scholarly journals Nuclear and chloroplast DNA differentiation in Andean potatoes

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 46-56 ◽  
Author(s):  
Thitaporn Sukhotu ◽  
Osamu Kamijima ◽  
Kazuyoshi Hosaka
Keyword(s):  
High Resolution ◽  
Chloroplast Dna ◽  
Wild Species ◽  
Nuclear Dna ◽  
Hybrid Origin ◽  
Strongly Correlated ◽  
Length Polymorphisms ◽  
Dna Restriction ◽  
Cultivated Species ◽  
Dna Microsatellite

Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T-type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry.Key words: potato, chloroplast DNA, microsatellite markers, nuclear DNA RFLPs.

scholarly journals 336 PHYLOGENETIC RELATIONSHIPS OF CELERY AND ITS WILD RELATIVES BASED ON RESTRICTION FRAGMENT LENGTH POLYMORPHISMS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 478f-478
Author(s):  
Gordon M. Huestis ◽  
Carlos F. Quiros
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Chloroplast Dna ◽  
Southern Hemisphere ◽  
Fragment Length ◽  
Wild Species ◽  
Phylogenetic Relationships ◽  
Wild Relatives ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Phylogenetic relationships of seven Apium species, including three horticultural types of A. graveolens, were assayed for RFLPs using cDNA, chloroplast DNA, and rDNA probes. Most of the probes had been previously mapped in celery. The three horticultural types of A. graveolens were found to be less polymorphic than the wild species and in phylogenetic analysis they clustered together. The wild species formed a cluster on the dendrogram corresponding to their origin in the southern hemisphere. A. nodiflorum, a wild species from Ethiopia formed a branch on the phylogenetic tree apart from all other species. This, along with morphological considerations, suggests that A. nodiflorum should be reclassified outside the genus Apium.

Hybridization and the origin of the arctic grass Poa hartzii (Poaceae): evidence from morphology and chloroplast DNA restriction site data

1997 ◽  
Vol 75 (11) ◽  
pp. 1978-1997 ◽  
Author(s):  
Lynn J. Gillespie ◽  
Laurie L. Consaul ◽  
Susan G. Aiken
Keyword(s):  
Chloroplast Dna ◽  
Restriction Enzyme ◽  
The Arctic ◽  
Hybrid Origin ◽  
Enzyme Analysis ◽  
Restriction Enzyme Analysis ◽  
Dominant Type ◽  
Morphological Studies ◽  
Poa Secunda ◽  
Dna Restriction

The hypothesized hybrid origin of Poa hartzii Gand. (Poaceae) was investigated by analysis of morphological and molecular data. This endemic nearctic caespitose grass has been considered to be a hybrid between two of the three sympatric arctic species, Poa glauca M. Vahl, Poa arctica R. Br., and Poa abbreviata R. Br. Field observations and morphological studies indicate that Poa hartzii is a morphologically distinct apomictic species that reproduces and disperses by seed. Restriction enzyme analysis of polymerase chain reaction amplified chloroplast DNA revealed the presence in Poa hartzii of two very different haplotypes. One haplotype is identical to the dominant type found in Poa glauca, while the second is identical to the haplotype of Poa secunda J. Presl., located south of the arctic region. These results are consistent with an hypothesis of ancient hybrid origin involving Poa glauca and Poa secunda, but not Poa arclica nor Poa abbreviata. They are also consistent with an hypothesis of cytoplasmic transfer via hybridization and introgression from Poa glauca to an ancestral Poa hartzii in the Poa secunda complex. Direction of transfer is suggested by the widespread occurrence of the Poa secunda haplotype in Poa hartzii and by closer morphological similarity with Poa secunda than Poa glauca. The origin of Poa hartzii provides an excellent example of reticulate evolution and the importance of hybridization in the speciation of arctic grasses. Key words: Poa hartzii, arctic Poa, chloroplast DNA, restriction enzyme analysis, hybridization, introgression.

Molecular phylogenetics of Thlaspi s.l. (Brassicaceae) based on chloroplast DNA restriction site variation and sequences of the internal transcribed spacers of nuclear ribosomal DNA

1997 ◽  
Vol 75 (3) ◽  
pp. 469-482 ◽  
Author(s):  
Klaus Mummenhoff ◽  
Andreas Franzke ◽  
Marcus Koch
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Restriction Site ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Ploidy Levels ◽  
Restriction Site Variation ◽  
Its Regions ◽  
Site Variation ◽  
Dna Restriction

Systematics of the genus Thlaspi s.l. is difficult and controversial. Previous hypotheses have been based on morphological and anatomical data. We have analyzed sequence variation of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA) among 13 Thlaspi s.l. taxa, representing all sections of the genus. Phylogenetic relationships among ITS sequences of the Thlaspi s.l. taxa studied are in general concordance with a previously published chloroplast DNA based phylogeny of this group. Most-parsimonious trees from ITS and chloroplast DNA data support three groups that are congruent with lineages (Thlaspi s.str., Noccaea–Raparia, Microthlaspi) previously described by Meyer on the basis of seed anatomy. The ITS data grouped Microthlaspi granatense outside the Microthlaspi clade and, therefore, Microthlaspi appeared paraphyletic on the ITS tree, in contrast with the chloroplast DNA phylogeny. We speculate that concerted evolutionary forces have acted among different nrDNA arrays (brought together in M. granatense by hybridization with a related taxon), resulting in the fixation of the alien species nrDNA type in M. granatense, which, however, maintains a Microthlaspi chloroplast genome type. Both molecular data sets detected intraspecific variation among Microthlaspi perfoliatum accessions of different geographic origin and different ploidy levels. Our molecular evidence would suggest the hybrid origin of polyploid M. perfoliatum from diploid M. perfoliatum and M. natolicum. Key words: chloroplast DNA, restriction site variation, sequence analysis of nuclear ribosomal DNA ITS regions, Thlaspi s.l. (Brassicaceae), molecular phylogeny, congruence.

