Genetic relationships within and among Iberian fescues (Festuca L.) based on PCR-amplified markers

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1170-1183 ◽  
Author(s):  
Pedro J.G. de Nova ◽  
Marcelino de la Cruz ◽  
Juan V. Monte ◽  
Consuelo Soler
Keyword(s):  
Molecular Markers ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Species Level ◽  
Lolium Rigidum ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Molecular Genetic Variation

The genus Festuca comprises approximately 450 species and is widely distributed around the world. The Iberian Penninsula, with more than 100 taxa colonizing very diverse habitats, is one of its main centers of diversification. This study was conducted to assess molecular genetic variation and genetic relatedness among 91 populations of 31 taxa of Iberian fescues, based on several molecular markers (random amplified polymorphic DNA, amplified fragment length polymorphisms, and trnL sequences). The analyses showed the paraphyletic origin of the broad-leaved (subgenus Festuca , sections Scariosae and Subbulbosae, and subgenus Schedonorus ) and the fine-leaved fescues (subgenus Festuca, sections Aulaxyper, Eskia, and Festuca). Schedonorus showed a weak relationship with Lolium rigidum and appeared to be the most recent of the broad-leaved clade. Section Eskia was the most ancient and Festuca the most recent of the fine-leaved clade. Festuca and Aulaxyper were the most related sections, in concordance with their taxonomic affinities. All taxa grouped into their sections, except F. ampla and F. capillifolia (section Festuca), which appeared to be more closely related to Aulaxyper and to a new independent section, respectively. Most populations clustered at the species level, but some subspecies and varieties mixed their populations. This study demonstrated the value in combining different molecular markers to uncover hidden genetic relationships between populations of Festuca.

scholarly journals Genetic Relationships among Schizolobium parahybum (Vell.) Blake (Leguminosae) Ecotypes from Ecuador and other Countries

2007 ◽  
Vol 56 (1-6) ◽  
pp. 214-221 ◽  
Author(s):  
H. F. Canchignia-Martínez ◽  
S. Hernández-Delgado ◽  
M. González-Paz ◽  
E. Motte ◽  
N. Mayek-Pérez
Keyword(s):  
Costa Rica ◽  
Fragment Length ◽  
Geographical Origin ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Aflp Markers ◽  
Diversity Patterns ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Genetic Status

Abstract Fifteen ecotypes of Schizolobium parahybum (Vell.) Blake collected in Ecuador (9), Brazil (3), Bolivia (1) Costa Rica (1), and Peru (1) were analyzed using Random Amplified Polymorphic DNA (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs) and microsatellites (SSRs) in order to determine their genetic relationships and diversity patterns among ecotypes and to identify the origin of cultivated germplasm in Ecuador. Although AFLP markers were the most informative technique based on amplified products, SSRs clearly differentiated the ecotypes of Ecuador based on their geographical origin or genetic status into two groups: commercial ecotypes growing at western Ecuador very similar to the ecotype from Costa Rica, and native germplasm from eastern Ecuador and ecotypes from Brazil, Peru and Bolivia.

Tracing the remnants of medieval raspberries using molecular markers

2015 ◽  
Vol 14 (2) ◽  
pp. 149-156
Author(s):  
Vesna Novak ◽  
Anton Ivancic ◽  
Andrej Susek ◽  
Metka Sisko
Keyword(s):  
Molecular Markers ◽  
Genetic Analysis ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Molecular Study ◽  
Molecular Genetic Analysis ◽  
Microsatellite Data ◽  
Clustering Method ◽  
Natural Conditions ◽  
Fruit Setting

Our investigation was based on a molecular study of the genetic relationships among raspberry genotypes collected around selected medieval castles, Carthusian monasteries and nearby villages. We assumed that the hypothetical medieval raspberry genotypes could be traced to isolated medieval settlements that used to be highly prosperous during the feudal era but were later abandoned. Some of these genotypes could have survived in natural conditions without seed multiplication for at least three centuries. The molecular genetic analysis was based on microsatellite data. A total of 155 alleles were detected at 18 microsatellite loci. The clustering method grouped the analysed genotypes into seven main clusters. The analyses indicated that the most probable medieval genotypes had been collected around the ruins of two abandoned Carthusian monasteries: Zice and Jurkloster. They were morphologically very similar, vigorous and primitive but obviously not wild genotypes. The plants could be more than 2.3 m high, the canes were medium waxy, the lower and upper parts of the canes were covered by sparse short spines, the mid part was more or less completely smooth, the fully developed leaves were 15–25 cm long and the inflorescences were loose. In addition, the flowers were relatively small, the fruit setting was poor and the fruits were small, ovoid to conical and more aromatic than those of modern cultivars.

