Genetic diversity in <i>Arabidopsis thaliana</i> L. Heynh. investigated by cleaved amplified polymorphic sequence (CAPS) and inter‐simple sequence repeat (ISSR) markers

Barth, Susanne; Melchinger, Albrecht E.; Lübberstedt, T.

doi:10.1046/j.0962-1083.2002.01466.x

Cited by 83 publications

(55 citation statements)

References 46 publications

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“…Inter-simple sequence repeat (ISSR) markers permit the detection of polymorphic loci without knowing the DNA sequences of species (Barth et al, 2002). At the same time, the cost of the analyses is relatively lower than that of other markers such as amplified fragment length polymorphisms (AFLPs) and microsatellites (Fang and Roose, 1997).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Broussonetia papyrifera populations in southwest China

et al. 2014

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ABSTRACT. Broussonetia papyrifera is an important native tree species with high economic value in southwest China. Its resources are drastically reduced because of over-harvesting and habitat fragmentation. In this study, 17 natural populations of B. papyrifera were analyzed using inter-simple sequence repeat (ISSR) markers to assess the genetic diversity and population structure. In total, 100 bands were obtained from 16 ISSR primers. The B. papyrifera populations showed relatively high genetic diversity at the species level [percentage of polymorphic bands (PPB): 96%; Nei's genetic diversity (H E ): 0.3074; Shannon's information index (I): 0.4617], while the genetic diversity at the population level was relatively low (PPB: 53.2%; H E : 0.1826; I: 0.2735). Relatively high level of genetic differentiation among populations (41%) was disclosed by analysis of molecular variance, which agrees with the Nei's genetic diversity statistics (40.59%) and Shannon's information measure (40.76%). Gene flow among populations (N M ) was only 0.7318. A significant correlation was observed between genetic and geographic distance among the studied populations (r = 0.2948). We conjectured that the genetic diversity of B. papyrifera resulted from human disturbance, habitat fragmentation, small effective population size, and geographic barrier. Given the high genetic differentiation among populations, some utilization and conservation strategies were proposed. This study provides a reference for the sustainable use of the species in southwest China.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity of Broussonetia papyrifera populations in southwest China

et al. 2014

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Section: Introductionmentioning

confidence: 99%

“…The multilocus dominant marker phenotypes of individuals are then used to generate a genetic distance matrix. This information is subjected to phenetic analysis to produce a visual representation (a tree-based diagram or principal coordinates plot (PCO)) of the genetic relationships among individuals in the sample (eg Winfield et al, 1998;Clausing et al, 2000;Drummond et al, 2000;van der Merwe et al, 2000;Sawkins et al, 2001;Barth et al, 2002;Nan et al, 2003).The shape of the tree or PCO plot then forms the basis for making population genetic inferences about the populations from which the individuals were derived. For instance, grouping of individuals from different populations in the same cluster of a tree has been interpreted as evidence for gene flow between these populations; location of individuals from different populations in mutually exclusive clusters has been taken as evidence for genetic isolation of the populations.…”

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confidence: 99%

Neighbour joining trees, dominant markers and population genetic structure

Hollingsworth

Ennos

2004

Heredity

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Population genetic theory for 'traditional' codominant loci showing low levels of allelic diversity (eg allozymes) has been well characterised and evaluated. In contrast, appropriate methods for the analysis of data from more recently developed marker systems are still being refined. For multilocus dominant markers such as amplified fragment length polymorphisms (AFLPs) and randomly amplified polymorphic DNA (RAPDs), the methods of data analysis can be split into two main categories. In population-based approaches, population allele frequencies are compared to obtain some measure of the partitioning of genetic diversity into within-and between-population components. In contrast, individual-based approaches use individual multilocus genotypes as the unit of analysis. Inferences on population processes such as gene flow are based on inter-relationships among individual samples as visualised on phenetic diagrams such as neighbour joining trees. Using a simulation approach coupled with neighbour joining analyses, we show that while the underlying population genetic structure is an important determinant of tree shape in the analysis of dominant data, the number of loci examined also affects the topology. At low levels of population differentiation (eg F ST ¼ 0.07), mutually exclusive clustering of individuals into their respective populations can occur when sufficiently large numbers of loci are scored (eg 250 loci, typical of many AFLP studies). In contrast, unresolved star-shaped topologies can be recovered at higher levels of population differentiation (F ST ¼ 40.15) when lower numbers of loci are employed (eg 50 loci, typical of many RAPD studies). Thus, the relationship between tree topology and the extent of genetic structuring of populations is contingent upon the number of dominant loci scored. The consequences of these findings for the biological interpretation of individual-based analysis of dominant data sets are discussed. IntroductionTraditional descriptors of population genetic structure (eg F ST ) were developed for the analysis of population samples scored for genetic markers showing codominant inheritance and low levels of allelic diversity (typically two to four alleles per locus). A substantial body of population genetic theory appropriate for such markers has provided us with an understanding of how estimates of F ST are influenced by parameters such as migration rate, population size and mutation rate (Wright, 1978;Nei, 1987). Using this knowledge, it is now possible (with caution, and making a number of assumptions) to infer biological processes such as dispersal patterns from estimates of F ST calculated from traditional codominant markers (eg allozymes) in natural populations.In recent years, a much wider range of genetic markers with significantly different properties have become available (Karp et al, 1998). These can be divided into two main classes: (1) locus-specific hypervariable microsatellite markers and (2) multilocus arbitrary fingerprinting techniques (eg randomly amplified polymor...

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“…However, the number of fragments detected depends on the size of the genome, the frequency of the sequences repeated in the genome and the detection method (Barth et al 2002). In the present study, the primers used to amplify the microsatellite loci (Table 1) generated one to five fragments per loci, depending on the primers.…”

Section: Genetic Diversitymentioning

confidence: 94%