Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants

Phenotypic variation seems not to be associated with the genetic profile in Zygopetalum (Orchidaceae): a case study of a high-elevation rocky complex

BACKGROUND

Hybridization associated with polyploidy studies is rare in the tropics. The genus Zygopetalum (Orchidaceae) was investigated here as a case study of Neotropical plants. In the rocky highlands of the Ibitipoca State Park (ISP), southeast Brazil, individuals with intermediate colors and forms between the species Z. maculatum and Z. triste were commonly identified.

METHODS AND RESULTS

Chromosomal analysis and DNA quantity showed a uniform population. Regardless of the aspects related to the color and shape of floral structures, all individuals showed 2n = 96 chromosomes and an average of 14.05 pg of DNA. Irregularities in meiosis associated with chromosome number and C value suggest the occurrence of polyploidy. The genetic distance estimated using ISSR molecular markers revealed the existence of genetic variability not related to morphological clusters. Morphometric measurements of the flower pieces revealed that Z. maculatum shows higher variation than Z. triste although lacking a defined circumscription.

CONCLUSION

The observed variation can be explained by the polyploid and phenotypic plasticity resulting from the interaction of the genotypes with the heterogeneous environments observed in this habitat.

Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies

Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.

Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan

Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.

Comparative analysis of molecular and morphological diversity in two diploid Paspalum species (Poaceae) with contrasting mating systems

KEY MESSAGE

Interspecific comparison of two Paspalum species has demonstrated that mating systems (selfing and outcrossing) contribute to variation (genetically and morphologically) within species through similar but mutually exclusive processes. Mating systems play a key role in the genetic dynamics of populations. Studies show that populations of selfing plants have less genetic diversity than outcrossing plants. Yet, many such studies have ignored morphological diversity. Here, we compared the morphological and molecular diversity patterns in populations of two phylogenetically-related sexual diploids that differ in their mating system: self-sterile Paspalum indecorum and self-fertile P. pumilum. We assessed the morphological variation using 16 morpho-phenological characters and the molecular diversity using three combinations of AFLPs. We compared the morphological and molecular diversity within and among populations in each mating system. Contrary to expectations, selfers showed higher morphological variation within populations, mainly in vegetative and phenological traits, compared to outcrossers. The high morphological variation within populations of selfers led to a low differentiation among populations. At molecular level, selfing populations showed lower levels of genotypic and genetic diversity than outcrossing populations. As expected, selfers showed higher population structure than outcrossers (PhiST = 0.301 and PhiST = 0.108, respectively). Increased homozygous combinations for the same trait/locus enhance morphological variation and reduce molecular variation within populations in selfing P. pumilum. Thus, selfing outcomes are opposite when comparing morphological and molecular variation in P. pumilum. Meanwhile, pollen flow in obligate outcrossing populations of P. indecorum increases within-population molecular variation, but tends to homogenize phenotypes within-population. Pollen flow in obligate outcrossers tends to merge geographically closer populations; but isolation by distance can lead to a weak differentiation among distant populations of P. indecorum.

Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China

Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.

Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers

BACKGROUND

Rhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources.

RESULTS

In the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity.

CONCLUSIONS

This is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.

The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its first sources of diversity and little is known about the genetic origin and genetic variability. Thus, this study aimed to investigate the genetic diversity and genetic population structure existing in a representative teak germplasm bank collection. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 3 giga bases per sample, the sequences are aligned using the genome, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four populations with considerable genetic variability between and within them. While the genetic variability in teak is generally known to be narrow, this study confirmed the presence of genetic variability scale in teak, which is contrary to what was initially expected.

