The transferability of microsatellite loci from a homoploid to a polyploid hybrid complex: an example from fine-leaved Festuca species (Poaceae)

Background Microsatellite loci, or single sequence repeats (SSR), are widely used as powerful markers in population genetics. They represent an attractive tool for studying plants such as grasses, whose evolution is driven by hybridisation and polyploidization. However, the development of microsatellite markers has been challenging and time-consuming, especially for non-model organisms lacking available genome-wide sequence data. One straightforward and low-cost approach is to transfer the SSR loci developed for one species, or complex, to another closely-related one. This work evaluates the transferability of microsatellite loci from homoploid to allopolyploid complexes of fine-leaved Festuca species and to assess their use in two new species. The studied complex (F. amethystina—F. tatrae) is a useful model for research on the local adaptability of grasses with different ploidy levels. Since both species can be considered as rare or threatened (F. tatrae—as a mountain and narrow endemic species and F. amethystina—a mountain species with relict lowland populations), any tool enabling studies on genetic diversity and population genetics, such as SSR markers, could also be very useful in a conservation context. Methods The ploidy level within populations was estimated using flow cytometry. One diploid and one tetraploid population of F. amethystina and a diploid population of F. tatrae were chosen to test the transferability of SSR loci. Because our work describes the transfer of SSR nuclear markers designed originally for F. gautieri, a phylogenetic tree was prepared based on the ITS marker to assess the genetic distance between the studied complexes. The PCR products were separated on a high-resolution agarose gel, intended for SSR marker analysis. Appropriate solutions for the allotetraploid population and whole mixed-ploidy complex were implemented. Results Flow cytometry confirmed earlier data regarding DNA content in the investigated species and cytotypes. The phylogenetic ITS tree indicated a small genetic distance between F. gautieri complexes and the studied species. Ten microsatellite markers were successfully transferred. All markers were polymorphic. In total, 163 different alleles were scored from the 10 SSR loci. PCoA of accessions revealed well-separated groups corresponding to studied populations. Over 60% of the total variance is explained by differentiation within populations and one third among them. Conclusions The transferred markers are valid tools for the study of population genetics and inheritance relationships within cytotypes and species and between them. The presented markers can be used to study inbreeding depression in the Festuca species, and variations in the degrees of genetic diversity between different cytotypes in mountain and lowland areas. Our findings can also be applied to study conservation strategies for ensuring biodiversity at the genetic level in polyploid complexes.

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Microsatellite Markers Developed from `Bluecrop' Reveal Polymorphisms in the Genus Vaccinium and Are Suitable for Cultivar Fingerprinting

HortScience ◽

10.21273/hortsci.40.4.1122b ◽

2005 ◽

Vol 40 (4) ◽

pp. 1122B-1122 ◽

Cited By ~ 1

Author(s):

Peter Boches ◽

Lisa J. Rowland ◽

Kim Hummer ◽

Nahla V. Bassil

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Distance ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Distance Measures ◽

Hybrid Origin ◽

Pedigree Information ◽

Species Relationships ◽

Ssr Loci

Microsatellite markers for blueberry (Vaccinium L.) were created from a preexisting blueberry expressed sequence tag (EST) library of 1305 sequences and a microsatellite-enriched genomic library of 136 clones. Microsatellite primers for 65 EST-containing simple sequence repeats (SSRs) and 29 genomic SSR were initially tested for amplification and polymorphism on agarose gels. Potential usefulness of these SSRs for estimating species relationships in the genus was assessed through cross-species transference of 45 SSR loci and cluster analysis using genetic distance values from five highly polymorphic EST-SSR loci. Cross-species amplification for 45 SSR loci ranged from 17% to 100%, and was 83% on average in nine sections. Cluster analysis of 59 Vaccinium species based on genetic distance measures obtained from 5 EST-SSR loci supported the concept of V. elliotii Chapm. as a genetically distinct diploid highbush species and indicated that V. ashei Reade is of hybrid origin. Twenty EST-SSR and 10 genomic microsatellite loci were used to determine genetic diversity in 72 tetraploid V. corymbosum L. accessions consisting mostly of common cultivars. Unique fingerprints were obtained for all accessions analyzed. Genetic relationships, based on microsatellites, corresponded well with known pedigree information. Most modern cultivars clustered closely together, but southern highbush and northern highbush cultivars were sufficiently differentiated to form distinct clusters. Future use of microsatellites in Vaccinium will help resolve species relationships in the genus, estimate genetic diversity in the National Clonal Germplasm Repository (NCGR) collection, and confirm the identity of clonal germplasm accessions.

