Nuclear Simple Sequence Repeat Markers Research Articles

Analysis of genetic diversity and environmental associations of wild citron (Citrus medica L.) in northeast India

Citron (Citrus medica L.) is a major citrus fruit crop known for its medicinal, nutritional, and aromatic uses. Native to northeast India, Myanmar, and south China, citron is cultivated mostly in the Mediterranean and South Asian countries. The truly wild populations of citron are found in the hills and valleys of northeast India. The extent of genetic diversity in wild citron in relation to environmental variables has not been documented. In the present study, we analyzed genetic diversity and environmental association of wild populations of C. medica in northeast India using 15 polymorphic nuclear SSR (simple sequence repeat) markers and 21 environmental variables. SSR profiling revealed a moderate genetic diversity (Ho = 0.40; He = 0.41; I = 0.70). Neighbor-joining (NJ) and principal coordinate analysis (PCoA) grouped 16 natural populations into two genetic clusters. Bayesian structure results showed two genetic populations with a high admixture of individuals. Analysis of molecular variance (AMOVA) revealed low genetic differentiation (Fst = 0.14; P < 0.001), indicative of high gene flow (Nm = 1.53) in citron. The isolation by distance (IBD) analysis showed a weak correlation, indicating that geographic distance was not a determining factor for genetic distance in C. medica populations. The higher metrics of outcrossing rate (tm > 0.9) revealed outbreeding nature of the species. The genetic diversity of citron showed a positive correlation with precipitation of driest month and precipitation of coldest quarter, but negative with mean diurnal range and isothermality. Overall, the results of the present study could benefit the conservation and management of citron resources and their natural habitat in northeast India. Genetically highly diverse populations identified in the present study can be used for conservation and utilization of citron genetic resources.

Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado.

Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.

Population genetic diversity and conservation priority of prince’s pine Chimaphila umbellata populations around the south margin of their distribution

How genetic diversity is maintained within a range of species is one of the crucial pieces of information in species conservation. Although the classical central-marginal hypothesis assumes genetic paucity in peripheral populations, this pattern is not always the case. The semi-shrub Chimaphila umbellata subsp. umbellate, population of which are located in the southernmost part of the subspecies distribution, is considered to be a threatened species in Japan. Thus, this study aimed to examine which populations should be preferentially conserved and if the central-marginal hypothesis can be applied to this case. Genetic diversity was examined in 15 populations of C. umbellata subsp. umbellata in Japan using 16 nuclear simple sequence repeat markers. Overall, the genetic diversity values within the populations did not correlate with the latitude of the population locality, although those of the southern marginal populations tended to be lower than those of populations in other regions. While the populations are genetically differentiated from each other, recent population size declines were only detected in a few cases. Bayesian inference of population structure revealed three genetically distinct groups. An approximate Bayesian computation revealed that these three genetic groups were derived from the ancient population in a recent times. The contribution of each population to total genetic diversity was estimated by removing a given population and recalculating the total genetic diversity. Only one population contributed to both gene diversity and allelic diversity, while several populations contributed to one or the other. Considering genetic diversity and structure, the conservation priority of Japanese populations of C. umbellata to preserve genetic diversity is discussed.

Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers.

Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial timber species, especially in perspective to climate warming that makes more regions in Germany suitable for its growing. The well performing trees in colder Germany could be potential frost resistant genotypes, but their genetic properties and origin are mostly unknown. Within the natural range in southern Oregon and northern California, only two relatively weak clusters were identified, one northern and one southern, separated by the San Francisco Bay. High genetic diversity, but low differentiation was found based on the 12 nuclear SSR markers for all three data sets F, C and G. We found that investigated 147 German trees represented only 37 different genotypes. They showed genetic diversity at the level less than diversity observed within the natural range in the northern or southern cluster, but more similar to the diversity observed in the southern cluster. It was difficult to assign German trees to the original single native populations using the six cpSSR markers, but rather to either the northern or southern cluster. The high number of haplotypes found in the data sets based on six cpSSR markers and low genetic differentiation based on 12 nuclear SSRs found in this study helps us study and better understand population genetic structure of this complex polyploid tree and supports the selection of potential genotypes for German forestry.

Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing

BackgroundLiriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm.ResultsWe performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79.ConclusionsThe genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.

Origins of weedy rice revealed by polymorphisms of chloroplast DNA sequences and nuclear microsatellites

AbstractConspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.