Genetic relationships among napiergrass (Pennisetum purpureum Schum.) nursery accessions using AFLP markers

2009 ◽  
Vol 8 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Karen Harris ◽  
William Anderson ◽  
Ravindra Malik
Keyword(s):  
Genetic Relatedness ◽  
Pennisetum Glaucum ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Perennial Grass ◽  
Morphological Data ◽  
Pennisetum Purpureum ◽  
Group Method ◽  
Heterotic Groups ◽  
Arithmetic Average

Pennisetum purpureum Schum. (napiergrass) is a perennial grass used for forage especially in South America and Africa. Over the last 30 years, a USDA–ARS nursery containing accessions collected from all over the world has been established in Tifton, Georgia. The study reported here was conducted to assess the molecular genetic variation and genetic relatedness among 89 accessions from the Tifton nursery using amplified fragment length polymorphism markers, morphological data and ploidy level. Using 218 polymorphic markers from eight selective primer combinations, the 89 accessions were clustered into five groups using a principal components analysis and a dendrogram based on Dice similarity estimates and unweighted pair group method with arithmetic average clustering. These five groups include three groups collected from Kenya, a group from Puerto Rico, and accessions derived from the cultivar Merkeron. This research provides the first molecular characterization of the Tifton nursery, displays the relationships between accessions, and provides potential heterotic groups for napiergrass and pearl millet (Pennisetum glaucum (L.) R. Br.) breeding improvement.

Evaluating the Taxonomic Status of the Globally Rare Carex roanensis and Allied Species Using Morphology and Amplified Fragment Length Polymorphisms

2008 ◽  
Vol 33 (3) ◽  
pp. 525-535 ◽  
Author(s):  
Tyler W. Smith ◽  
Marcia J. Waterway
Keyword(s):  
Fragment Length ◽  
Taxonomic Status ◽  
Principal Coordinate Analysis ◽  
Species Level ◽  
Morphological Data ◽  
Aflp Data ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
The Common ◽  
Geographic Regions

We used a combination of amplified fragment length polymorphisms (AFLP) and morphological data from 272 individuals from 59 populations to investigate the species-level taxonomy of Carex roanensis and allied species. There were two taxonomic problems in this group: identifying the appropriate taxonomic status for Carex roanensis, and clarifying the distinctions (if any) between C. virescens and C. swanii. Principal coordinate analysis of the morphological data suggested four entities corresponding to C. aestivalis, C. roanensis, C. swanii, and C. virescens, but clear discrimination was not possible. In contrast, the AFLP data showed marked discontinuities among these four species, placing even morphological intermediates into one of four groups. Analysis of molecular variance revealed significant population differentiation within each species, but only C. virescens had any detectable differentiation between geographic regions. This study confirms the species-level distinction between the common and widespread taxa C. swanii and C. virescens, as well as that of the globally rare Appalachian endemic C. roanensis.

AFLP-based molecular characterization of Brassica rapa and diversity in Canadian spring turnip rape cultivars

2008 ◽  
Vol 6 (1) ◽  
pp. 11-21 ◽  
Author(s):  
S. I. Warwick ◽  
T. James ◽  
K. C. Falk
Keyword(s):  
Genetic Diversity ◽  
Brassica Rapa ◽  
Genetic Relationships ◽  
Aflp Data ◽  
Distance Information ◽  
Breeding Lines ◽  
Cultivar Development ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Aa Genome