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Genetic Divergence of Flax Genotypes (Linum Usitatissimum L.) Utilizing Microsatellite Markers

Current Agriculture Research Journal ◽

10.12944/carj.5.1.14 ◽

2017 ◽

Vol 5 (1) ◽

pp. 123-129 ◽

Cited By ~ 1

Author(s):

Sumita Nag ◽

Jiban Mitra

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Linum Usitatissimum ◽

Rank Correlation ◽

Natural Fibre ◽

Similarity Coefficients ◽

Oilseed Crops ◽

Linum Usitatissimum L ◽

Ssr Primers ◽

Ssr Loci

Flax (Linum usitatissimum L.), stoods in position third, being the largest natural fibre crop and simultaneously one of the five preeminent oilseed crops in the world. SSR/microsatellite markers are extensively utilized for genetic diversity analysis and cultivar identification considering their myriad abundance, co-dominant inheritance, steep polymorphism, reproducibility, and comfort of assay by PCR. Ten microsatellites were amplified in 27 genotypes of Flax. The study was undertaken to assess the genetic diversity in flax and to select most diverse genotypes for future breeding program. Primer efficiency parameters were studied. The 10 SSR loci amplified a total of 41 alleles that were used for genetic analysis. Most primers have PIC value greater than 0.5 and the LU6 marker was highly polymorphic PIC = 0.95. Estimates of RP̅ were highest for the primer LU1 (0.68). The maximum MI was observed for the primer LU10 (3.56). The H and D ranged from 0.26 to 1.78 and 0.36 to 5.40, respectively. According to Spearman rank correlation, PIC and MI were most important parameters in assessing the efficiency of whole set of 10 SSR primers. Dendrogram was constructed using the genetic similarity coefficients using UPGMA. PCo-A was also performed in support. Genetic diversity in Flax was revealed at molecular level.

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Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽

10.7717/peerj.2936 ◽

2017 ◽

Vol 5 ◽

pp. e2936 ◽

Cited By ~ 13

Author(s):

Caroline E. Dubé ◽

Serge Planes ◽

Yuxiang Zhou ◽

Véronique Berteaux-Lecellier ◽

Emilie Boissin

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Natural Populations ◽

454 Sequencing ◽

Genetic Distances ◽

Null Alleles ◽

Future Research ◽

Significant Linkage ◽

Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

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Study of genetic differences among Slovak Tsigai populations using microsatellite markers

Czech Journal of Animal Science ◽

10.17221/1670-cjas ◽

2009 ◽

Vol 54 (No. 10) ◽

pp. 468-474 ◽

Cited By ~ 3

Author(s):

S. Kusza ◽

E. Gyarmathy ◽

J. Dubravska ◽

I. Nagy ◽

A. Jávor ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Microsatellite Markers ◽

Mating System ◽

Population Differentiation ◽

Genetic Relationships ◽

The Other ◽

Potential Risks ◽

Substantial Degree

In this study genetic diversity, population structure and genetic relationships of Tsigai populations in Slovakia were investigated using microsatellite markers. Altogether 195 animals from 12 populations were genotyped for 16 microsatellites. 212 alleles were detected on the loci. The number of identified alleles per locus ranged from 11 to 35. In the majority of the populations heterozygosity deficiency and potential risks of inbreeding could be determined. High values of <I>F</I><sub>ST</sub> (0.133) across all the loci revealed a substantial degree of population differentiation. The estimation of genetic distance value showed that the Slovak Vojin population was the most different from the other populations. The 12 examined populations were able to group into 4 clusters. With this result our aim is to help the Slovak sheep breeders to establish their own mating system, to avoid genetic loss and to prevent diversity of Tsigai breed in Slovakia.

