Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data

Chloroplast DNA Diversity in Populations of P. sylvestris L. from Middle Siberia and the Romanian Carpathians

Scots pine is one of the dominant conifer species in forest ecosystems of the boreal zone in Eurasia. Knowledge of the genetic structure and the level of genetic variability of Scots pine populations is relevant for the development of measures aimed at conservation of species’ diversity. In this study, we used ten paternally inherited chloroplast microsatellite loci to investigate the genetic diversity of nineteen Scots pine populations from Middle Siberia and the Romanian Carpathians. The results of the study showed high genetic diversity (HCP = 0.91–1.00) in all of the investigated populations. The cpSSR analysis yielded a total of 158 haplotypes. The majority of the haplotypes (85%) were detected only once (unique haplotypes). Three common haplotypes were found between the Carpathian and the Siberian populations of Scots pine. Analysis of molecular variance (AMOVA) showed that only 3% of the variation occurred among populations from Middle Siberia and 6% of the variation existed among populations from the Carpathian Mountains. Overall, we found a weak geographic population structure in Scots pine from Middle Siberia and the Romanian Carpathians. The present study on genetic diversity in the Siberian and the Carpathian populations of Scots pine may contribute to the sustainable management and conservation of Scots pine genetic resources in Middle Siberia and the Romanian Carpathians.

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.

Testing the Effect of Mountain Ranges as a Physical Barrier to Current Gene Flow and Environmentally Dependent Adaptive Divergence in Cunninghamia konishii (Cupressaceae)

Populations can be genetically isolated by differences in their ecology or environment that hampered efficient migration, or they may be isolated solely by geographic distance. Moreover, mountain ranges across a species’ distribution area might have acted as barriers to gene flow. Genetic variation was quantified using amplified fragment length polymorphism (AFLP) and 13 selective amplification primer combinations used generated a total of 482 fragments. Here, we tested the barrier effects of mountains on gene flow and environmentally dependent local adaptation of Cunninghamia konishii occur in Taiwan. A pattern of genetic isolation by distance was not found and variation partitioning revealed that environment explained a relatively larger proportion of genetic variation than geography. The effect of mountains as barriers to genetic exchange, despite low population differentiation indicating a high rate of gene flow, was found within the distribution range of C. konishii. Twelve AFLP loci were identified as potential selective outliers using genome-scan methods (BAYESCAN and DFDIST) and strongly associated with environmental variables using regression approaches (LFMM, Samβada, and rstanarm) demonstrating adaptive divergence underlying local adaptation. Annual mean temperature, annual precipitation, and slope could be the most important environmental factors causally associated with adaptive genetic variation in C. konishii. The study revealed the existence of physical barriers to current gene flow and environmentally dependent adaptive divergence, and a significant proportion of the rate of gene flow may represent a reflection of demographic history.

Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites

The relict character of the Scots pine populations from the Tatra Mts. (Western Carpathians) was formed on scarcely accessible, ecologically extreme habitats, in areas which were not under human activity. An exhaustive genetic analysis of the Scots pine populations from the refugial locations in the Tatra Mts. (Poland) had not yet been. In this study, we characterize the genetic variation and differentiation of the relict Scots pine populations from the Tatra Mts., to provide information on their genetic resources and the conservation implications. Eight paternally inherited chloroplast microsatellite loci were used to investigate the genetic structure of 4 relict populations, which were compared with the natural populations from the Baltic region (5 populations from Lithuania, Latvia and Estonia) and to a northern range from Russia (5 populations from the Kola Peninsula and Arkhangelsk Oblast). The four relict pine populations were characterized by a lower level of genetic variation when compared to the Baltic and northern populations, which was expressed in lower values of particular genetic parameters: numbers of alleles and haplotypes, haplotype genetic diversity, haplotype differentiation, and mean genetic distance between individuals in the population. Our results revealed a very high and significant genetic differentiation between all the analyzed populations, as well as between the three analyzed regions (PhiPT = 8%). Furthermore, the relict populations within a close geographic location showed higher differentiation (PhiPT = 5%) compared to the northern Russian and Baltic populations that were separated by tens and hundreds of kilometers. The relict populations of P. sylvestris from the Tatra Mts. deserve conservation efforts due to the fact that they are an important component if the species-poor Tatra forests.

Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR) and chloroplast single nucleotide polymorphism (cpSNP). In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA). The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM) in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats

BACKGROUND

Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions.

RESULTS

An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria.

CONCLUSIONS

Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

BACKGROUND

Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton.G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. Present study was conducted in order to analyse the sequence of its chloroplast.

OBJECTIVES

Present study was conducted to study and compare the complete chloroplast sequence of G. thurberi, analyses of its genome structure, gene content and organization, repeat sequence and codon usage and comparison with two cultivated allotetraploid sequenced cotton species.

MATERIALS AND METHODS

The available sequence was assembled by DNAman (Version 8.1.2.378). Gene annotation was mainly performed by DOGMA. The map of genome structure and gene distribution were carried out using OGDRAW V1.1. Relative synonymous codon usage (RSCU) of different codons in each gene sample was calculated by codonW in Mobyle. To determine the repeat sequence and location, an online version of REPuter was used.

RESULTS

The G. thurberi chloroplast (cp) genome is 160264 bp in length with conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 88,737 bp, and the small single copy region is 20,271 bp whereas the inverted repeat is 25,628 bp each. The plastidic genome has 113 single genes and 20 duplicated genes. The singletones encode 79 proteins, 4 ribosomal RNA genes and 30 transfer RNA genes.

CONCLUSIONS

Amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with cpDNA of two cultivated allotetraploid, rps18 was the only duplicated gene in G.thurberi. Despite the high level of conservation in cp genome SSRs ,these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs. Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair.

Limited genetic variability and phenotypic plasticity detected for cavitation resistance in a Mediterranean pine

Resistance to cavitation is a major determinant of plant survival under severe drought and can be used to quantify species adaptive potential. Interspecific variation in this key trait is well defined in woody species, but intraspecific variation (level and structure) resulting from standing genetic variation and phenotypic plasticity has never been determined. Combining for the first time in situ characterization of natural populations and two reciprocal common gardens in dry and wet sites, we estimated variance components (phenotypic, genetic, environmental, and genetic × environmental) of cavitation resistance based on 513 genotypes of a Mediterranean pine, Pinus pinaster. Despite the selected populations being climatically contrasted, phenotypic plasticity in resistance to cavitation remained low and was essentially attributed to family level. Between-population variation in cavitation resistance for both phenotypic and genetic variation was limited. These results strongly suggest that cavitation resistance is buffered against genetic and to a lesser extent environmental variation (canalization) in maritime pine. Consequently, in a drier world, the increasing drought tolerance of Pinus species might be severely constrained by the low level of cavitation resistance variation, resulting in a large-scale loss of productivity.

Effect of latitudinal gradient and impact of logging on genetic diversity of Cedrela lilloi along the Argentine Yungas Rainforest

Cedrela lilloi C. DC. (cedro coya, Meliaceae), an important south American timber species, has been historically overexploited through selective logging in Argentine Yungas Rainforest. Management and conservation programs of the species require knowledge of its genetic variation patterns; however, no information is available. Molecular genetic variability of the species was characterized to identify high-priority populations for conservation and domestication purposes. Fourteen native populations (160 individuals) along a latitudinal gradient and with different logging's intensities were assessed by 293 polymorphic AFLP (amplified fragment length polymorphism) markers. Genetic diversity was low (Ht = 0.135), according to marginal location of the species in Argentina. Most of the diversity was distributed within populations (87%). Northern populations showed significant higher genetic diversity (R(2)= 0.69) that agreed with latitudinal pattern of distribution of taxonomic diversity in the Yungas. Three clusters were identified by Bayesian analysis in correspondence with northern, central, and southern Yungas. An analysis of molecular variance (AMOVA) revealed significant genetic differences among latitudinal clusters even when logging (Φ(RT) = 0.07) and unlogging populations (Φ(PT) = 0.10) were separately analyzed. Loss of genetic diversity with increasing logging intensity was observed between neighboring populations with different disturbance (Φ(PT) = 0.03-0.10). Bottlenecks in disturbed populations are suggested as the main cause. Our results emphasize both: the necessity of maintaining the genetic diversity in protected areas that appear as possible long-term refuges of the species; and to rescue for the national system of protected areas some high genetic diversity populations that are on private fields.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

BACKGROUND

Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers.