GenoSSRFinder: a tool for rapid, precise, and targeted simple sequence repeat detection in genomic studies

The GenoSSRFinder is a new tool enables the research of Simple Sequence Repeats (SSRs) in DNA sequences and genomes much simpler and more precise in short time. The analysis is carried out by targeting a certain SSR in genome and gene sequences. This utility is quick, accurate, and does its function quite well. It quickly goes across the sequence, revealing all of the locations at which the selected SSR may be found. This tool will tell researchers where selected SSR begins and where it stops, how long it is, how often it repeats, and how long each repetition is. GenoSSRFinder gets the findings quickly, and they will be simple to comprehend. Therefore, when studying SSRs, researchers will have more time to use to thorough work as a result of this time savings. In addition, it provides a valuable information since it is highly precise. GenoSSRFinder is simple to use and produces high-quality findings. It is also accelerating SSRs gene research, which is a direct result of the new approach we use to analyse SSRs. Three case studies in this study demonstrated the usefulness of this program by immediately studying a particular SSR that was associated with genetic illness, biodiversity and criminal science in living organisms. This demonstration explains that GenoSSRFinder might be utilized in a wide variety of fields, such as the research of genetic illnesses, the biodiversity and genetic studies, or even in criminal investigations.

Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations

BACKGROUND

Climate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles.

METHODS

In this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera.

RESULTS

The genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding.

CONCLUSION

Our study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.

Population structure and genetic diversity of Tamarix chinensis as revealed with microsatellite markers in two estuarine flats

Background

Tamarix chinensis Lour. is a 3-6-meter-tall small tree with high salt- and alkali- tolerance and aggressive invasiveness, mainly distributed in the eastern part of China in warm-temperate and subtropical climate zones, yet there is little information available regarding genetic diversity and population structure.

Methods

A total of 204 individuals of nine T. chinensis populations were investigated for genetic diversity and population structure using a set of 12 highly polymorphic microsatellite markers.

Results

The total number of alleles detected was 162, the average number of effective allele was 4.607, the average polymorphism information content (PIC) value of the 12 loci was 0.685, and the mean observed heterozygosity (Ho) and the mean expected heterozygosity (He) was 0.653 and 0.711, respectively. Analysis of molecular variance (AMOVA) showed a 5.32% genetic variation among T. chinensis populations. Despite a low population differentiation, Bayesian clustering analysis, discriminant analysis of principal components (DAPC) and the unweighted pair group method with arithmetic mean (UPGMA) clearly identified three genetic clusters correlated to the populations' geographic origin: the northern populations including those from Yellow River Delta, the Fangshan (FS) population from Beijing, the Changyi (CY) population from Bohai Bay, the Huanjiabu (HHJ) population from Hangzhou Bay, and the remaining two populations from Hangzhou Bay. There was a significant relationship between the genetic distance and geographical distance of the paired populations. Gene flow (Nm) was 4.254 estimated from FST.

Conclusion

T. chinensis possessed high genetic diversity comparable to tree species, and although the population differentiation is shallow, our results classified the sampled populations according to sampling localities, suggesting the different origins of the study populations.

The Genetic Diversity and Genetic Structure of the Germplasm Resources of the Medicinal Orchid Plant Habenaria dentata

Habenaria dentata has medicinal and ornamental value, but the number of wild populations is decreasing dramatically. Thus, conducting research on its genetic diversity and structure is necessary to provide a basis for its conservation. This study aimed to explore the genetic diversity of the wild plant H. dentata and protect and optimize its wild resources. The genetic diversity of 133 samples from six wild populations of H. dentata was analyzed using Inter Simple Sequence Repeat molecular markers to provide a scientific basis for the screening of improved germplasm resources. The results showed that the average number of alleles was 1.765, the average number of effective alleles was 1.424, the average Nei's gene diversity index was 0.252, the average Shannon diversity index was 0.381, and the average percentage of polymorphic loci was 76.499%. The variation within the populations was 77.34%, and the variation between the populations was 22.66%. The gene flow was 1.705, which was greater than 1. The results of the cluster analysis showed that the six populations were mainly divided into four clusters and were not classified according to their geographical location. There was no significant correlation between the geographical location and genetic distance between the populations (r = 0.557, p > 0.05). The genetic diversity of H. dentata is high. Among the six wild populations, the genetic diversity of the Mulun population was the highest and this population can be used as a key protection unit. The study on the genetic diversity of H. dentata can not only reveal the reasons for the decrease in the number of individuals in the population to a certain extent, and put forward the protection strategy, but also provide a scientific basis for the breeding of excellent seed resources.

