PCR primers amplifying microsatellite loci of Quercus myrsinifolia Blume and their conservation between oak species

Hybridization and introgression in sympatric and allopatric populations of four oak species

BACKGROUND

Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization.

RESULTS

Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize.

CONCLUSIONS

Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.

Genetic, Morphological, and Environmental Differentiation of an Arid-Adapted Oak with a Disjunct Distribution

The patterns of genetic and morphological diversity of a widespread species can be influenced by environmental heterogeneity and the degree of connectivity across its geographic distribution. Here, we studied Quercus havardii Rydb., a uniquely adapted desert oak endemic to the Southwest region of the United States, using genetic, morphometric, and environmental datasets over various geographic scales to quantify differentiation and understand forces influencing population divergence. First, we quantified variation by analyzing 10 eastern and 13 western populations from the disjunct distribution of Q. havardii using 11 microsatellite loci, 17 morphological variables, and 19 bioclimatic variables. We then used regressions to examine local and regional correlations of climate with genetic variation. We found strong genetic, morphological and environmental differences corresponding with the large-scale disjunction of populations. Additionally, western populations had higher genetic diversity and lower relatedness than eastern populations. Levels of genetic variation in the eastern populations were found to be primarily associated with precipitation seasonality, while levels of genetic variation in western populations were associated with lower daily temperature fluctuations and higher winter precipitation. Finally, we found little to no observed environmental niche overlap between regions. Our results suggest that eastern and western populations likely represent two distinct taxonomic entities, each associated with a unique set of climatic variables potentially influencing local patterns of diversity.

WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes

Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.

Wind pollination over 70 years reduces the negative genetic effects of severe forest fragmentation in the tropical oak Quercus bambusifolia

Whether wind pollination in trees can offset the negative genetic consequences of anthropogenic forest fragmentation is not clearly established. To answer this question, we examined the demographic genetics of Quercus bambusifolia over a 70-year recovery period in highly fragmented forests in Hong Kong. We sampled 1138 individuals from 37 locations, and genetically analysed the chronosequence through the classification of tree diameters from the same populations using 13 microsatellite markers. Our study reveals that severe fragmentation caused a significant genetic bottleneck with very few remaining but genetically diverse individuals. We observed an enhanced genetic diversity during demographic recovery. We found full-sibs within populations and half-sibs across the study range. This reflects a limited seed dispersal and extensive pollen flow. Despite reduced genetic structure both among and within populations, overall a strong persisting genetic differentiation (F'_ST = 0.240, P < 0.01) and significant small-scale spatial genetic structure (F₍₁₎ = 0.13, Sp = 0.024, P < 0.01) were observed. Existing bottlenecks and low effective population sizes within the temporal chronosequence suggest that the long-term effect of severe fragmentation cannot be entirely eliminated by wind pollination with demographic recovery in the absence of effective seed dispersal. Our results lead to recommendations for forest management.

The draft genome sequence of cork oak

Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

Genetic variation and structure of Ubame oak, Quercus phillyraeoides, in Japan revealed by chloroplast DNA and nuclear microsatellite markers

Genetic variation and structure of Ubame oak (Quercus phillyraeoides A. Gray), a shrub tree on the Pacific coast of Japan, were examined to elucidate historical population dynamics using five chloroplast DNA (cpDNA) marker regions and 11 nuclear microsatellite loci. Three cpDNA haplotypes (A, B and C) were identified in a screen of 41 populations across the entire distribution range in Japan. Haplotype A was the most prevalent and was found in the entire range. Haplotype B was locally restricted to the Kii Peninsula, while haplotype C was restricted to the southwestern part of Japan. These haplotypes corresponded with the nuclear genetic constitution revealed by microsatellite markers. Two genetically differentiated major groups were identified by STRUCTURE analysis applied to 536 individuals from 28 populations, and they mostly corresponded with the two major cpDNA haplotypes, A and C. These populations were further divided into three geographically identified groups: group 1 in the area including Kanto and Tokai regions, the Kii Peninsula and the Muroto-misaki Cape on the Pacific coast; group 2 in the Bungo-suido Channel area; and group 3 in southern Kyushu and Okinawa. Populations in the Seto Inland Sea were divided into two groups: one was included in group 1 and appears to have originated from last glacial maximum (LGM) refugia located in the Kii Peninsula, while the other was included in group 2 and appears to have originated from LGM refugia located in southern Kyushu. These groups can be considered as conservation units for the preservation of unique seashore ecosystems, or as a seed source to foster coastal protection forests and next-generation production forests. Considerable care should be taken to protect isolated populations that may be specialized to unique local environments, such as those on the islands of Koshikijima and Izenajima.

Comparative mapping in the Fagaceae and beyond with EST-SSRs

BACKGROUND

Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species.

RESULTS

We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype.

CONCLUSIONS

This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.

Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.

