identification and characterization of plants. They are an integral part of the plant and they are not subject to environmental modification. There are relatively reliable, generally applicable methods to obtain large samples of markers from any species of plant. However, each marker system samples a different fraction of the genome and therefore has a different resolving power, range of applicability and probability of homology. Standard measures (e.g. "genetic distance") are dependent on the marker system and on the group under study. Taxa of similar rank may differ greatly in the variability of molecular marker systems. This is illustrated with examples from the genus Allium. At the IPK, a unique living collection of about 300 species of the genus, many collected at type localities, and a large collection of accessions of the cultivated species has been studied with a range of molecular markers: isozymes, RAPDs, ITS-sequences, PCR-RFLPs of variable regions of chloroplast DNA, and genome in situ hybridization (GISH). Molecular marker studies have necessitated changes in the subgeneric classification of the genus but have confirmed the monophyly of most sections within subgenera. The origin of various cultivated groups has been elucidated, especially where material of native origin was available, since garden-grown Allium are very liable to genetic introgression. Introgression in nature between species from various sections has been demonstrated. Microsatellite primers have been developed for the characterization of individual accessions of Allium cepa and for molecular genetic mapping experiments.
... Screening for drought tolerance and diversity among different cultivars based on morphological characterization is not enough, as these traits are more sensitive to environmental changes (Fufa et al., 2005). Therefore, the DNA molecular markers have been used as an accurate tool that are not influenced by environmental effects (Bachmann et al., 2001;Tatikonda et al., 2009). In addition, they can easily detect polymorphism that may result from nucleotide change or mutation in the genome loci (Hartl and Clark, 1997). ...
... Рід Allium родини Alliaceae у світовій флорі нараховує понад 500 видів, за даними Bachmann K. et al. їх нараховується близько 700 видів [BACHMANN et al., 2001], у флорі України описано 42 види [OPREDELITEL', 1987;. За результатами молекулярних досліджень видів підродини Melanocrommyum, що походять з Євразії, встановлено 160 видів та підвидів [FRITSCH et al., 2010, Shaw et al., 2007, LI Q. et al., 2010. ...
... It is used to monitor variation on DNA sequence in the species and also to manipulate genetic variation by introducing desired characters. Molecular marker can be an alternative system to be used in gene mapping, tracing genetic relationship, marker for selection for qualitative as well as quantitative characteristics (Araki et al., 2010;Arifin, Ozaki, & Okubo, 2000;Bachmann et al., 2001;Cunha, Hoogerheide, Zucchi, Monteiro, & Pinheiro, 2012;Masuzaki et al., 2006;Song et al., 2004). This approach especially is required to trace clone or accession selected for parents in hybridization that can create a wide variability and expected characteristics of both parents. ...
The escalating demand of shallot has forced the increase of domestic production, including through extension of harvest area by utilization of arable land on peatland. This study was aimed to analyze genetic profile of shallot adapted in peatland areas using SSR markers. Twenty-one shallot genotypes were tested in the field and eighteen primers dispersed throughout the genome was applied to analyze genetic diversity of the peatland-adapted shallots. Phenotypic evaluation revealed that shallot yield potential ranged from 6.66 to 14.21 t/ha. Of these, seven shallot clones (11 NA, 1111 TA, 12 NA, 12 NC, 20 NA and 22 N) had good yield potential and comparable with those of five released shallot varieties. Nine out of 12 shallot clones were moderately resistant to Alternaria porii. Clustering analysis showed that shallot genotypes were clustered into two main groups, Clustered I and II which consisted of 13 and 8 genotypes, respectively. The closest genetic relatedness was observed between 8NC and 8NA (0.85), while the farthest ones was between 11NA and Kramat2 (0.51). This result implies that cross combination between 11NA and Kramat2 is valuable and suitable for breeding programs aimed at improving shallot potential yield in the future.
... DNA polymorphisms are the markers of choice for identification and characterization of plants. They may be representative of the whole genome and they are not subject to environmental modification (Bachmann et al., 2001 ). Different molecular techniques have been developed to G study garlic diversity, mostly Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP). ...
