Chloroplast Simple Sequence Repeat Markers Research Articles

Molecular Detection for Identification and Seed Adulteration of Camellia Oils Based on Chloroplast Simple Sequence Repeat Markers

Molecular Detection for Identification and Seed Adulteration of Camellia Oils Based on Chloroplast Simple Sequence Repeat Markers

Analysis of Latvian and Belarusian Oak (Quercus robur L.) Population Provenance and Genetic Structure Using Chloroplast Markers

Abstract In this study, oak specific chloroplast simple sequence repeat (SSR) markers were used to analyse Latvian and Belarusian oak (Quercus robur L.) population provenance and genetic structure. Chloroplast haplotypes were compared between Latvian and Belarusian pedunculate oak, and several common haplotypes were identified. The SSR haplotypes were compared to previously reported PCR-RFLP haplotypes, and haplotypes from the A (eastern European) and C (central European) lineages were identified. C lineage haplotypes were only found in the western region of Latvia. Haplotypes shared between Latvia and Belarus were all from the A lineage. Despite the much smaller population size of oak in Latvia in comparison to Belarus, the level of genetic diversity identified using the chloroplast SSR markers is similar. Provenance trials will need to be established in order to determine the suitability of Belarusian oak reproductive material for deployment in Latvia. Based on the results from this comparison of chloroplast haplotypes, as well as climatic similarities, it is probable that Belarusian oak material will be better suited to the eastern regions of Latvia compared to the western regions of Latvia.

Genetic Diversity and Population Structure of Wild Sunflower (Helianthus annuus L.) in Argentina: Reconstructing Its Invasion History.

Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and approximate Bayesian computation (ABC) modeling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and 3 chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of 3 genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated 2 invasive populations from the rest. ABC modeling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared with US populations, suggesting a role for seed-mediated gene flow in Argentina.

Development of novel polymorphic nuclear and chloroplast microsatellite markers in coast redwood (Sequoia sempervirens)

AbstractThe range-wide genetic structure of the highly productive and valuable timber species Sequoia sempervirens (D. Don) Endl. is still insufficiently studied, although published data based on different genetic markers (nuclear and chloroplast microsatellites, AFLP, RFLP and isozymes) demonstrated relatively low population structure. However, more genetic markers are needed to increase the efficiency of population genetic studies in coast redwood. Therefore, we developed seven nuclear and five chloroplast microsatellite or simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) and the complete chloroplast genome sequence, respectively. All selected markers were tested in a range-wide sample representing trees from 16 locations. They are highly polymorphic microsatellite loci with the number of alleles ranging from 3 to 17, and the number of effective alleles from 1.1 to 2.48. Coast redwood is a hexaploid species, and its chloroplasts are paternally inherited. Therefore, the chloroplast SSR markers are especially useful for this species, because their genotyping is not affected by nuclear genome ploidy. Moreover, they showed high gene diversity for each locus within and across all populations and can be used to study range-wide population genetic structure, pollen-based gene flow and long-distance gene transfer. Coast redwood can propagate clonally, and nuclear polymorphic EST-SSRs can be used for clonal identification. They are linked with expressed genes and their variation can reflect variation in genes under selection, including those that could be potentially important for local adaptation of coast redwood considering the threat of climate change.

Development and characterization of chloroplast simple sequence repeat markers for Prunus taxa (eleven Japanese native taxa and two foreign taxa)