Assessment of Genetic Diversity and Genetic Structure of Saussurea medusa (Asteraceae), a "Sky Island" Plant in the Qinghai-Tibet Plateau, Using SRAP Markers

Saussurea medusa Maxim. is a typical "sky island" species and one with the highest altitude distributions among flowering plants. The present study aimed at analyzing the genetic diversity and population structure of 300 S. medusa accessions collected from 20 populations in the Qilian Mountains in the northeastern Qinghai-Tibet Plateau (QTP), using sequence-related amplified polymorphism (SRAP) markers. A total of 14 SRAP primer combinations were employed to analyze genetic diversity and population structure across all accessions. Out of 511 amplified bands, 496 (97.06%) were polymorphic. The populations in the eastern Qilian Mountains had significantly higher genetic diversity than those in the central and western groups. Population structure analysis revealed greater genetic differentiation among populations with a Gst of 0.4926. UPGMA-based clustering classified the 300 S. medusa accessions into 3 major clusters, while the Bayesian STRUCTURE analysis categorized them into 2 groups. Correlation analyses showed that the genetic affinity of the populations was based on differences in geographical distance, moisture conditions, and photothermal conditions between the habitats. This study represents the first comprehensive genetic assessment of S. medusa and provides important genetic baseline data for the conservation of the species.

Multi-character approach reveals a new mangrove population of the Yellow Warbler complex, Setophaga petechia, on Cozumel Island, Mexico

The Setophaga petechia complex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean: Setophaga petechia bryanti a mangrove subspecies belonging to the erithachorides group resident on the mainland of the Yucatan Peninsula and Setophaga petechia rufivertex endemic to Cozumel Island and belonging to the petechia group. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies, S. p. rufivertex and to the mainland subspecies, S. p. bryanti while demonstrating finite differences. We conclude that the new population of S. petechia on Cozumel Island is a well-established population with high level of differentiation.

Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum

BACKGROUND

Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.

METHODS

In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.

RESULTS

The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization.

CONCLUSIONS

Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.

Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

Water yam (Dioscorea alata L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about Dioscorea species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 D. alata accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.20to 0.76, with a mean of 0.53, which suggests moderate genetic diversity of D. alata accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 54% of the variation was attributed to within individual, 39% was attributed to among individual while among population contributed 7% of the total variation. The highest Nei's genetic distance (0.43) was for accessions sampled from Kilimanjaro and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D. alata accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of D. alata accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of D. alata accessions for breeding programs in Tanzania.

Genome-Wide Development of Polymorphic Microsatellite Markers and Genetic Diversity Analysis for the Halophyte Suaeda aralocaspica (Amaranthaceae)

Suaeda aralocaspica, which is an annual halophyte, grows in saline deserts in Central Asia with potential use in saline soil reclamation and salt tolerance breeding. Studying its genetic diversity is critical for effective conservation and breeding programs. In this study, we aimed to develop a set of polymorphic microsatellite markers to analyze the genetic diversity of S. aralocaspica. We identified 177,805 SSRs from the S. aralocaspica genome, with an average length of 19.49 bp, which were present at a density of 393.37 SSR/Mb. Trinucleotide repeats dominated (75.74%) different types of motifs, and the main motif was CAA/TTG (44.25%). We successfully developed 38 SSR markers that exhibited substantial polymorphism, displaying an average of 6.18 alleles with accompanying average polymorphism information content (PIC) value of 0.516. The markers were used to evaluate the genetic diversity of 52 individuals collected from three populations of S. aralocaspica in Xinjiang, China. The results showed that the genetic diversity was moderate to high, with a mean expected heterozygosity (He) of 0.614, a mean Shannon's information index (I) of 1.23, and a mean genetic differentiation index (Fst) of 0.263. The SSR markers developed in this study provide a valuable resource for future genetic studies and breeding programs of S. aralocaspica, and even other species in Suaeda.

Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes

The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.

Isolation of Pseudomonas syringae pv. Tomato strains causing bacterial speck disease of tomato and marker-based monitoring for their virulence

BACKGROUND

The bacterial speck disease of tomato caused by a bacterial pathogen Pseudomonas syringae pv. tomato is a most important disease causing severe crop losses.

METHODS AND RESULTS

Present study was conducted to investigate and characterize the population diversity of P. syringae pv. tomato pathogen isolated from infected tomato plants from various regions of Egypt. Significant variation among the isolates was observed which demonstrated considerable virulence. All isolates were pathogenic and the CFU population recovered from inoculate tomato leaves by isolate Pst-2 was higher than other isolates. Genetic disparity among the isolates was investigated by PCR analysis by amplifying hrpZ gene using random amplified polymorphic DNA (RAPD), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeats (ISSR) markers. The amplified products for ITS1 were found to have 810 bp length whereas 536 bp length was observed for hrpZ gene using primer pairs (1406-f/23S-r) and (MM5-F, MM5-R) respectively. The restriction analysis of amplified regions "ITS" and hrpZ by using 5 and 4 endonucleases respectively demonstrated slight variation among the bacterial isolates. The results of RAPD, ISSR and SRAP showed higher polymorphism (60.52%) within the isolates which may assist for successful characterization by unique and specific markers based on geographical distribution, origin and virulence intensity.

CONCLUSION

The results of present study suggested that the use of molecular approach may provide successful and valuable information to differentiate and classify P. syringae pv. tomato strains in future for the detection and confirmation of pathogenicity.

Genetic Diversity of Oxytropis Species from the Center of the Genus Origin: Insight from Molecular Studies

The genus Oxytropis (Fabaceae) was formed from the ancient species of Astragalus presumably approximately 5.6 Ma ago in Southern Siberia. Our study summarized data on the genetic diversity of 69 populations of 31 Oxytropis species in the center of origin of the genus based on the sequencing of plastid genome markers. Most of the populations (82.6%) are characterized by high gene diversity (0.600–1.000), which indicates a relatively stable state. Phylogenetic relationships between most Oxytropis species remain unresolved. Three genetic complexes and four phyletic lineages have been identified. Some species form weakly differentiated complexes, which is probably caused by their relatively recent divergence and the demography processes, as well as interspecific hybridization and polyploidy characteristic of Oxytropis species.

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.

Genotyping by sequencing and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)

The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost complexity reduced mRNA analysis (mRNA-GBS) and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but due to site-specific multifactorial influences of environmental responses as well as conceptual and methodological limitations of mRNA-GBS, it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. Nevertheless, the use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Nevertheless, our study design across different regions in Germany was also challenging. The use of reduced complexity differential expression analyses most likely overlays site-specific patterns due to highly complex plant responses under natural conditions.

Bioinformatic analysis of the coding region of the melatonin receptor 1b gene as a reliable DNA marker to resolve interspecific mammal phylogenetic relationships

This research looks into the main DNA markers and the limits of their application in molecular phylogenetic analysis. Melatonin 1B (MTNR1B) receptor genes were analyzed from various biological sources. Based on the coding sequences of this gene, using the class Mammalia as example, phylogenetic reconstructions were made to study the potential of mtnr1b as a DNA marker for phylogenetic relationships investigating. The phylogenetic trees were constructed using NJ, ME and ML methods that establish the evolutionary relationships between different groups of mammals. The resulting topologies were generally in good agreement with topologies established on the basis of morphological and archaeological data as well as with other molecular markers. The present divergences provided a unique opportunity for evolutionary analysis. These results suggest that the coding sequence of the MTNR1B gene can be used as a marker to study the relationships of lower evolutionary levels (order, species) as well as to resolve deeper branches of the phylogenetic tree at the infraclass level.

Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens

Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-F_ST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.

Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains

Investigating the genetic diversity and population structure is important in conserving narrowly distributed plants. In this study, 90 Clematis acerifolia (C. acerifolia) plants belonging to nine populations were collected from the Taihang Mountains in Beijing, Hebei, and Henan. Twenty-nine simple sequence repeats (SSR) markers developed based on RAD-seq data were used to analyze the genetic diversity and population structure of C. acerifolia. The mean PIC value for all markers was 0.2910, indicating all SSR markers showed a moderate degree of polymorphism. The expected heterozygosity of the whole populations was 0.3483, indicating the genetic diversity of both C. acerifolia var. elobata and C. acerifolia were low. The expected heterozygosity of C. acerifolia var. elobata (He = 0.2800) was higher than that of C. acerifolia (He = 0.2614). Genetic structure analysis and principal coordinate analysis demonstrated that C. acerifolia and C. acerifolia var. elobata showed great genetic differences. Molecular variance analysis (AMOVA) demonstrated that within-population genetic variation (68.31%) was the main contributor to the variation of the C. acerifolia populations. Conclusively, C. acerifolia var. elobata had higher genetic diversity than C. acerifolia, and there are significant genetic differences between C. acerifolia and C. acerifolia var. elobata, and small genetic variations within the C. acerifolia populations. Our results provide a scientific and rational basis for the conservation of C. acerifolia and provide a reference for the conservation of other cliff plants.

Multivariate analysis of chemical and genetic diversity of wild Humulus lupulus L. (hop) collected in situ in northern France

The hop plant (Humulus lupulus L.) has been exploited for a long time for both its brewing and medicinal uses, due in particular to its specific chemical composition. These last years, hop cultivation that was in decline has been experiencing a renewal for several reasons, such as a craze for strongly hopped aromatic beers. In this context, the present work aims at investigating the genetic and chemical diversity of fifty wild hops collected from different locations in Northern France. These wild hops were compared to ten commercial varieties and three heirloom varieties cultivated in the same sampled geographical area. Genetic analysis relying on genome fingerprinting using 11 microsatellite markers showed a high level of diversity. A total of 56 alleles were determined with an average of 10.9 alleles per locus and assessed a significant population structure (mean pairwise F_ST = 0.29). Phytochemical characterization of hops was based on volatile compound analysis by HS-SPME GC-MS, quantification of the main prenylated phenolic compounds by UHPLC-UV as well as untargeted metabolomics by UHPLC-HRMS and revealed a high level of chemical diversity among the assessed wild accessions. In particular, analysis of volatile compounds revealed the presence of some minor but original compounds, such as aromadendrene, allo-aromadendrene, isoledene, β-guaiene, α-ylangene and β-pinene in some wild accessions; while analysis of phenolic compounds showed high content of β-acids in these wild accessions, up to 2.37% of colupulone. Genetic diversity of wild hops previously observed was hence supported by their chemical diversity. Sample soil analysis was also performed to get a pedological classification of these different collection sites. Results of the multivariate statistical analysis suggest that wild hops constitute a huge pool of chemical and genetic diversity of this species.

Genetics and epigenetics of Pinus nigra populations with differential exposure to air pollution

Forest species in the course of their evolution have experienced several environmental challenges, which since historic times include anthropogenic pollution. The effects of pollution on the genetic and epigenetic diversity in black pine (Pinus nigra) forests were investigated in the Amyntaio - Ptolemais - Kozani Basin, which has been for decades the largest lignite mining and burning center of Greece, with a total installed generating capacity of about 4.5 GW, operating for more than 70 years and resulting in large amounts of primary air pollutant emissions, mainly SO₂, NOx and PM10. P. nigra, a biomarker for air pollution and a keystone species of affected natural ecosystems, was examined in terms of phenology (cone and seed parameters), genetics (283 AFLP loci) and epigenetics (606 MSAP epiloci), using two populations (exposed to pollution and control) of the current (mature trees) and future (embryos) stand. It was found that cone, seed, as well as genetic diversity parameters, did not show statistically significant differences between the exposed population and the control. Nevertheless, statistically significant differences were detected at the population epigenetic level. Moreover, there was a further differentiation regarding the intergenerational comparison: while the epigenetic diversity does not substantially change in the two generations assessed in the control population, epigenetic diversity is significantly higher in the embryo population compared to the parental stand in the exposed population. This study sheds a light to genome dynamics in a forest tree population exposed to long term atmospheric pollution burden and stresses the importance of assessing both genetics and epigenetics in biomonitoring applications.