Sixteen Simple Sequence Repeats (SSR) and three Inter Simple Sequence Repeats (ISSR) primers were used to es-timate the genetic diversity and its distri-bution in twenty garlic clones. A high level of polymorphism amongst studied clones was found with both SSR and ISSR markers. The total number of bands that were detected by all used primers was 75 including 6 monomorphic, 5 unique and 64 polymorphic. The percentage of poly-morphism identified by SSR primers were varied between 33.3 and 100. However, all of the studied ISSR primers were pol-ymorphic conferring a 100% of polymor-phism. Results showed that each of the Asa14, Asa17, Asa18 and Asa59 primers generated one monomorphic band of 77, 120, 102 and 113 bp, respectively, in all of the studded garlic clones. Two monomor-phic bands of 104 and 177 bp were gener-ated by using Asa24 primer. Asa17 and Asa59 SSR primers produced only one unique band of 154 (Egaseed 2) and 646 bp (EGA 1), respectively. Two unique bands of 225 and 250 bp were detected for Egaseed 2 (ft) by using HB 13 ISSR pri-mer. The highest similarity value (0.969) was found between AZO 2 and AZO 3, while the lowest value (0.482) was found between AZO 4 and EGA 5 clones. Dendrogram of genetic distances amongst all tested clones showed two distinct ma-jor clusters with overlapping. In general, the present results reveal the importance of using molecular markers to assess ge-netic diversity among such closely related genotypes which were difficult to distin-guish with other markers.
... Reviews about the different methods applied in Gatersleben and elsewhere to Allium and their main results were recently presented (Bachmann et al., 2001;Bachmann, 1998, 2000;Klaas, 1998;Klaas and Friesen, 2002). The resulting new views about the phylogeny of the genus, and some more details, will be given in the next sections dealing with taxonomy and classification at different levels. ...
Variation of approximately 20 kb of non-coding regions of the chloroplast genome of 29 species of Allium and 7 species of related genera have been cladistically analyzed. Both restriction site mutations and length mutations have been included in these analyses. The cladograms obtained with both types of mutation are highly similar topologically and display similar levels of homoplasy. No indication of significant between-data-set incongruence was found. The results of Wagner, Dollo and weighted parsimony indicate that recognition of the monotypic Nectaroscordum siculum renders Allium paraphyletic. The two large subgenera Rhizirideum and Bromatorrhiza are probably not monophyletic. Two strongly supported clades, both of which comprise species of different subgenera, are not characterized by morphological synapomorphies when analyzed a posteriori. Furthermore, the position of Allium tuberosum (subg. Rhizirideum) and A. fimbriatum (subg. Amerallium) changes considerably with different types of analysis, which suggests that inclusion of these and affiliated taxa may strongly influence the relationships found among chloroplast types in the genus. The highly artificial nature of the subgenera (subg. Bromatorrhiza is also indicated to be para-or polyphyletic) is not unexpected given the taxonomic complexity of Allium. As a consequence, however, many more taxa have to be included in an analysis of the phylogenetic relationships of chloroplast DNA's in the genus. The trnK, trnC - trnD, psbA - trnS, and rbcL - ORF106 regions are most suited for further use because these regions are easily amplified and exhibit a considerable level of sequence variation with a restricted degree of length variation.
Sequences of the ITS region of nrDNA were analyzed for the seven genera of Papaveraceae subf. Chelidonioideae s.str. Three major clades can be recognized. These are 1.Chelidonium/Hylomecon/Stylophorum, 2.Eomecon/Sanguinaria, and 3.Bocconia/Macleaya. The monophyly of genera in the first of these three clades is doubtful, and clades two and three are sister to each other. Use of the ITS phylogeny of the subfamily to trace its morphological and ecological evolution shows that morphological change is concentrated in theBocconia/Macleaya clade, and probably related to the evolution of wind-pollination from insect-pollination in these two genera after habitat shift.
Random amplified polymorphic DNA (RAPD) and genomic in situ hybridization (GISH) methods have been used to verify the hybridogenic
origin and to identify the parental species of some ornamental cultivars in the subgenus Melanocrommyum of the genus Allium. The cultivars had been selected from seed obtained after uncontrolled pollination in breeders’ fields. The combination of
GISH analysis with RAPD markers is very suitable for testing the hybridogenic origin of plants and to ascertain the parental
species of the hybrids in such cases. As suspected, A. macleanii and A. cristophii are the parental species of ‘Globemaster’. The parental species of cultivar ‘Globus’ are A. karataviense and A. stipitatum, and not A. cristophii and A. giganteum as has been assumed on morphological grounds. Cultivars ‘Lucy Ball’ and ‘Gladiator’ are of hybrid origin, though only one
of the parental species, A. hollandicum, could be confirmed. The cultivars ‘Purple Sensation’, ‘Mount Everest’, ‘White Giant’, ‘Michael H. Hoog’ and ‘Mars’ are not
hybrids since neither GISH nor RAPD suggest the presence of a second genome. ‘Purple Sensation’ belongs to A. hollandicum, ‘Mount Everest’, ‘White Giant’ and ‘Mars’ to A. stipitatum,‘Michael H. Hoog’ to A. rosenorum.
