Multilocus structure in the Pinus contorta – Pinus banksiana complex

2007 ◽  
Vol 85 (8) ◽  
pp. 774-784 ◽  
Author(s):  
Rong-Cai Yang ◽  
Francis C. Yeh ◽  
Terrance Z. Ye
Keyword(s):  
Population Structure ◽  
Pinus Banksiana ◽  
Pinus Contorta ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Natural Hybridization ◽  
Gene Pools ◽  
Different Populations ◽  
Multilocus Associations ◽  
Gametic Disequilibria

Natural hybridization between lodgepole pine ( Pinus contorta Dougl. ex Loud.) and jack pine ( Pinus banksiana Lamb.) in western Canada provides a distinct opportunity to infer evolutionary and demographic determinants of nonrandom associations of the alleles at different loci occurring in this Pinus contorta – Pinus banksiana complex (PCBC). Here, we investigated multilocus associations among and within 40 PCBC populations sampled from central and northwestern Alberta, using 39 random amplified polymorphic DNA (RAPD) markers. For each of the 40 PCBC populations, we examined distributions of 741 pairs of linkage (gametic) disequilibria (LD) between the 39 RAPDs and measured the “average” multilocus associations using the summary statistics that allow for packaging of individual LD in each population. We then partitioned the variance of LD in the total population to assess the causes of multilocus population structure. The results showed that (i) LD were more prominent in hybrid populations than in parental populations; (ii) multilocus Wahlund effect was a much more important determinant of population structure than its single-locus counterpart, particularly in hybrid populations; and (iii) considerable mutlilocus associations across the populations within each taxa group was due to the presence of different multilocus haplotypes in different populations. Such results are best explained by the fact that PCBC populations are geographically and ecologically marginal and are produced at the balance between mixing of two distinct gene pools creating new recombinants and selection in favor of parental gametes, but against the recombinants.

Population structure of a lodgepole pine (Pinus contorta) and jack pine (P. banksiana) complex as revealed by random amplified polymorphic DNA

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 530-540 ◽  
Author(s):  
Terrance Z Ye ◽  
Rong-Cai Yang ◽  
Francis C Yeh
Keyword(s):  
Population Structure ◽  
Pinus Banksiana ◽  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Random Amplified Polymorphic Dna ◽  
Introgressive Hybridization ◽  
Jack Pine ◽  
Natural Hybridization ◽  
Secondary Contact ◽  
Putative Hybrid

We studied the population structure of a lodgepole (Pinus contorta Dougl.) and jack pine (Pinus banksiana Lamb.) complex in west central Alberta and neighboring areas by assessing random amplified polymorphic DNA (RAPD) variability in 23 lodgepole pine, 9 jack pine, and 8 putative hybrid populations. Of 200 random primers screened, 10 that amplified 39 sharp and reproducible RAPDs were chosen for the study. None of the 39 RAPDs were unique to the parental species. RAPD diversity ranged from 0.085 to 0.190 among populations and averaged 0.143 for lodgepole pine, 0.156 for jack pine, 0.152 for hybrids, and 0.148 for all 40 populations. The estimated population differentiation based on GST was 0.168 for hybrids, 0.162 for lodgepole pine, 0.155 for jack pine, and 0.247 across all 40 populations. Cluster analysis of genetic distances generally separated jack pine from lodgepole pine and hybrids, but no division could be identified that further separated lodgepole pine from hybrids. The observed weak to mild trend of "introgression by distance" in the complex and neighbouring areas was consistent with the view that introgressive hybridization between lodgepole and jack pines within and outside the hybrid zone may have been through secondary contact and primary intergradation, respectively.Key words: introgression, lodgepole–jack pine complex, natural hybridization, random amplified polymorphic DNA.

Identification and characterization of RAPD markers inferring genetic relationships among Pine species

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 51-58 ◽  
Author(s):  
K K Nkongolo ◽  
P Michael ◽  
W S Gratton
Keyword(s):  
Pinus Banksiana ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Rflp Analysis ◽  
Pinus Monticola ◽  
Species Specific ◽  
Specific Sequences ◽  
Pine Species

