An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation

Merritt, Benjamin J.; Culley, Theresa M.; Avanesyan, Alina; Stokes, Richard L.; Brzyski, Jessica R.

doi:10.3732/apps.1500025

Cited by 46 publications

(34 citation statements)

References 57 publications

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“…The present study is a first broad genetic survey of North American chicory placed into a global framework of the species’ natural history. The genetic diversity for the 12 SSR markers was high ( H e = 0.61), similar to another North American non‐native taxon in the Asteraceae (Eriksen et al., ) and higher then mean values (0.56) from a recent compilation of 1512 species of Asteriods (Merritt, Culley, Avanesyan, Stokes, & Brzyski, ). cpDNA variation in populations is generally low, but it serves as a useful tool for monitoring seed dispersal and maternal contributions (Ennos, Sinclair, Hu, & Langdon, ; Wallace et al., ).…”

Section: Discussionsupporting

confidence: 73%

“…The genetic diversity for the 12 SSR markers was high (H e = 0.61), similar to another North American non-native taxon in the Asteraceae (Eriksen et al, 2014) and higher then mean values (0.56) from a recent compilation of 1512 species of Asteriods (Merritt, Culley, Avanesyan, Stokes, T A B L E 6 Analysis of molecular variance and population pairwise F ST values among three groups (Group 1 CC-chicory cultivars, Group 2 EU-wild Eurasian chicory, Group 3 NA-North American chicory from Arlequin v. 3.5.1.3 & Brzyski, 2015). cpDNA variation in populations is generally low, but it serves as a useful tool for monitoring seed dispersal and maternal contributions (Ennos, Sinclair, Hu, & Langdon, 1999;Wallace et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

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Population structure in chicory (Cichorium intybus): A successful U.S. weed since the American revolutionary war

Závada

Malik

Kesseli

2017

Ecology and Evolution

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Plant invasions are recognized as major drivers of ecosystem change, yet the precise cause of these invasions remains unknown for many species. Frequency and modes of introductions during the first, transport and colonization, stages of the invasion process as well as phenotypic changes due to plasticity or changing genetic diversity and adaptation during later establishment and expansion stages can all influence the “success” of invasion. Here, we examine some of these factors in, and the origin of, a very successful weed, Cichorium intybus (chicory) which was introduced to North America in the 18th century and which now can be found in all 48 continental U.S. states and much of Canada. We genotyped a Eurasian collection of 11 chicory cultivars, nine native populations and a North American collection of 20 introduced wild populations which span the species range (592 individuals in total). To detect the geographic sources of North American chicory populations and to assess the genetic diversity among cultivars, native, and introduced populations, we used both a sequenced cpDNA region and 12 nuclear simple sequence repeat (SSR), microsatellite loci. Four cpDNA haplotypes were identified and revealed clear geographic subdivisions in the chicory native range and an interspecific hybrid origin of Radicchio group. Nuclear data suggested that domesticated lines deliberately introduced to North America were major contributors to extant weedy populations, although unintended sources such as seed contaminants likely also played important roles. The high private allelic richness and novel genetic groups were detected in some introduced populations, suggesting the potential for local adaptation in natural sites such as deserts and nature reserves. Our findings suggest that the current populations of weedy U.S. chicory have evolved primarily from several sources of domesticated and weedy ancestors and subsequent admixture among escaped lineages.

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Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Population structure in chicory (Cichorium intybus): A successful U.S. weed since the American revolutionary war

Závada

Malik

Kesseli

2017

Ecology and Evolution

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“…These markers will likely continue to be widely used because budgets are affordable once a set of SSRs is characterized for a taxon (Jennings et al., ). Although several studies in the past decade have focused on SSR isolation and characterization strategies (Zane et al., ; Viruel et al., , ; Meglécz et al., ; Merritt et al., ), few improvements on the genotyping procedures of microsatellite markers can be found in the literature (e.g., Suez et al., ).…”

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confidence: 99%

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

et al. 2018

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Premise of the StudySimple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.MethodsIn this study, we implemented a next‐generation sequencing–based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results.ResultsThe analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single‐nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates.DiscussionNext‐generation sequencing allows the detection and scoring of SSRs, single‐nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.

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“…Characterization using molecular markers is currently widely practiced in agriculture, especially for providing complementary data supplementing morphological characterization. Microsatellite or simple sequence repeat (SSR) is one of the molecular markers consisting of short tandem repeat sequences of 1-6 bps and are widely distributed in the eukaryotic genome-including the plant genome [13]. This marker has the following advantages: it is codominant, locus-specific, and has both a high level of polymorphism and high reproducibility [14].…”

Section: Introductionmentioning

confidence: 99%

The Use of Molecular Markers to Analyze the Genetic Diversity of Indonesian Pepper (Capsicum spp.) Varieties Based on Anthracnose Resistance

Nugroho¹,

Terryana²,

Manzila³

et al. 2019

Makara J. Sci

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Anthracnose is an important disease affecting the pepper plant and can lead to significant decreases in harvest yield. In this study, the genetic diversity of Indonesian pepper varieties was analyzed based on anthracnose resistance using molecular markers. DNA collected from 15 pepper varieties belonging to two species-Capsicum annuum L. and C. frutescens L.-were amplified using 14 molecular markers. The fungal isolate Colletotrichum capsici was inoculated into ripe harvested pepper fruits to observe their resistance to anthracnose as indicated by lesion size. Phylogenetic analysis revealed that the 15 pepper varieties could be classified into two major clusters with a genetic similarity coefficient of 0.63, and the pepper varieties exhibited varying degrees of resistance to anthracnose based on lesion size. Using the molecular markers, we were able to differentiate the species of pepper varieties, but not their resistance to anthracnose. All markers used in this study were confirmed to be highly informative (PIC > 0.5), suggesting their potential use in genetic studies on peppers. The marker GPMS29 was found to be significantly associated (P < 0.05) with anthracnose resistance. This information about the genetic diversity of peppers-along with the molecular markers used in our study-could prove to be useful in the further development of breeding programs of pepper plants in terms of anthracnose resistance in Indonesia.

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An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation

Cited by 46 publications

References 57 publications

Population structure in chicory (Cichorium intybus): A successful U.S. weed since the American revolutionary war

Population structure in chicory (Cichorium intybus): A successful U.S. weed since the American revolutionary war

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

The Use of Molecular Markers to Analyze the Genetic Diversity of Indonesian Pepper (Capsicum spp.) Varieties Based on Anthracnose Resistance

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