scholarly journals Diversity of Virulence in Phytophthora parasitica on Tobacco, as Reflected by Nuclear RFLPs

1998 ◽  
Vol 88 (3) ◽  
pp. 205-212 ◽  
Author(s):  
V. Colas ◽  
I. Lacourt ◽  
P. Ricci ◽  
F. Vanlerberghe-Masutti ◽  
A. Poupet ◽  
...  
Keyword(s):  
Disease Management ◽  
Nuclear Dna ◽  
Clonal Evolution ◽  
Black Shank ◽  
Length Polymorphisms ◽  
Dna Restriction ◽  
Tobacco Cultivation ◽  
First Time ◽  
Highly Virulent ◽  
Restriction Fragment Length

A worldwide collection of P. parasitica isolates was investigated for the ability to infect tobacco and tomato, as related to elicitin production. Elicitin was produced by all nontobacco isolates, and nonproducing strains all were isolated from tobacco. In addition, producing strains were isolated from tobacco and coexisted with nonproducing (TE¯) strains. Elicitin production generally was associated with low virulence on tobacco and frequent pathogenicity on tomato, whereas TE¯ isolates generally were highly virulent and specialized to tobacco. Analysis of both mitochondrial and nuclear DNA restriction fragment length polymorphisms indicated, for the first time, that black shank isolates can be distinguished from other P. parasitica isolates on the basis of genetic criteria. Our results suggest that severe black shank is caused by a limited number of TE¯ strains that have been disseminated by clonal evolution. Mutations in the TE¯ phenotype seem to have arisen independently in several genetic backgrounds and distinct geographic areas. The fortuitous absence of elicitin production has precluded population replacements in areas of intensive tobacco cultivation. Thus, monitoring the loss of elicitin production in developing tobacco areas should be considered in disease management.

scholarly journals Chloroplast DNA Restriction Fragment Variation among Strawberry (Fragaria spp.) Taxa

1997 ◽  
Vol 122 (1) ◽  
pp. 63-68 ◽  
Author(s):  
Richard E. Harrison ◽  
James J. Luby ◽  
Glenn R. Furnier
Keyword(s):  
Nicotiana Tabacum ◽  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Restriction Fragment ◽  
Restriction Enzymes ◽  
Closely Related Species ◽  
Length Polymorphisms ◽  
Phylogenetic Resolution ◽  
Dna Restriction ◽  
Restriction Fragment Length

Restriction fragment-length polymorphisms (RFLPs) of chloroplast DNA (cpDNA) were used to study phylogenetic relationships among twenty-six Fragaria taxa and two closely related species, Potentilla fruticosa L. and Duchesnea indica (Andrews) Focke. Sixteen restriction enzymes and probes of the entire Nicotiana tabacum L. chloroplast genome revealed a very low level of variation among the Fragaria taxa, limiting phylogenetic resolution. However, Fragaria appears to be more closely related to Potentilla than Duchesnea. The diploid taxa, F. iinumae Makino, F. nilgerrensis Schlect. and F. vesca L. were the most divergent Fragaria taxa and F. iinumae appears to be the most ancestral taxon. Little variation was revealed within the economically important octoploid group of taxa, which gave rise to the cultivated strawberry, and no progenitor taxa to the octoploid group could be identified. The lack of variation in the chloroplast genome suggests that these Fragaria species may be of relatively recent evolutionary origin.

scholarly journals Origin and evolution of Andigena potatoes revealed by chloroplast and nuclear DNA markers

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 636-647 ◽  
Author(s):  
Thitaporn Sukhotu ◽  
Kazuyoshi Hosaka
Keyword(s):  
Chloroplast Dna ◽  
Wild Species ◽  
Nuclear Dna ◽  
Solanum Tuberosum L ◽  
Diploid Species ◽  
Evolutionary Process ◽  
Principal Component ◽  
Rflp Markers ◽  
Origin And Evolution ◽  
Multiple Origins

Andigena potatoes (Solanum tuberosum L. subsp. andigena Hawkes) (2n = 4x = 48) are important, native-farmer-selected cultivars in the Andes, which form a primary gene pool for improving a worldwide grown potato (S. tuberosum subsp. tuberosum). To elucidate the origin of Andigena, 196 Andigena accessions were compared with 301 accessions of 33 closely related cultivated and wild species using several types of chloroplast DNA (ctDNA) markers and nuclear DNA (nDNA) restriction fragment length polymorphism (RFLP) markers. Fourteen ctDNA types (haplotypes) and 115 RFLP bands were detected in Andigena, of which the main haplotypes and frequent RFLP bands were mostly shared with a cultivated diploid species, S. stenotomum Juz. et Buk. Principal component analysis of nDNA polymorphisms revealed a progressive and continuous variation from Peruvian wild species with C-type ctDNA to a group of wild species having S-type ctDNA in its variation range (S. bukasovii, S. canasense, S. candolleanum, and S. multidissectum), to cultivated diploid potatoes (S. phureja and S. stenotomum), and to cultivated tetraploid potatoes (Andigena and Chilean S. tuberosum subsp. tuberosum). These results suggest that the initial Andigena population arose with multiple origins exclusively from S. stenotomum. The overall evolutionary process toward the present-day Andigena was discussed.Key words: Andigena, chloroplast DNA, nuclear DNA RFLPs, origin, sexual tetraploidization.

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