East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity

Background

Cashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring.

Methods

A total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses.

Results

The population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement.

Conclusions

Crop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data is also important to creating a country-specific genetic cashew signature to increase cashew market value.

Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing

Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (G_IS that was close to or even below zero in all populations), and a high level of genetic differentiation (F_ST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.

Assessment of Genetic Diversity among Wild Ruta chalepensis L. from the North of Jordan

Ruta chalepensis, known as Fringed Rue, is a small shrub of the Rutaceae family. To date, there is no record of its natural distribution across Jordan, a country located in the eastern part of the Mediterranean basin, and there are no previous studies on its genetic diversity in the region. Therefore, this study was conducted to assess the genetic diversity of R. chalepensis in the northern parts of Jordan using morphological trait and amplified fragment length polymorphism (AFLP) analyses. For the morphological traits, the analysis of variance indicated that there were significant differences between the identified populations. The Shannon diversity indices showed relatively high values, indicating the existence of a high variability among the identified populations. The principal component analysis explained 82% of the variation between the collected plants, and a clear separation of the collected individuals from the Jarash-A, Jarash-B and Ajloun-B populations from the rest of the populations was observed. The heatmap clustering was in general agreement with the results of the principal component analysis, with the plant height, rachis length and plant width considered as the discriminative traits. The AFLP analysis using eight different primer combinations generated 59 polymorphic bands, with an average polymorphism information content value of 0.32. The phylogenetic analysis identified three main clusters, with the first cluster including 65% of the individuals collected from the Jarash and Ajloun provinces, with a clear separation of the Jarash-B population. The AMOVA revealed that the genetic variation between the populations contributed 30% of the total genetic variation, while the variation within the populations explained 70%. In conclusion, morphological traits and molecular markers were used successfully to assess the genetic diversity among wild R. chalepensis from the north of Jordan, and such data can be used for future conservation plans and utilization purposes.

Interspecific Gene Flow and Selective Sweeps in Picea wilsonii, P. neoveitchii and P. likiangensis

Genome-wide single nucleotide polymorphism (SNP) markers were obtained by genotyping-by-sequencing (GBS) technology to study the genetic relationships, population structure, gene flow and selective sweeps during species differentiation of Picea wilsonii, P. neoveitchii and P. likiangensis from a genome-wide perspective. We used P. jezoensis and P. pungens as outgroups, and three evolutionary branches were obtained: P. likiangensis was located on one branch, two P. wilsonii populations were grouped onto a second branch, and two P. neoveitchii populations were grouped onto a third branch. The relationship of P. wilsonii with P. likiangensis was closer than that with P. neoveitchii. ABBA-BABA analysis revealed that the gene flow between P. neoveitchii and P. wilsonii was greater than that between P. neoveitchii and P. likiangensis. Compared with the background population of P. neoveitchii, the genes that were selected in the P. wilsonii population were mainly related to plant stress resistance, stomatal regulation, plant morphology and flowering. The genes selected in the P. likiangensis population were mainly related to plant stress resistance, leaf morphology and flowering. Selective sweeps were beneficial for improving the adaptability of spruce species to different habitats as well as to accelerate species differentiation. The frequent gene flow between spruce species makes their evolutionary relationships complicated. Insight into gene flow and selection pressure in spruce species will help us further understand their phylogenetic relationships and provide a scientific basis for their introduction, domestication and genetic improvement.

