Nuclear- and chloroplast-microsatellite variation in A-genome species of rice

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 658-666 ◽  
Author(s):  
T Ishii ◽  
Y Xu ◽  
S R McCouch
Keyword(s):  
Oryza Sativa ◽  
Length Polymorphism ◽  
Allelic Diversity ◽  
Sequence Length ◽  
Chloroplast Microsatellites ◽  
Microsatellite Variation ◽  
Chloroplast Microsatellite ◽  
Genome Species ◽  
A Genome ◽  
Simple Sequence

Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.Key words: simple sequence length polymorphism, SSLP, microsatellite marker, rice, Oryza sativa, allelic diversity, phylogenetics.

Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 786-798 ◽  
Author(s):  
T Kyndt ◽  
B Van Droogenbroeck ◽  
A Haegeman ◽  
I Roldán-Ruiz ◽  
G Gheysen
Keyword(s):  
Population Genetics ◽  
Chloroplast Microsatellites ◽  
Microsatellite Data ◽  
Chloroplast Microsatellite ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Polymorphism Rate ◽  
Nuclear Ssr ◽  
Simple Sequence ◽  
Future Population

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.

Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 336-344 ◽  
Author(s):  
F Viard ◽  
Y A El-Kassaby ◽  
K Ritland
Keyword(s):  
Pseudotsuga Menziesii ◽  
Random Amplified Polymorphic Dna ◽  
Douglas Fir ◽  
Pinus Thunbergii ◽  
Chloroplast Microsatellites ◽  
Nuclear Markers ◽  
Chloroplast Microsatellite ◽  
High Pollen ◽  
Historical Factors ◽  
Simple Sequence

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.Key words: chloroplast microsatellites, isozymes, RAPDs, gene flow, pollen flow.

scholarly journals Genetic analysis of European common ash (Fraxinus excelsior L.) populations affected by ash dieback

2014 ◽  
Vol 63 (1-6) ◽  
pp. 198-212 ◽  
Author(s):  
Barbara Fussi ◽  
M. Konnert
Keyword(s):  
Forest Ecosystems ◽  
Mixed Forest ◽  
Genetic Differences ◽  
Chloroplast Microsatellites ◽  
Microsatellite Variation ◽  
Chloroplast Microsatellite ◽  
Ash Dieback ◽  
Genetic Base ◽  
Genetic Potential ◽  
Adaptation Processes

AbstractEuropean common ash is an important component of mixed forest ecosystems in Bavaria and is considered a valuable tree species under climate change. The first aim of the present study was to assess the genetic diversity within and between ash populations in Bavaria in comparison with neighboring regions. Because ash stands have been heavily attacked by ash shoot disease in the last few years, the second aim of the study was to detect genetic differences between susceptible and less susceptible trees (trees with defoliation up to 30%) within populations. Altogether 41 populations were investigated using nuclear and chloroplast microsatellites. The results showed high genetic variation within and high genetic differentiation between ash populations. Higher chloroplast microsatellite variation was detected instead populations from south-eastern Bavaria compared to other regions. The comparison of susceptible and less susceptible groups of individuals within each population revealed medium to high genetic differences in some cases. For the observed heterozygosity, higher values were found for the group of less susceptible trees compared to the group of all trees or to the group of susceptible trees within populations. This could be a first indication that individuals with a higher heterozygosity might be able to withstand ash dieback in a better way compared to homozygotic individuals. Within the group of less susceptible trees a relatively wide genetic base exists whereupon a future breeding programme can be built. Thus it is of utmost importance for the species to maintain less affected trees in order to keep the genetic potential for future adaptation processes within ash populations, seed production and regeneration.

Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 715-723 ◽  
Author(s):  
P. J. Maughan ◽  
M. A. Saghai Maroof ◽  
G. R. Buss
Keyword(s):  
Genetic Markers ◽  
Glycine Soja ◽  
Wild Soybean ◽  
Allelic Diversity ◽  
Sequence Length ◽  
Length Polymorphisms ◽  
Ssr Loci ◽  
Low Levels ◽  
Cultivated Soybean ◽  
Simple Sequence

The objectives of this study were to (i) assess the extent of genetic variation in soybean microsatellites (simple sequence repeats or SSRs), (ii) assay for amplified sequence length polymorphisms (ASLPs), and (iii) evaluate the usefulness of SSRs and ASLPs as genetic markers. Five microsatellites detected a total of 79 variants (alleles) in a sample of 94 accessions of wild (Glycine soja) and cultivated soybean (G. max). F2 segregation analysis of four of the five microsatellites identified these variants (alleles) with four loci located in independent linkage groups. The number of alleles per microsatellite locus ranged from 5 to 21; to our knowledge these are the largest numbers of alleles for single Mendelian loci reported in soybean. Allelic diversity for the SSR loci was greater in wild than in cultivated soybean. Overall, 43 more SSR alleles were detected in wild than in cultivated soybean. These results indicate that SSRs are the marker of choice, especially for species with low levels of variation as detected by other types of markers. Two alleles were detected at each of the three ASLP loci examined. A total of six ASLP alleles were observed in cultivated soybean and five were observed in wild soybean; all alleles detected in wild soybean were present in cultivated soybean. Allelic diversity values for the ASLP loci were near previous estimates for restriction fragment length polymorphisms and therefore ASLPs may be useful as genetic markers in site-directed mapping.Key words: microsatellite, simple sequence repeat, soybean, amplified sequence length polymorphism, genetic mapping.

scholarly journals Genetic Characterization and Curation of Diploid A-Genome Wheat Species

2021 ◽  
Author(s):  
Laxman Adhikari ◽  
John Raupp ◽  
Shuangye Wu ◽  
Duane Wilson ◽  
Byron Evers ◽  
...  
Keyword(s):  
Population Analysis ◽  
Allelic Diversity ◽  
Genomic Analysis ◽  
Individual Species ◽  
Wheat Species ◽  
Phenotypic Data ◽  
Genome Species ◽  
Core Set ◽  
Population Structure Analysis ◽  
A Genome

The A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum. monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.) and T. urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC), using genotyping-by-sequencing (GBS) and identified 13,089 curated SNPs. Genomic analysis detected misclassified and duplicated accessions with most duplicates originated from the same or a nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were duplicates supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that the T. urartu as the closest A-genome diploid to wheat through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring domestication selection signature (Btr1) on the short arm of chromosome 3Am at ~ 70 Mb. We established A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 80% of allelic variants in the A-genome collection and constitute a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.

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