Development and characterization of 17 microsatellite markers for Sonchus oleraceus.

PremiseThe common sowthistle, Sonchus oleraceus (Asteraceae), is a globally invasive weedy species. In order to investigate its genetic diversity, population genetic structure, and evolutionary history, we developed and characterized nuclear simple sequence repeat markers (SSRs or microsatellites).Methods and ResultsSeventeen microsatellite primer pairs were developed based on the Illumina sequence data. Ten developed SSR loci were polymorphic in four populations sampled from broad geographical regions. The number of alleles per locus ranged from one to 11, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.801, respectively. Up to 82% of the newly developed primer pairs were successfully amplified in the congeneric taxa S. asper, S. asper subsp. glaucescens, S. canariensis, and S. palmensis.ConclusionsThe SSR markers developed in this study will be useful for future population genetic studies on S. oleraceus and other congeneric species.

Genetic Diversity and Population Structure of Natural Pinus koraiensis Populations

Studying the genetic diversity and population structure of natural forest populations is essential for evaluating their ability to survive under future environmental changes and establishing conservation strategies. Pinus koraiensis is a conifer species with high ecological and economic value in Northeast China. However, its natural forests have been greatly reduced in recent years, mostly due to over exploitation and over utilization. Here, we evaluated the genetic diversity and population structure of seven populations of P. koraiensis located throughout its native distribution. A total of 204 samples were genotyped with nine polymorphic nuclear SSR (simple sequence repeat) markers. The results showed high genetic diversity in all populations, with an average expected heterozygosity of 0.610, and the northern-most populations (Dailin (DL) and Fenglin (FL)) showed slightly higher diversity than the other five populations. The level of genetic differentiation among populations was very low (FST = 0.020). Analysis of molecular variance (AMOVA) showed that only 2.35% of the genetic variation existed among populations. Moreover, STRUCTURE analysis clearly separated the seven populations into two clusters. Populations DL and FL from the Xiaoxinganling Mountains comprised cluster I, while cluster II included the five populations from the Changbai Mountains and adjacent highlands. Our research on the genetic diversity and population structure of P. koraiensis in natural forests of China can provide a basis for the implementation of programs for the conservation and utilization of P. koraiensis genetic resources in the future.

Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm

BackgroundCommon bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.ResultsWe conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).ConclusionsThis study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.

Late Pleistocene speciation of three closely related tree peonies endemic to the Qinling-Daba Mountains, a major glacial refugium in Central China.

Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China.

Development of Nuclear Microsatellite Markers with Long (Tri-, Tetra-, Penta-, and Hexanucleotide) Motifs for Three Larch Species Based on the de novo Whole Genome Sequencing of Siberian Larch (Larix sibirica Ledeb.)

Siberian larch (Larix sibirica Ledeb.) is one of the major boreal tree species in Eurasia and has a considerable economic and ecological value. Despite that importance, the development and use of microsatellite markers in this species remain limited. Microsatellite markers are considered to be a valuable tool for estimation of population diversity and structure. Availability of a draft reference assembly of the Siberian larch genome allowed us to identify 1015 microsatellite loci or simple sequence repeats (SSRs) with tri-, tetra-, penta-, and hexanucleotide motifs. For 60 of them PCR primers were designed and tested for amplification in L. sibirica and for their within-genus transferability to L. gmelinii (Rupr.) Rupr. and L. cajanderi Mayr. Here, we present a set of 14 reliable and polymorphic new nuclear SSR markers that can be used for further population genetic studies, breeding programs, and timber origin identification.

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.

Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

AbstractAccurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes.

Development and validation of Acacia koa and A. koaia nuclear SSRs using Illumina sequencing

Abstract Koa (Acacia koa) and sub-species koaia (A. koaia) are two of more than 1,200 species from the genus Acacia within the Leguminosae (also designated Fabaceae) family. In the past, koa and koaia forests were found throughout the Hawaiian archipelago but populations have dramatically decreased. Comprehensive analyses of simple sequence repeats (SSRs) have not been published previously. Here we use genome sequencing and bioinformatics tools to report development of 100,000+ nuclear SSR (nuSSR) markers for use in koa and koaia genome studies with transcriptome SSR information was inclu­ded for comparison. Over 10,000 high-value SSRs (40-60 % GC content) were isolated with 3,600+ further validated by ePCR. SSRs generated in this work can assist current efforts to sustai­nably increase in koa and koaia populations.