Genetic Diversity in Marginal Populations of Nitraria schoberi L. from Romania

Nitraria schoberi L. (Nitrariaceae) is a halophytic plant with a continuous range in Central Asia and with only two populations in the westernmost distribution limit of species, in Romania. Currently, there is no documented explanation for the species’ presence in Europe, outside the main distribution area. Considering that marginal populations genetics are important in establishing range limits and species adaptative potential, genetic diversity was assessed using Inter-simple sequence repeat markers (ISSR). Both the Shannon’s Information Index (I) and Expected Heterozygosity (He) suggested a relatively low level of genetic diversity within the two populations. However, the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and Principal Coordinates Analysis clearly distinguished the two populations. Our presumptions, based on current results, are that the marginal westernmost population of N. schoberi was established due to the unique conditions from the “islands of desert” developed in a temperate continental climate. The European establishment of this species was likely accidental and probably due to ornithochory. Genetic relatedness between populations could be a consequence of their common origin, presumably from proximal Asian N. schoberi populations, while the separation can be explained by the lack of genetic material exchange between the two populations.

Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (Sassafras tzumu) Revealed by Novel Nuclear Microsatellite (nSSR) Markers

Sassafras tzumu (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of S. tzumu are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of S. tzumu via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of S. tzumu. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean PIC = 0.356), and the transferability of these markers in other Sassafras species was high (85.19%). A moderately low level of genetic diversity and a high variation (F_ST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (H_E) of 0.430 at the species level and H_E ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six S. tzumu populations into two clusters, and the further strong population subdivision appeared from K = 2 to K = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (r = 0.742, p = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (N_m = 0.625), a relatively high degree of inbreeding (F_IS = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of S. tzumu and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of S. tzumu and other Sassafras (Lauraceae) species.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

BACKGROUND

Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.

RESULTS

A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.

CONCLUSIONS

Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

Pattern of Adaptive Divergence in Zingiber kawagoii Hayata (Zingiberaceae) along a Narrow Latitudinal Range

Ecological and evolutionary processes linking adaptation to environment are related to species’ range shifts. In this study, we employed amplified-fragment-length-polymorphism-based genome scan methods to identify candidate loci among Zingiber kawagoii populations inhabiting varying environments distributed at low to middle elevations (143–1488 m) in a narrow latitudinal range (between 21.90 and 25.30° N). Here, we show evidence of selection driving the divergence of Z. kawagoii. Twenty-six F_ST outliers were detected, which were significantly correlated with various environmental variables. The allele frequencies of nine F_ST outliers were either positively or negatively correlated with the population mean F_ST. Using several independent approaches, we found environmental variables act in a combinatorial fashion, best explaining outlier genetic variation. Nonetheless, we found that adaptive divergence was affected mostly by annual temperature range, and it is significantly positively correlated with latitude and significantly negatively correlated with the population mean F_ST. This study addresses a latitudinal pattern of changes in annual temperature range (which ranged from 13.8 °C in the Lanyu population to 18.5 °C in the Wulai population) and emphasizes the pattern of latitudinal population divergence closely linked to the allele frequencies of adaptive loci, acting in a narrow latitudinal range. Our results also indicate environmentally dependent local adaptation for both leading- and trailing-edge populations.

Population history, genetic variation, and conservation status of European white elm (Ulmus laevis Pall.) in Poland

KEY MESSAGE

The core populations of the European white elm (Ulmus laevis Pall.) located in Poland maintained slightly higher level of genetic diversity compared to the peripheral populations of this species.

CONTEXT

The most severe threat to elms is the loss of natural habitat under the pressures of agriculture and forestry as well as urbanization. The reductions in European white elm populations as well as populations of other elm species have also been caused by Dutch elm disease (DED). Previous studies have indicated a low level of genetic variation in Ulmus leavis Pall. However, in Poland, the genetic resources and demographic history of U. laevis populations remain poorly documented.

AIMS

The genetic resources of U. laevis in Poland were identified and characterized. Additionally, tests were performed to identify potential bottleneck signatures and effective population sizes of the examined populations.

METHODS

Polymorphism was analyzed using a set of six nuclear microsatellite markers (nSSRs) for 1672 individuals from 41 populations throughout the species range in Poland.