Total genomic DNAs were extracted from several populations of pine species and amplified using oligonucleotides of random sequences. Polymorphism in random amplified polymorphic DNA (RAPD) markers was high and sufficient in distinguishing each of the species. Genetic relationships among eight pine species (Pinus sylvestris, Pinus strobus, Pinus rigida, Pinus resinosa, Pinus nigra, Pinus contorta, Pinus monticola, and Pinus banksiana) from different provenances were analyzed. The degree of band sharing was used to evaluate genetic distance between species and to construct a phylogenetic tree. In general, the dendrogram corroborated the description of relationships based on morphological characteristics and crossability, but also provided new insights into pine taxonomy. RAPD markers specific to some pine species were cloned and sequenced. PCR amplifications using pairs of designed specific primers revealed that all the cloned sequences were likely genus specific because they were not found in spruce or larch. True species-specific sequences were identified using designed primers flanking cloned RAPD fragments. The analysis of RAPD fragment sequences confirmed the genetic relationships among species. A 2281-bp RAPD band called PI-Mt-Stb-23 from P. strobus was used as a probe in restriction fragment length polymorphism (RFLP) analysis and produced distinct banding patterns for each species examined, consistent with the highly polymorphic character of DNA-fingerprinting probes.Key words: Pine, RAPD, RFLP, cloning, species-specific sequences.

scholarly journals Random Amplified Polymorphic DNA (RAPD) Marker Variability between and within Gene Pools of Common Bean

1994 ◽  
Vol 119 (1) ◽  
pp. 122-125 ◽  
Author(s):  
Scott D. Haley ◽  
Phillip N. Miklas ◽  
Lucia Afanador ◽  
James D. Kelly
Keyword(s):  
Common Bean ◽  
Gene Pool ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Major Gene ◽  
Rapd Marker ◽  
Gene Pools ◽  
Navy Bean ◽  
Breeding Programs ◽  
Polymerase Chain

The objective of this study was to evaluate the degree of RAPD marker variability between and within commercially productive market classes representative of the Andean and Middle American gene pools of common bean (Phaseolus vulgaris L.). Six sets of near-isogenic lines were screened with oligonucleotide primers in the polymerase chain reaction-based RAPD assay. Simultaneous analyses with at least three sets of lines enabled us to score RAPD markers between the two major gene pools, races within the same gene pool, and different genotypes of the same race (within race). A “three-tiered” pattern of polymorphism was observed: between gene pools> between races> within races. The overall level of polymorphism between the Andean and Middle American gene pools was 83.4%. The overall level of polymorphism between races within the same gene pool was similar for Andean races (60.4%) and Middle American races (61.7%). The level of polymorphism between related commercial navy bean lines was 39.2% and between related commercial snap bean lines was 53.6 %. The inherent simplicity and efficiency of RAPD analyses, coupled with the number of polymorphisms detectable between related commercial genotypes, should facilitate the construction of RAPD-based genetic linkage maps in the context of populations representative of most bean breeding programs.

Susceptibility of Pinus contorta - Pinus banksiana complex to Endocronartium harknessii: host-pathogen interactions

1999 ◽  
Vol 77 (7) ◽  
pp. 1035-1043 ◽  
Author(s):  
Rong-Cai Yang ◽  
Zhihong Ye ◽  
Yasu Hiratsuka
Keyword(s):  
Pinus Banksiana ◽  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Rust Fungus ◽  
Jack Pine ◽  
Natural Hybridization ◽  
Host Group ◽  
Group Interactions ◽  
Endocronartium Harknessii ◽  
Rust Susceptibility

Lodgepole (Pinus contorta Dougl. ex Lound.) and jack (Pinus banksiana Lamb.) pines occur sympatrically and hybridize in central and northwestern Alberta, providing opportunities for studying unique ecological and evolutionary interactions. We conducted a greenhouse inoculation experiment to investigate interactions between 40 populations of lodgepole and jack pines and their putative hybrids across this hybrid zone and two sources of the western gall rust fungus, Endocronartium harknessii (J.P. Moore) Y. Hiratsuka, one from lodgepole pine and the other from jack pine. Rust susceptibility and height were assessed when the seedlings were 6 months and 1 year old. Lodgepole pine and the hybrids were significantly more susceptible to the rust infection than jack pine. Jack pine grew significantly faster than the hybrids and lodgepole pine. In addition, the seedlings infected with spores from lodgepole pine grew significantly slower than those with spores from jack pine. While the overall rust scores indicated that spores from lodgepole pine was more virulent to the hosts than those from jack pine, both spore sources were better adapted to their own host species, causing significant spore source × host group interactions. However, such host specificity in the western gall rust is far from stabilized (equilibrium) because of continued gene exchanges among the two parental species and their hybrids.Key words: Pinus contorta - Pinus banksiana complex, western gall rust, natural hybridization, coevolutionary genetics.