Abstract Japanese flowering cherry (Prunus subgenus Cerasus; Rosa­ceae) cultivars, which are characterized by beautiful flowers, have been generated through hybridization among wild Pru­nus taxa. The analysis of polymorphisms in the maternally inhe­rited chloroplast DNA is an effective complementary approach for tracing the origins of these cultivars. Thus, a set of novel chloroplast simple sequence repeat (cpSSR) markers was deve­loped for the Prunus taxa, and their utility in cross-species amp­lification was evaluated. Five markers were designed from the partial chloroplast genome sequences of thirteen Prunus taxa. In all, we found 19 haplotypes among the 311 individuals tes­ted. The number of haplotypes, haplotype richness and haplo­type diversity in each taxon ranged from 1 to 8, from 1 to 6.613 and from 0 to 0.758, respectively. The major proportion of the total diversity (HT = 0.831) was accounted for by intraspecific diversity (HS = 0.559), and the level of species subdivision, GST, was 0.327. These five cpSSR markers highly polymorphic, and they will be useful not only for tracing the origins of the culti­vars but also for studying the population structure, diversity, and phylogeography of Prunus.

Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum.

Well-characterized examples of homoploid hybrid speciation (HHS) are rare in nature, yet they offer the potential to study a number of evolutionary processes. In this study, we investigate putative homoploid hybrid species in the genus Argyranthemum (Asteraceae), a group of plants endemic to the Macaronesian archipelagos of the North Atlantic Ocean. We specifically address a number of knowledge gaps surrounding the origin(s) of A.sundingii and A.lemsii, which are thought to be derived from the same parental cross. Comparisons of leaf morphology suggest that A.sundingii and A.lemsii are distinct from their parental progenitors and distinguishable from each other based on leaf area. Ecological niche modelling (ENM) demonstrated that the homoploid hybrid species occupy novel habitats that are intermediate relative to the parental species. Nuclear simple sequence repeat markers (SSRs) and single nucleotide polymorphism (SNP) data indicate that the homoploid hybrid species are distinct from the parental taxa, while population-level sampling of chloroplast SSRs and approximate Bayesian computation show that A.sundingii and A.lemsii are independently derived from the same parental cross. As such, Argyranthemum represents an example of independent homoploid hybrid speciation events with evidence of divergence in leaf morphology and adaptation to novel intermediate habitats. On oceanic islands, which are often typified by steep ecological gradients and inhabited by recently derived species with weak reproductive barriers, multiple HHS events from the same parental cross are not only possible but also likely to have played a more important role in oceanic island radiations than we currently think.

Development and characterization of chloroplast microsatellite markers for Pinus massoniana and their application in Pinus (Pinaceae) species

Pinus massoniana is one of the important afforestation and pioneer tree species, which is widely distribute in southern China. Chloroplast simple sequence repeat markers (cpSSRs) have been widely used in studies of tree genetics, phylogenetic and breeding. We sequenced the whole chloroplast genome sequences of P. massoniana using PCR and Sanger sequencing. A total of 71 cpSSRs were identified, among which mononucleotide repeats were predominant (70.42%). Seventeen primer pairs were developed and amplification tests were conducted with 15 P. massoniana individuals. Also, cross-species amplification tests were conducted among 15 individuals per Pinus species, including P. elliottii, P. bungeana, P. armandii, P. caribaea, P. tabulaeformis, P. taiwanensis and P. yunnanensis which revealed polymorphic information content ranging from 0.2 to 0.8 and average of haploid diversity (h) ranging from 0.29 to 0.63. In addition, the polymorphic cpSSRs were useful in distinguishing the sampled pine species, and could be powerful tool in phylogenetic studies.

Evidence of Low Chloroplast Genetic Diversity in Two Carpinus Species in the Northern Balkans

Genetic diversity and differentiation in two Carpinus species (C. betulus and C. orientalis) occurring in Romania was investigated by using three chloroplast Simple Sequence Repeat markers (cpSSRs). A total of 96 and 32 individuals were sampled in eighteen C. betulus and six C. orientalis populations, respectively. A total of four chloroplast haplotypes were observed. Two haplotypes were specific for C. betulus and two for C. orientalis. Most of C. betulus populations were fixed for the predominant haplotype (H1), which was observed in 82% of the individuals. All C. orientalis populations were fixed for one haplotype or the other. Populations with haplotype (H3) are spread in southern Romania and the haplotype (H4) was observed at the northern limit of C. orientalis natural distribution range. Genetic differentiation among populations was moderate in C. betulus (GST = 0.422), compared to the high value observed in C. orientalis (GST = 1.000), which can be explained by the occurrence of a distinct haplotype in the peripheral population. RST values for both species suggest low levels of recurrent gene flow through seeds among populations. Our data on geographic distribution of chloroplast DNA haplotypes may be useful for the identification and conservation of distinct genetic resources of the two Carpinus species.

