scholarly journals Chloroplast microsatellite polymorphisms in Vitis species

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1142-1149 ◽  
Author(s):  
Rosa Arroyo-García ◽  
Francois Lefort ◽  
María Teresa de Andrés ◽  
Javier Ibáñez ◽  
Joaquín Borrego ◽  
...  
Keyword(s):  
Variable Number ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Consensus Primer ◽  
Chloroplast Microsatellite ◽  
Vitis Species ◽  
Vitis Riparia ◽  
Chloroplast Genomes ◽  
Growth Area ◽  
Chloroplast Haplotypes

The use of consensus chloroplast microsatellites primers for dicotyledonous chloroplast genomes revealed the existence of intra and interspecific length variation within the genus Vitis. Three chloroplast microsatellite loci were found to be polymorphic in samples of Vitis vinifera, Vitis berlandieri, Vitis riparia, and Vitis rupestris out of a total of 10 consensus primer pairs tested. These polymorphisms were always due to a variable number of mononucleotide residues within A and (or) T stretches in the amplified regions. Chloroplast microsatellite polymorphisms were used to demonstrate the maternal inheritance of chloroplast in V. vinifera and to characterise the chloroplast haplotypes present in wine grape cultivars of this species grown in Spain and Greece. The different distribution of haplotype frequencies in the two ends of the Mediterranean growth area suggests the existence of independent domestication events for grapevine.Key words: Vitis, grapevine, chloroplast microsatellites, chloroplast haplotypes, chloroplast inheritance, grapevine domestication.

scholarly journals Characterization of Polymorphic Chloroplast Microsatellites in Prunus Species and Maternal Lineages in Peach Genotypes

2017 ◽  
Vol 142 (3) ◽  
pp. 217-224
Author(s):  
Chunxian Chen ◽  
William R. Okie
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Microsatellites ◽  
Nucleotide Polymorphisms ◽  
Chloroplast Microsatellite ◽  
Single Nucleotide ◽  
Chloroplast Genomes ◽  
Genome Features ◽  
Genomic Locations ◽  
Representative Material

Several available Prunus chloroplast genomes have not been exploited to develop polymorphic chloroplast microsatellites that could be useful in Prunus phylogenetic analysis and maternal lineage group (MLG) categorization. In this study, using available bioinformatics tools, 80, 75, and 78 microsatellites were identified from the chloroplast genome of P. persica (CPpe), P. kansuensis (CPka), and P. mume (CPmu), respectively. The genome features and polymorphism status of these microsatellites were characterized. The genomic locations and motif types of most chloroplast microsatellites were conserved in CPpe, CPka, and CPmu. Of the 67 microsatellites with primer sequences and names, 57 were polymorphic for their in silico motif, amplicon lengths, or both among the three genomes. Based on the genotyping data of eight most polymorphic microsatellites, eight unique MLGs were found among the 736 peach materials in a breeding program. Most peach cultivars (111 of 161 genotyped) belong to MLG-1, the Chinese Cling-derived group reflecting the heavy use of this germplasm in early peach development. Forty-one cultivars belong to MLG-2, the European-derived group of peaches. MLG-3 consists of ornamental accessions. MLG-4 and MLG-5 contain only ‘Flordaking’ and ‘Reliance’, respectively. MLG-6 to MLG-8 consists of selections derived from P. tangutica, P. davidiana, and P. mira, respectively. These amplicons from the representative material for each MLG were sequenced, revealing additional single nucleotide polymorphisms (SNPs) within the amplicons. With the polymorphism status and amplification reliability validated, these new polymorphic chloroplast microsatellite markers may be useful in Prunus phylogenetic analysis.

scholarly journals The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew Pathogen Plasmopara viticola

2021 ◽  
Vol 22 (2) ◽  
pp. 940
Author(s):  
Elodie Vandelle ◽  
Pietro Ariani ◽  
Alice Regaiolo ◽  
Davide Danzi ◽  
Arianna Lovato ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Ubiquitin Ligase ◽  
Control Measure ◽  
Durable Resistance ◽  
Genetic Resistance ◽  
E3 Ubiquitin Ligase ◽  
Plasmopara Viticola ◽  
Vitis Vinifera L ◽  
Vitis Species ◽  
Vitis Riparia

Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine (Vitis vinifera L.). Genetic resistance is an effective and sustainable control strategy, but major resistance genes (encoding receptors for specific pathogen effectors) introgressed from wild Vitis species, although effective, may be non-durable because the pathogen can evolve to avoid specific recognition. Previous transcriptomic studies in the resistant species Vitis riparia highlighted the activation of signal transduction components during infection. The transfer of such components to V. vinifera might confer less specific and therefore more durable resistance. Here, we describe the generation of transgenic V. vinifera lines constitutively expressing the V. riparia E3 ubiquitin ligase gene VriATL156. Phenotypic and molecular analysis revealed that the transgenic plants were less susceptible to P. viticola than vector-only controls, confirming the role of this E3 ubiquitin ligase in the innate immune response. Two independent transgenic lines were selected for detailed analysis of the resistance phenotype by RNA-Seq and microscopy, revealing the profound reprogramming of transcription to achieve resistance that operates from the earliest stages of pathogen infection. The introduction of VriATL156 into elite grapevine cultivars could therefore provide an effective and sustainable control measure against downy mildew.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

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.

Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 237-247 ◽  
Author(s):  
Ted HM Mes ◽  
Reinhard M Fritsch ◽  
Sven Pollner ◽  
Konrad Bachmann
Keyword(s):  
Concerted Evolution ◽  
Morphological Evolution ◽  
Restriction Analysis ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Border Region ◽  
Chloroplast Genomes ◽  
Central Asian ◽  
Its Regions ◽  
Chloroplast Haplotypes

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.Key words: polymorphic, phylogeny, restriction analysis.

scholarly journals Features of identification grape varieties and clones of Western European origin

2021 ◽  
pp. 125-133
Author(s):  
Г.Ю. Спотарь ◽  
С.А. Блинова ◽  
А.А. Шварцев ◽  
Я.И. Алексеев ◽  
С.М. Гориславец
Keyword(s):  
Ssr Markers ◽  
Gene Locus ◽  
Molecular Genetic ◽  
Pinot Noir ◽  
Chloroplast Microsatellite ◽  
European Origin ◽  
Vitis Riparia ◽  
Economically Valuable Traits ◽  
The Difference ◽  
The Cost

С помощью молекулярно-генетических и ампелографических методов проведена идентификация сортов винограда, относящихся к наиболее распространенным в мире техническим сортам западно-европейского происхождения. Генотипирование образцов проводилось с использованием 9-ядерных и 3-хлоропластных микросателлитных маркеров. На основании полученных профилей, по данным базы VIVC было установлено, что образец № 2 является сортом Каберне-Совиньон, образец № 4 - сортом Рисланер. Профиль образца № 1 совпадает с профилем сорта Мерло, за исключением разницы в двух парах нуклеотидов (п.н.) в одном аллеле локуса VVMD27, что можно объяснить редким случаем мутации в микросателлитной последовательности и не является достаточным основанием утверждать, что образец № 1 и Мерло являются разными сортами. Генетические профили образцов № 3 и № 6 соответствовали сортам сортогруппы Темпранильо, № 5 - сортам сортогруппы Рислинг рейнский, №7 - сортам сортогруппы Пино черный. Сорта в сортогруппах, полученные в результате соматических мутаций (связанных в основном с окраской ягод), имели одинаковый профиль. Принадлежность образцов к указанным сортам в сортогруппах была подтверждена ампелографическим методом. Использование для идентификации сортов в сортогруппах 6-9-ти SSR-маркеров в сочетании с ампелографическими методами позволяет получить достоверные результаты без удорожания работ. Однако дифференциация клонов и сортов, полученных в результате соматических мутаций, только SSR-маркерами потребует значительного увеличения их количества на 1-2 порядка либо использования высоковариабельных SSR-маркеров, таких как VRG ( Vitis riparia Götzhof). Таким образом, целесообразен более целенаправленный поиск полиморфизмов непосредственно в генах, отвечающих за определенные хозяйственно ценные признаки. В случае возникновения отличия в окраске ягод для дифференциации возможно использовать полиморфизм локуса гена VvMybA1, при изменении во вкусе и аромате ягод - в локусе гена VviDXS, при изменении лигнификации семян - в локусе гена VviAGL11, при повышении устойчивости к заболеваниям - в локусах соответствующих генов резистентности. The identification of grapes related to the most widespread wine varieties of West-European origin was carried out using molecular-genetic and ampelographic methods. Genotyping of samples was provided using 9- nuclear and 3-chloroplast microsatellite markers. Basing on the profiles obtained according to the VIVC database, it was established that Sample No. 2 is a ‘Cabernet-Sauvignon’ variety, and Sample No. 4 is a ‘Rieslaner’ variety. The profile of Sample No. 1 coincides with the ‘Merlot’ profile, except for the difference in 2 base pairs (bp) in one allele of the VVMD27 locus, which can be explained by a rare case of mutation in microsatellite sequence, and is not a sufficient reason to insist that Sample No. 1 and the ‘Merlot’ are different varieties. The genetic profiles of Samples No. 3 and No. 6 corresponded to the varieties of ‘Tempranillo’ group, No. 5 - to the varieties of ‘Rhein Riesling’ group, and No. 7 - to the varieties of ‘Pinot Noir’ group. The varieties of the groups, obtained as a result of somatic mutations (mainly associated with color of berries), had the same profile. The ampelographic method confirmed the origin of samples in the mentioned groups of varieties. Using of 6-9-SSR-markers in combination with ampelographic methods to identify the varieties of groups allows obtaining reliable results without increasing the cost of work. However, differentiation of clones and varieties in groups with only SSR-markers will require a significant increase in their number by 1-2 orders, or using of highly variable SSR-markers, such as VRG ( Vitis riparia Götzhof). Thus, a more targeted search for polymorphisms directly in genes responsible for certain economically valuable traits is advisable. In case of occurrence a difference in the color of berries, it is possible to use for differentiation the polymorphism of VvMybA1 gene locus, when flavor and aroma of berries change - to use the VviDXS gene locus, when seed lignification changes - the VviAGL11 gene locus, when disease resistance increases - the loci of the corresponding resistance genes.

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.

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.

Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.)

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 68-78 ◽  
Author(s):  
G G Vendramin ◽  
M Anzidei ◽  
A Madaghiele ◽  
C Sperisen ◽  
G Bucci
Keyword(s):  
Picea Abies ◽  
Norway Spruce ◽  
Glacial Refugia ◽  
Population Subdivision ◽  
Chloroplast Microsatellites ◽  
Gene Pools ◽  
Chloroplast Microsatellite ◽  
Haplotypic Diversity ◽  
Main Gene ◽  
Degree Of Differentiation

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine - Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands. Key words: haplotypic diversity, phylogeography, chloroplast microsatellites, recolonization.

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