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Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

Journal of Scientific Research ◽

10.3329/jsr.v4i3.10416 ◽

2012 ◽

Vol 4 (3) ◽

pp. 757-767 ◽

Cited By ~ 1

Author(s):

M. M. Hassan ◽

A. K. M. Shamsuddin ◽

M. M. Islam ◽

K. Khatun ◽

J. Halder

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Gene Diversity ◽

Allele Number ◽

Rice Landraces ◽

Efficient Management ◽

Ssr Loci ◽

Pattern Of Variation ◽

Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

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Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

Author(s):

S Islam ◽

MS Haque ◽

RM Emon ◽

MM Islam ◽

SN Begum

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Genetic Distance ◽

Microsatellite Markers ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Triticum Aestivum L ◽

Allele Number ◽

Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

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Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

BioMed Research International ◽

10.1155/2013/317912 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 8

Author(s):

Suping Feng ◽

Helin Tong ◽

You Chen ◽

Jingyi Wang ◽

Yeyuan Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genomic Library ◽

Trinucleotide Repeats ◽

The Other ◽

Diversity Analysis ◽

Dominant Type ◽

Genetic Diversity Analysis ◽

Ssr Loci ◽

Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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The Genetic Diversity and Geographic Differentiation of the Wild Soybean in Northeast China Based on Nuclear Microsatellite Variation

International Journal of Genomics ◽

10.1155/2018/8561458 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Hongkun Zhao ◽

Yumin Wang ◽

Fu Xing ◽

Xiaodong Liu ◽

Cuiping Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Northeast China ◽

Wild Soybean ◽

Population Level ◽

Mantel Test ◽

Microsatellite Variation ◽

Information Index ◽

Ssr Loci ◽

The Mean

In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index (I) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes. The greater the difference in latitude was, the greater the genetic distance was, whereas a similar trend was not found in longitude populations. Three main clusters (1N, <41°N-42°N; 2N, 43°N-44°N; and 3N, 45°N–>49°N) were assigned to populations. AMOVA analysis showed that the genetic differentiation among latitude and longitude populations was 0.088 and 0.058, respectively, and the majority of genetic variation occurred within populations. The Mantel test revealed that genetic distance was significantly correlated with geographical distance (r=0.207, p<0.05). Furthermore, spatial autocorrelation analysis showed that there was a spatial structure (ω=119.58, p<0.01) and the correlation coefficient (r) decreased as distance increased within a radius of 250 km.

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Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [Cynodon dactylon (L.) Pers.] along longitude gradients

PeerJ ◽

10.7717/peerj.11953 ◽

2021 ◽

Vol 9 ◽

pp. e11953

Author(s):

Jing-Xue Zhang ◽

Miaoli Wang ◽

Jibiao Fan ◽

Zhi-Peng Guo ◽

Yongzhuo Guan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Genetic Distance ◽

Ploidy Level ◽

Population Genetic ◽

Annual Precipitation ◽

Mean Annual Precipitation ◽

Ploidy Levels ◽

Population Genetic Diversity

Background Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure. Methods Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E). Results There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.

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Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758)

PeerJ ◽

10.7717/peerj.2019 ◽

2016 ◽

Vol 4 ◽

pp. e2019 ◽

Cited By ~ 5

Author(s):

Christine Ewers-Saucedo ◽

John D. Zardus ◽

John P. Wares

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Next Generation Sequencing Data ◽

Model Organisms ◽

Next Generation ◽

Sequencing Data ◽

Genetic Studies ◽

Evolutionary Features ◽

Generation Sequencing

Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacleChelonibia testudinaria(Linnaeus, 1758).Chelonibia testudinariaappears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies onC. testudinaria.

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