Recovery of citrus cybrid plants with diverse mitochondrial and chloroplastic genome combinations by protoplast fusion followed by in vitro shoot, root, or embryo micrografting

Somatic embryogenesis and plant regeneration are basic processes for the success of citrus somatic hybridization via protoplast fusion. In many cases, few embryos develop normally and only a small number of plants are recovered. The development of methodologies able to increase the recovery of plants after protoplast fusion experiments it is an important requirement to improve the efficiency of the procedure. Here, plants were regenerated at high efficiency using in vitro micrografting of shoots, roots, and embryos recovered after different somatic hybridizations. Hybridizations were performed using protoplasts isolated from Chios mandarin callus with protoplasts isolated from Clementine mandarin leaves and from Sanguinelli sweet orange callus. Recovered plants were analyzed with flow cytometry and nuclear simple sequence repeat (SSR), mitochondrial InDel, and chloroplast SSR markers to determine genomic structure. One tetraploid cybrid and numerous diploid cybrids were recovered, and these exhibited a range of mitochondrial and chloroplastic genome combinations.

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.

Polymorphic chloroplast microsatellite loci in Nelumbo (Nelumbonaceae)

To study population genetics, phylogeography, and hybridization of Nelumbo (Nelumbonaceae), chloroplast microsatellite markers were developed. Seventeen microsatellite loci were identified from the chloroplast genomes of N. nucifera and N. lutea. Polymorphisms were assessed in three populations of N. nucifera and one population of N. lutea. Nine loci were found to be polymorphic in N. nucifera, and all 17 loci were found to be polymorphic in N. lutea. In N. nucifera, the number of alleles per locus ranged from two to six, and the unbiased haploid diversity per locus ranged from 0.198 to 0.790. In N. lutea, the number of alleles ranged from two to four, and the unbiased haploid diversity per locus ranged from 0.245 to 0.694. The identified chloroplast simple sequence repeat markers will be useful for the study of genetic diversity, phylogeography, and identification of Nelumbo cultivars.

Genetic diversity in mandarin landraces and wild mandarins from China based on nuclear and chloroplast simple sequence repeat markers

SummaryLandraces and wild germplasm are important citrus genetic resources. Knowledge of the genetic diversity of this germplasm provides an opportunity both to mandarin breeding programmes and to germplasm conservation strategies. Genetic diversity of 33 loose-skin mandarin landraces and 19 wild mandarin accessions were analysed with ten nuclear simple sequence repeat (nSSR) and eight chloroplast simple sequence repeat (cpSSR) markers. Our analysis of nuclear and chloroplast genome polymorphism showed that the genetic diversity in wild populations was slightly higher than that found in landraces, with polymorphic information content values of 0.6138 and 0.5091 at nSSR loci, and 0.4921 and 0.3769 at cpSSR loci, respectively. Overall, 60 nSSR alleles and 19 cpSSR haplotypes were identified, and all but seven accessions were unambiguously discriminated by nSSR markers. Five groups of landraces and two groups of wild mandarins were identified based on the nSSR data, and two groups each of landraces and wild mandarins were identified at the cpSSR loci. Different distribution patterns of landraces and wild mandarins were observed between dendrograms constructed using these two marker systems, and hybrid origins for several landraces were suggested by these results. Combined analysis also suggested that, among wild mandarin, ‘Chongyi’ showed the closest relationship to landraces, and that landrace ‘Chazhigan’ was the primary genotype among landraces.