Identity and parentage of some South American grapevine cultivars present in Argentina

Background and Aims Based on 19 nuclear simple sequence repeat markers and parental analysis, we aimed to identify and propose the pedigree of different accessions held at the Estacion Experimental Agropecuaria Mendoza of the Instituto Nacional de Tecnologia Agropecuaria germplasm collection. The results were compared with data recorded in large, international databases. Methods and Results We identified 37 different cultivars, of which 18 were original and not previously identified. The parentage analysis showed that European cultivars, such as Muscat of Alexandria, Muscat a Petits Grains, Listan Prieto, Mollar Cano and Malbec, were involved in natural crossings resulting in different South American cultivars. Conclusions Many of the cultivars identified here represent unique individuals based on their genotype. The number of cultivars that participated as progenitors in the origin of South American germplasm is higher than previously thought. Significance of the Study Germplasm collections planted many years ago play a key role in the conservation and characterisation of genotypes that otherwise may have been lost. It is highly probable that there might be other genotypes not identified and mixed in old vineyards. The identification, rescue and conservation of these genotypes are a challenge to preserve the existing genetic variability.

Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers.

To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR) markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA) revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3), with a few lines that instead grouped with L. multiflorum (C4) or Lolium rigidum (C6). Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.

The eastern part of the Fertile Crescent concealed an unexpected route of olive (Olea europaea L.) differentiation.

Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeo-botanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication.

An Irish perennial ryegrass genetic resource collection clearly divides into two major gene pools

This study assessed the genetic diversity in 928 individuals from 40 diploid populations ofLolium perenneusing nuclear simple sequence repeat markers, including 22 accessions of Irish ecotypes, seven European ecotypes and 11 released varieties. High levels of allelic and genetic diversity were determined, with intra-population variation accounting for the majority of the variation. The majority of the accessions deviated from Hardy–Weinberg equilibrium and had relatively high inbreeding coefficients. Two major gene pools of ecotypic accessions were defined by unweighted pair group method with arithmetic mean (UPGMA) and PCA analyses. One of these two gene pools accounted for two-thirds of the ecotypes and included most of the current Irish and Northern Irish breeding materials and about half of the European ecotypes included in this study; these European ecotypes performed well under Irish selection conditions. Population structure and differentiation analyses using Structure analysis and analysis of molecular variance confirmed the results found in the UPGMA and PCA analyses. These results will be useful for breeders who wish to exploit specific pools from ecotype collections.

Current Genetic Structure of Teak (Tectona Grandis) in Myanmar Based on Newly Developed Chloroplast Single Nucleotide Polymorphism and Nuclear Simple Sequence Repeat Markers

Teak ( Tectona grandis), which is among the most valuable tropical timber species, is under pressure from rapid deforestation and habitat fragmentation. Limited genetic information is available for Myanmar teak, which comes from the largest natural teak-bearing forest area in the world. To determine the phylogeographic patterns of Myanmar teak, we evaluated three newly developed chloroplast single nucleotide polymorphism (cpSNP) and 10 nuclear simple sequence repeat (nrSSR) markers in 480 individuals representing 20 natural populations. The cpSNP markers detected four haplotypes, each differing by a single mutation. The GST value was lower than the NST value and did not reveal a phylogeographic structure of Myanmar teak. Nuclear microsatellite analysis revealed high genetic diversity with the mean expected heterozygosity (0.652). The same level of genetic differentiation (4%) was observed for both cpSNP and nrSSR markers in different groups. Conservation of the HMB, TDG, KTA, and POL populations should receive highest priority because these contribute most to the total genetic diversity. The genetic boundaries of teak observed from combining the results of cpSNP and nrSSR marker barriers suggested four potential zones in the teak seed transfer guidelines of Myanmar. In light of our findings, we discussed appropriate gene conservation strategies and proposed seed zones to safeguard the current genetic resources of Myanmar teak.

High levels of gene flow and genetic diversity in Irish populations of Salix caprea L. inferred from chloroplast and nuclear SSR markers.

BackgroundSalix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs).ResultsA total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (HT = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean GST = 0.38). For the nuclear SSRs, GST was low at 0.07 and observed heterozygosity across populations was high (HO = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds.ConclusionsThe data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material.