Information on genetic diversity and genetic relationships among taxa of Brassica rapa (n = 10, AA genome) is currently limited. Grown for oil, vegetable and fodder use in Europe and Asia, previous studies have indicated western and eastern groups corresponding to independent centres of origin. This study evaluated patterns and levels of genetic diversity in 93 accessions [includes 25 Agriculture and Agri-Food Canada (AAFC) breeding lines (BL)] of B. rapa based on 307 amplified fragment length polymorphisms (AFLP), testing subspecific separateness and the affiliation of four previously unassigned AA genome species (B. perviridis, B. purpuraria, B. ruvo and B. septiceps). AFLP data revealed three main clusters (I, II, III) corresponding to European (I), Indian (III), and a mixed Asian/European/Indian (II) purported origins of the taxa, with several subclusters observed in I and II. Mean AFLP polymorphism levels for Asian, European, Indian and AAFC-BL accessions were 79, 74, 66 and 62%, respectively. Few of the subspecies formed unique clusters and some, particularly subspecies chinensis and pekinensis, were assigned to several clusters. AFLP-based genetic distance information can be used by breeders to select diverse genotypes for cultivar development and fingerprinting of genotypes/cultivars. For example, a single AFLP primer pair was sufficient to uniquely identify all breeding lines in the AAFC B. rapa breeding programme.

Edraianthus stankovicii (Campanulaceae), an overlooked taxon from the Balkan Peninsula—Evidence from morphometric, molecular and genome size studies

Phytotaxa ◽  
2016 ◽  
Vol 269 (2) ◽  
pp. 69
Author(s):  
DMITAR LAKUŠIĆ ◽  
SAŠA STEFANOVIĆ ◽  
SONIA SILJAK-YAKOVLEV ◽  
TAMARA RAKIĆ ◽  
NEVENA KUZMANOVIĆ ◽  
...  
Keyword(s):  
Genome Size ◽  
Phylogenetic Analyses ◽  
Conservation Status ◽  
Plastid Dna ◽  
Balkan Peninsula ◽  
Species Level ◽  
F Region ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
External Transcribed Spacer

The taxonomically intricate Edraianthus dalmaticus-serbicus group within E. tenuifolius-complex in the Balkan Peninsula is reviewed using morphological, molecular and genome size data based on extensive sampling of populations across the species’ range. The phylogenetic analyses based on Amplified Fragment Length Polymorphisms (AFLPs), plastid DNA (trnL-F region and rbcL-atpB spacer) and nuclear ribosomal external transcribed spacer (nrETS) sequences confirmed the monophyly of E. serbicus as traditionally defined but have also revealed the presence of two distinct and allopatrically distributed taxa. The genome size and morphological analyses, performed on the same widespread sample of populations, largely corresponded with molecular results, allowing us to raise the overlooked taxon E. serbicus subsp. stankovici, to the species level. The names Edraianthus serbicus and E. serbicus subsp. stankovicii (≡ E. stankovicii) are typified. Furthermore, a new differential diagnosis, description and illustration of E. stankovicii are provided, as well as its conservation status is assessed. Edraianthus stankovicii is a rare and critically endangered stenoendemic taxon, with the distribution limited only to Mts. Veliki Krš and Stol in NE Serbia.

scholarly journals Molecular markers based genetic relatedness studies in tissue culture propagated Japanese plum cultivars Santa Rosa and Frontier

2021 ◽  
Author(s):  
Manisha Thakur ◽  
Rakshandha Luharch ◽  
Vishal Sharma ◽  
Dharam Paul Sharma
Keyword(s):  
Molecular Markers ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Start Codon ◽  
Japanese Plum ◽  
Percent Similarity ◽  
Allelic Variations ◽  
Relationship Of

Abstract Santa Rosa and Frontier are the major Japanese plum cultivars grown throughout the world. The present investigation was performed to understand the genetic relatedness among in vitro propagated plum cultivars Santa Rosa and Frontier using PCR based molecular markers. For the study, three arbitrary markers viz. RAPD (Random amplified Polymorphic DNA), ISSR (Inter-Simple Sequence Repeats) and SCoT (Start Codon Targeted) were used. In RAPD analysis, 18 primers out of 28 amplified and generated 33 scorable bands. The allelic variations when analysed, revealed 84 percent similarity between these two cultivars with highest polymorphic information content of 0.78. Similarly, 15 ISSR primers produced 73 amplicons with an average of 4.86 amplicon per primer and similarity coefficient ranging from 62 to 67 percent. Seven SCoT primers out of 26 resulted in a total of twenty- six scorable bands with 24 polymorphic bands. Cluster analysis from all the three markers used broadly divided plum cultivars santa rosa and frontier into two major clusters containing in vitro shoots, their progenies and mother trees of respective genotypes. The study concluded that these three marker systems were found to be effective in revealing genetic relationship of these two commercially important plum cultivars.