Restriction enzyme (RE) analysis of both chloroplast (cpDNA) and nuclear ribosomal DNA ( rDNA ) was used to establish the phylogeny of the diploid viviparous onion [ Allium × proliferum (Moench) Schrad. syn. Allium cepa L. var. viviparum (Metzger) Alefeld]. Six mutations at RE sites in the cpDNA demonstrated that the seed parent of two accessions of diploid viviparous onions (TS6007 and JS01) was identical to A. fistulosum . Variability at RE sites in the nuclear rDNA demonstrated that TS6007 and JS01 always possessed fragments of both A. cepa and A. fistulosum . In contrast, mutations in the cpDNA of Pran, a triploid viviparous onion, were different from A. fistulosum . Equally sized rDNA fragments were always shared by Pran and A. cepa . Only two rDNA fragments were shared by Pran and A. fistulosum , contradicting previous reports that Pran is an interspecific hybrid between A. cepa and A. fistulosum . Therefore, Pran arose from hybridization of A. cepa with an unresolved seed parent. This study confirms that more than one interspecific hybridization occurred in the evolution of the viviparous onion.
The cultivation of the triploid viviparous onion is reported from Tibet, Kashmir, Jammu, Croatia, Germany, The Netherlands, France, Guadeloupe, and Canada. Because of certain resemblance to the diploid top onion, Allium x proliferum, it was assumed that the parents of triploids might be also A. cepa and A. fistulosum. Accessions of A. altaicum, A. cepa, A. fistulosum, A. galanthum, A. oschaninii, A. x proliferum, A. pskemense, A. roylei, A. schoenoprasum, and A. vavilovii were investigated by isozyme analysis. The results confirmed only one species of sect. Cepa, either A. cepa, A. oschaninii or A. vavilovii, as parent of the triploid onions. A. fistulosum was excluded from the ancestry. The second parent remains still unknown. Two rare species of sect. Cepa s.l., A. farctum from Pakistan and Afghanistan and A. rhabdotum from Bhutan, were not studied. They could have been involved in the evolution of the triploids and should be analysed in this respect.
The results of the isozyme analysis suggest a closer genetical connection of the French grey shallot to Allium oschaninii and A. vavilovii than to A. cepa.
Random amplified polymorphic DNA (RAPD) analysis was used to study the phylogenetic relationships between species in Allium section Schoenoprasum and for the investigation of the intraspecific differentiation of A. schoenoprasum. RAPD analysis of 39 samples representing eight species of sect. Schoenoprasum and one sample of A. atrosanguineum (sect. Annuloprasum) resulted in 233 interpretable RAPD bands. The analysis clearly distinguishes the species of section Schoenoprasum. The arrangement of the accessions of A. schoenoprasum in all dendrograms mirrors the geographical distribution, with a clear differentiation between an Asian and European subgroup. Within the European group, Scandinavian material is clearly distinct from S and E European material. Informally described morphological types of A. schoenoprasum could not be confirmed by RAPD analysis but represent recurrent ecological adaptations. A combination of phenetic (UPGMA, neighbour-joining analysis), cladistic (parsimony analysis), and statistical (PCA) methods of data analysis resulted in clearer phylogenetic interpretations than each of the methods facilitates when used separately.
Polymorphisms for six enzyme systems (GPI, IDH, PDG, PGM, SKD, and TPI) were analysed in the top onion,Allium proliferum. Five multilocus isozyme genotypes were found. The banding patterns of top onions were compared with those ofA. wakegi, A. cepa, A. fistulosum, A. altaicum, and artificial hybrids between these three species. One top onion type and one artificial hybrid had identical banding patterns. Shallots andA. altaicum, the wild progenitor ofA. fistulosum, cannot be distinguished from the common onion andA. fistulosum, respectively; these species are also potential contributors to the top onion''s gene pool.