scholarly journals Assessment of genetic diversity of Curcuma aromatica from eastern India using ISSR and RAPD markers

2018 ◽  
Vol 1 (1) ◽  
pp. 24
Author(s):  
Reena Parida ◽  
Sujata Mohanty ◽  
Sanghamitra Nayak
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Different Populations ◽  
Clustering Pattern ◽  
Simple Sequence ◽  
Important Medicinal Plant

Application of Inter Simple Sequence Repeats and Random Amplified Polymorphic DNA markers in Curcuma aromatica collected from 4 different populations of Odisha. A dendrogram was constructed through sequential agglomerative hierarchial and nested (SAHN) clustering and unweighted pair group method with arithmetic mean (UPGMA) analysis using Jaccard’s similarity coefficient of combined markers using this particular species. Two major clusters were found i.e., cluster-I (Koraput-1, Koraput-2, Koraput-3, G.Udaigiri-1, G.Udaigiri-2, G.Udaigiri-3 and Phulabani-1, Phulabani-2, Phulabani-3) and cluster-II (Raikia-1, Raikia-2 and Raikia-3). The clustering pattern also revealed moreover the extent of genetic similarity between germplasms collected from those populations. This technique would be further utilized for identification and tagging of important novel gene present in different taxa or improvement work in family Zingiberaceae. This study would be of immense significance for conservation and characterization of important medicinal plant species.

scholarly journals Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1125
Author(s):  
Carla L. Saldaña ◽  
Johan D. Cancan ◽  
Wilbert Cruz ◽  
Mirian Y. Correa ◽  
Miriam Ramos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Tree Species ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Population Divergence ◽  
Eastern Region ◽  
Peruvian Amazon

Capirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.

Construction of a framework map in Pinus contorta subsp. latifolia using random amplified polymorphic DNA markers

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 147-153 ◽  
Author(s):  
Changxi Li ◽  
Francis C Yeh
Keyword(s):  
Pinus Contorta ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Lod Score ◽  
Chain Reaction ◽  
Base Pairs ◽  
Oligonucleotide Primers ◽  
Polymerase Chain ◽  
Genomic Map

We report on the construction of the first random amplified polymorphic DNA (RAPD) framework map in Pinus contorta subsp. latifolia. Genomic DNA of haploid megagametophytes from 90 open-pollinated seeds originating from a single tree were amplified with 840 random decamer oligonucleotide primers by the polymerase chain reaction. Three-hundred twenty-eight RAPD markers with fragment sizes that ranged between 260 and 3080 base pairs were found segregating at 110 random decamer oligonucleotide primers. Of these 328 RAPD markers, 148 were mapped to 16 framework linkage groups and 77 were mapped as accessory markers onto the framework linkage groups, on a support interval of minimal LOD score of 3. The 16 framework maps cover a distance of 2287 cM. The estimate of genome size was 2407 cM with a 95% confidence interval of 2304–2459 cM.Key words: framework genomic map, RAPD, Pinus contorta subsp. latifolia.

scholarly journals Assessment of genetic diversity of Curcuma aromatica from eastern India using ISSR and RAPD markers

2018 ◽  
Vol 3 (1) ◽  
pp. 24
Author(s):  
Reena Parida ◽  
Sujata Mohanty ◽  
Sanghamitra Nayak
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Different Populations ◽  
Clustering Pattern ◽  
Simple Sequence ◽  
Important Medicinal Plant

Application of Inter Simple Sequence Repeats and Random Amplified Polymorphic DNA markers in Curcuma aromatica collected from 4 different populations of Odisha. A dendrogram was constructed through sequential agglomerative hierarchial and nested (SAHN) clustering and unweighted pair group method with arithmetic mean (UPGMA) analysis using Jaccard’s similarity coefficient of combined markers using this particular species. Two major clusters were found i.e., cluster-I (Koraput-1, Koraput-2, Koraput-3, G.Udaigiri-1, G.Udaigiri-2, G.Udaigiri-3 and Phulabani-1, Phulabani-2, Phulabani-3) and cluster-II (Raikia-1, Raikia-2 and Raikia-3). The clustering pattern also revealed moreover the extent of genetic similarity between germplasms collected from those populations. This technique would be further utilized for identification and tagging of important novel gene present in different taxa or improvement work in family Zingiberaceae. This study would be of immense significance for conservation and characterization of important medicinal plant species.

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