scholarly journals 078 Mapping of the Citrullus Genome using Populations Segregating for Fusarium Wilt Resistance

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 454E-454
Author(s):  
Leigh K. Hawkins ◽  
Fenny Dane ◽  
Thomas L. Kubisiak ◽  
Billy Rhodes
Keyword(s):  
Fusarium Wilt ◽  
Citrullus Lanatus ◽  
Random Amplified Polymorphic Dna ◽  
Dominant Gene ◽  
Wilt Resistance ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Race 2 ◽  
Serious Disease ◽  
Simple Sequence

Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f.sp. niveum (FON), is a serious disease of the watermelon (Citrullus lanatus). Three races of this pathogen (races 0, 1, and 2) have been identified based on differential pathogenicity assays. Most commercially available cultivars are resistant to races 0 and 1. Inheritance for resistance to these races is thought to be controlled by a single dominant gene. No cultivars are resistant to race 2 and resistance is thought to be a quantitative trait. F2 lines derived from a cross between the Fusarium-resistant Citrullus lanatus PI296341, and the Fusarium-susceptible watermelon cultivar `New Hampshire Midget' were used to generate a RAPD-based map of the Citrullus genome. F2:3 families were assayed in the greenhouse for resistance to races 1 and 2. Those families that were either highly resistant or highly susceptible were used in identifying markers linked to Fusarium wilt resistance. A preliminary map of the Citrullus genome based on random amplified polymorphic DNA (RAPD) markers has been expanded with the inclusion of simple sequence repeats (SSRs), amplified fragment length polymorphisms (AFLPs), and isozymes.

Genetic Relatedness among Environmental, Clinical, and Diseased-Eel Vibrio vulnificus Isolates from Different Geographic Regions by Ribotyping and Randomly Amplified Polymorphic DNA PCR

1998 ◽  
Vol 64 (9) ◽  
pp. 3403-3410 ◽  
Author(s):  
Covadonga R. Arias ◽  
María Jesús Pujalte ◽  
Esperanza Garay ◽  
Rosa Aznar
Keyword(s):  
Genetic Relatedness ◽  
Vibrio Vulnificus ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Mediterranean Coast ◽  
Universal Primers ◽  
23S Rrna ◽  
Rrna Gene ◽  
Conserved Sequence ◽  
Rapd Pcr

ABSTRACT Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with KpnI and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high level of homogeneity of diseased-eel isolates in contrast to the genetic heterogeneity of Mediterranean isolates. The latter suggests the existence of autochthonous clones present in Mediterranean coastal waters. Both techniques have revealed a genetic proximity among Spanish fish farm isolates and a close relationship between four Spanish eel farm isolates and some Mediterranean isolates. Whereas the differentiation within diseased-eel isolates was only possible by ribotyping, RAPD PCR was able to differentiate phenotypically atypical isolates of V. vulnificus. On the basis of our results, RAPD PCR is proposed as a better technique than ribotyping for rapid typing in the routine analysis of new V. vulnificusisolates.

scholarly journals Does Primula intricata Gren. et Godr. Merit Species Rank? A Taxonomic Revision Based on nrDNA, cpDNA and AFLP Data

2011 ◽  
Vol 39 (1) ◽  
pp. 24
Author(s):  
Dana ŞUTEU ◽  
Mihai PUSCAS ◽  
Ioan BĂCILĂ ◽  
Ana COSTE ◽  
Liviu FILIPAS ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Taxonomic Status ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Valid Species ◽  
Aflp Data ◽  
Genetic Studies ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

Primula intricata Gren. et Godr. has an unclear taxonomic status: it was originally described as a distinct species but subsequently was considered a subspecies (Primula elatior subsp. intricata) or even a variety (P. elatior var. intricata ) of Primula elatior (L.) Hill. No prior genetic studies were performed on this group of Primulaceae, therefore we considered useful to investigate taxonomies boundaries within the P. elatior-intricata group. We explored genetic differences between Primula intricata and Primula elatior group by applying three different types of molecular markers: nuclear ribosomal DNA (ITS1), chloroplast DNA (spacer trnH-psbA and intron trnL) and Amplified Fragment Length Polymorphisms (AFLP). We found a solid differentiation between P. intricata and P. elatior group, differentiation that was confirmed by all the employed molecular markers. This finding enabled us to propose a valid species rank for Primula intricata, as a separate taxon from the P. elatior group.

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