Application of plant DNA markers in forensic botany: Genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites

As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

Interannual genetic heterogeneity of pollen pools accepted by Quercus salicina individuals

Since flowering often varies among years in wind-pollinated woody species, the genetic composition of pollen pools accepted by seed parents can differ between years. The interannual heterogeneity of pollen flow may be important for maintaining genetic diversity within populations because it can increase genetic variation within populations and the effective sizes of the populations. In this study we examined heterogeneity, using paternity analysis and analysis of molecular variance, in the genetic composition of pollen pools among different reproductive years for six Quercus salicina seed parents in an 11.56-ha plot in a temperate old-growth evergreen broadleaved forest. The genotypes at seven microsatellite loci were determined for 111 adult trees and 777 offspring of the six seed parents in 2-5 reproductive years. Genetic differentiation of pollen pools among different reproductive years for each seed parent was significant over all seed parents and for each of four seed parents that were analysed for more than 2 years, but not for either of the other two seed parents (analysed for 2 years). For both the pollen pools originating from inside the plot and those originating from outside it, genetic differentiation among different reproductive years for each seed parent was significant over all seed parents. However, among-year genetic differentiation in the pollen pools originating from within the plot was detected for all four of the seed parents that were analysed for more than 2 years, but for only one of the four in the pools originating from outside the plot. Genetic diversity (estimated as allelic richness and gene diversity) was higher for pollen pools over all reproductive years than for pollen pools in single years. These results indicate that the year-to-year genetic variation of pollen pools increases genetic diversity in offspring and is strongly affected by the variation in pollen parents within the plot because of their high pollination contributions. The high year-to-year variation in pollen parents within the plot and overall supports the hypothesis that the offspring produced across years represent a larger genetic neighbourhood.

Source populations of Quercus glauca in the last glacial age in Taiwan revealed by nuclear microsatellite markers

In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (H(E) = 0.741) and low population differentiation (F(ST) = 0.042) but shows isolation by distance. The most divergent populations, according to the average F(ST) for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversities that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers.

Cross-species amplification of microsatellite loci within the dioecious, polyploid genus Actinidia (Actinidiaceae)

Microsatellite marker transfer across species in the dioecious genus Actinidia (kiwifruit) could offer an efficient and time-effective technique for use during trait transfer for vine and fruit improvement in breeding programmes. We evaluated the cross-species amplification of 20 EST-derived microsatellite markers that were fully informative in an Actinidia chinensis mapping family. We tested all 20 markers on 120 genotypes belonging to 21 species, 5 with varieties and/or chromosome races. These 26 taxa included 16 diploids, 7 tetraploids, 2 hexaploids and 1 octaploid, and represented all four taxonomic sections in the genus. All 20 markers showed some level of cross-species amplification. The most successful marker amplified in all genotypes from all species from all sections of the genus, the least successful amplified fragments only in A. chinensis and A. deliciosa. One species, A. glaucophylla, failed to amplify with all but 2 markers. PIC (Polymorphism information content) values were high, with 14 of 17 markers recording values of 0.90 and above. Sequence data demonstrated the presence of the microsatellite in all the amplified products. Sequence homology was less 5' of the microsatellite and increased toward the start codon of the translated region of the EST from which the marker was derived. The data confirm that EST-derived microsatellite markers from Actinidia species show cross-species amplification with high levels of polymorphism which could make them useful markers in breeding programmes.

Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica

We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (approximately 30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (P<0.01) deviation from the expected segregation ratio. In total, 136 polymorphic markers were developed using C. japonica-based STS primers without any sequence modification. In addition, the applicability of STS-based markers developed in one species to other species was found to closely reflect the evolutionary distance between the species, which is roughly concordant with the difference between their rbcL sequences. We plan to use these markers for genetic studies in C. obtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.

Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives

The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He +/- SE = 0.58 +/- 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.

Cross-species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: allelic polymorphism and degree of relationship

Microsatellite amplification was performed on cassava (Manihot esculenta) and six other different species (all wild) of the Manihot genus. We used ten pairs of microsatellite primers previously developed from cassava, detecting 124 alleles in a sample of 121 accessions of the seven species. The number of alleles per locus ranged from four to 21 alleles, and allelic diversity was greater in the wild species than in cassava. Seventy-nine alleles, including unique ones, were detected in the wild species but were not found in the crop. The lower level of heterozygosity in some wild species probably resulted from a combination of fine-scale differentiation within the species and the presence of null alleles. Overall, microsatellite primers worked across the genus, but, with increasing genetic distance, success in amplifying loci tended to decrease. No accession of M. aesculifolia, M. carthaginensis, and M. brachyloba presented a banding pattern at locus Ga-140; neither did one appear for M. aesculifolia at locus Ga-13. Previous work with amplified fragment length polymorphism (AFLP) markers and this microsatellite analysis show that these three wild taxa are the most distant relatives of the crop, whereas the wild forms M. esculenta subsp. flabellifolia and M. esculenta subsp. peruviana appear to be the closest.

Comparative study of genetic variation and differentiation of two pedunculate oak (Quercus robur) stands using microsatellite and allozyme loci

In a comparative study four codominant microsatellite loci and seven allozyme gene loci have been used to investigate the genetic variation and differentiation of two pedunculate oak stands in North Germany. Both number and effective number of alleles were five to six times higher and the observed heterozygosity was three times higher for the microsatellite than for the allozyme loci. One stand showed an overall excess of homozygotes. In general the microsatellites were closer to Hardy-Weinberg expectation. The genetic distances between the two stands were distinctly higher for microsatellites. For most parameters microsatellites exhibited smaller interlocus variation than the allozymes. The different impact of population genetic processes on the genetic structure as assessed by microsatellites or allozymes is discussed.