RESULTS

We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency.

CONCLUSIONS

This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Variation of selfing rate and inbreeding depression among individuals and across generations within an admixed Cedrus population

We investigated the variation and short-term evolution of the selfing rate and inbreeding depression (ID) across three generations within a cedar forest that was established from admixture ca 1860. The mean selfing rate was 9.5%, ranging from 0 to 48% among 20 seed trees (estimated from paternally inherited chloroplast DNA). We computed the probability of selfing for each seed and we investigated ID by comparing selfed and outcrossed seeds within progenies, thus avoiding maternal effects. In all progenies, the germination rate was high (88-100%) and seedling mortality was low (0-12%). The germination dynamics differed significantly between selfed and outcrossed seeds within progenies in the founder gene pool but not in the following generations. This transient effect of selfing could be attributed to epistatic interactions in the original admixture. Regarding the seedling growth traits, the ID was low but significant: 8 and 6% for height and diameter growth, respectively. These rates did not vary among generations, suggesting minor gene effects. At this early stage, outcrossed seedlings outcompeted their selfed relatives, but not necessarily other selfed seedlings from other progenies. Thus, purging these slightly deleterious genes may only occur through within-family selection. Processes that maintain a high level of genetic diversity for fitness-related traits among progenies also reduce the efficiency of purging this part of the genetic load.

Chloroplast diversity in a putative hybrid swarm of Ponderosae (Pinaceae)

The Ponderosae subsection of the genus Pinus contains numerous taxa in disjunct mountain ranges of southern Arizona and New Mexico, differing for several leaf and cone traits, key among which is the number of leaf needles per fascicle. Trees with three needles are often found together with trees having five needles and mixed numbers. One taxonomic hypothesis is that there are swarms of hybrids between P. ponderosa and P. arizonica. A second hypothesis is that there are spatial mixtures of two separate taxa, five-needle P. arizonica and a "taxon X" containing three needle and mixed needle trees. We genotyped chloroplasts in one putative hybrid swarm on Mt. Lemmon using microsatellite markers and show that cpDNA is almost completely differentiated between two separate morphotypes corresponding to P. arizonica and "taxon X." Little if any introgression has occurred on Mt. Lemmon, and the simplest explanation is that little or no effective hybridization has occurred. Further results indicate that not only is taxon X not of hybrid origin, it is more closely related to nonregional Ponderosae other than P. ponderosa and P. arizonica. The results further suggest that other putative hybrid swarms in the region are also spatial mixtures of distinct taxa.

Molecular and phenotypic profiling from the base to the crown in maritime pine wood-forming tissue

Environmental, developmental and genetic factors affect variation in wood properties at the chemical, anatomical and physical levels. Here, the phenotypic variation observed along the tree stem was explored and the hypothesis tested that this variation could be the result of the differential expression of genes/proteins during wood formation. Differentiating xylem samples of maritime pine (Pinus pinaster) were collected from the top (crown wood, CW) to the bottom (base wood, BW) of adult trees. These samples were characterized by Fourier transform infrared spectroscopy (FTIR) and analytical pyrolysis. Two main groups of samples, corresponding to CW and BW, could be distinguished from cell wall chemical composition. A genomic approach, combining large-scale production of expressed sequence tags (ESTs), gene expression profiling and quantitative proteomics analysis, allowed identification of 262 unigenes (out of 3512) and 231 proteins (out of 1372 spots) that were differentially expressed along the stem. A good relationship was found between functional categories from transcriptomic and proteomic data. A good fit between the molecular mechanisms involved in CW-BW formation and these two types of wood phenotypic differences was also observed. This work provides a list of candidate genes for wood properties that will be tested in forward genetics.

Genetic variation in the invasive process of Bursaphelenchus xylophilus (Aphelenchida: Aphelenchoididae) and its possible spread routes in China

Pinewood nematode (Bursaphelenchus xylophilus) is an invasive species that causes a destructive forest disease-pine wilt disease. This disease has been prevalent in some countries in Asia since the 1970s. An amplified fragment length polymorphism survey was used to compare the genetic variation of native and invasive nematode populations in China and to examine the changes in genetic diversity during the invasion process. The genetic diversity of Chinese populations was slightly higher than that of American populations. Analysis of groups sampled from different invasive stages in China, showed that no obvious change in genetic diversity. Hence, genetic drift and founder effects are not obvious in the invasion process. Phylogenetic analysis showed that Chinese pinewood nematode populations were closer to Japanese populations than to American populations. On the basis of the genetic relationships among samples, two major invasion pathways in China are suggested. One is from Guangdong to Anhui and Zhejiang, and the other is from Guangdong to Jiangsu and then from Jiangsu to Hubei, Guizhong and Congqing. The results imply that it is important to reinforce both domestic and international quarantine to control the spread of pinewood nematode.

Nucleotide variation in genes involved in wood formation in two pine species

Nucleotide diversity in eight genes related to wood formation was investigated in two pine species, Pinus pinaster and P. radiata. The nucleotide diversity patterns observed and their properties were compared between the two species according to the specific characteristics of the samples analysed. A lower diversity was observed in P. radiata compared with P. pinaster. In particular, for two genes (Pp1, a glycin-rich protein homolog and CesA3, a cellulose synthase) the magnitude of the reduction of diversity potentially indicates the action of nonneutral factors. For both, particular patterns of nucleotide diversity were observed in P. pinaster (high genetic differentiation for Pp1 and close to zero differentiation associated with positive Tajima's D-value for CesA3). In addition, KORRIGAN, a gene involved in cellulose-hemicellulose assembly, demonstrated a negative Tajima's D-value in P. radiata accompanied by a high genetic differentiation in P. pinaster. The consistency of the results obtained at the nucleotide level, together with the physiological roles of the genes analysed, indicate their potential susceptibility to artificial and/or natural selection.

Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation

Phylogeographical and mismatch analysis of chloroplast DNA (cpDNA) variation were used to infer the temporal dynamics of distributional and demographic history of Taiwan fir (Cunninghamia konishii). We examined 64 and 52 trees from 17 populations of C. konishii and 14 provenances of C. lanceolata, respectively, by sequencing three intergenic spacers and one intron using cpDNA universal primers. Of the aligned 1888 base pairs (bp) sequence, 30 varied among 28 haplotypes, which consisted of three transitions, 14 transversions and 13 indels. One ancestral haplotype was found in 86 individuals across the surveyed range of both species, C. konishii and C. lanceolata, which was distributed in all populations and provenances. The 28 haplotypes also included 15 C. konishii specific and 12 C. lanceolata-specific haplotypes. Ancestral haplotype was found fixed in five populations of C. konishii and five provenances of C. lanceolata. Other haplotypes occurred mainly as singletons. The levels of population differentiation studied are relatively low in both Cunninghamia species. The nucleotide diversity (theta) of chloroplast DNA sequences within C. konishii was slightly higher than that of C. lanceolata. Excess in singletons as well as star-like phylogeny of haplotypes suggested no clearcut migration patterns of C. konishii after glacial maximum. One probable demographic history of C. konishii is the postglacial population growth of C. konishii after a glacial bottleneck event. This inference is supported by the combined results of fossil pollen record, low nucleotide diversity, significant Tajima's d-value, phylogeographical analysis and unimodal mismatch distribution. Similarities and discrepancies between our results and those of Lu et al. (2001) are discussed.

Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria-Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre-date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria-Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans-species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.