RESULTS

(1) A moderate level of genetic variation was found. (2) A low genetic differentiation and lack of population structuring were identified. (3) Evidence of reduction in population size was found as a consequence of severe, past bottlenecks.

CONCLUSION

The loss of genetic diversity of U. laevis probably occurred in their refugia or shortly after the postglacial recolonization. This loss may have been affected by past DED pandemics similar to those seen at present.

Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools

A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.

Tracking population genetic signatures of local extinction with herbarium specimens

BACKGROUND AND AIMS

Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management.

METHODS

We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations.

KEY RESULTS

Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination.

CONCLUSIONS

Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

Genetic diversity and population structure of critically endangered Dactylorhiza hatagirea (D. Don) Soo from North-Western Himalayas and implications for conservation

Dactylorhiza hatagirea (D. Don) Soo is medicinally important herb, which is widely used in ayurveda, unani, and folk/traditional medicine system to cure diseases. Due to its immense ethno-botanical properties, the trade of D. hatagirea is estimated to be USD 1 billion/year in India. Unfortunately, due to overexploitation of the herb from the wild, has resulted in dwindling of its populations in their natural habitats, which has led to its critically endangered status. Molecular genetic studies are still scarce in D. hatagirea, therefore, in current study, genetic diversity and population structure analysis was carried out of 10 populations (48 individuals) collected from three cold desert regions (2527 m-3533 m amsl) of Himachal Pradesh. Mean observed heterozygosity (Ho) and expected heterozygosity (He) was recorded 0.185 and 0.158. The maximum values for Fst (fixation index) and Nm (gene flow) were recorded 0.945 at locus KSSR14 and 1.547 at locus KSSR 4 respectively. Mean genetic differentiation (Fst) coefficient was estimated to 0.542. Overall, low levels of genetic diversity was recorded in the populations of D. hatagirea, might be due to habitat specificity (alpine meadows ecosystem; humid laden undulating habitat), restricted distribution and high anthropogenic activities. However, two populations viz., Bathad and Rangrik were recorded with high diversity and largest number of private alleles, stipulates that these populations might have high evolutionary significance and response to selection. Dendrogram analysis revealed that the populations of D. hatagirea were clustered into four major clusters, which was supported by Bayesian based STRUCTURE predictions. Clustering pattern of majority individuals of different populations revealed consistency with their geographic origin. Outcomes of current study reveals the status of genetic diversity and population structure of endangered D. hatagirea, which can be futuristically utilised for appropriate planning of conservation strategies.

Limited phylogeographic and genetic connectivity in Acacia species of low stature in an arid landscape

Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co‐distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north‐western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, G_ST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, F_ST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon‐specific life history and ecological traits to seed and pollen dispersal.

Genetic diversity and population structure of Tunisian wild Kermes oak (Quercus coccifera L.): Assessment by ISSR molecular markers and implication for conservation

BACKGROUND

In Tunisia, Kermes oak (Quercus coccifera L.) populations are severely destroyed due to deforestation. Nowadays, no preservation programs are attempted, yet, to conserve and promote the potential value of this resource. In this work, we assessed the genetic diversity of seven natural Tunisian populations of Q. coccifera from different bioclimates using Inter-Simple Sequence Repeats molecular markers. The distribution of the genetic diversity of Q. coccifera constitutes the pioneer step in the process of the conservation of the species.

METHODS AND RESULTS

Nine selected ISSR markers were analyzed to characterize the genetic profiles of 70 different genotypes. The ISSR primers produced 64 loci ranging from 6 (UBC809 and UBC810) to 9 (UBC873) with an average of 7.11 at the species level. The average percentage of the polymorphic loci varied from 64.06% (Tabarka) to 76.56% (El Haouaria). The analyzed genotypes (70 individuals) revealed a high level of genetic diversity at species level (Na = 1.697; Ne = 1.517; He = 0.289; I = 0.418). The major proportion of the variation was attributable to individual differences within populations (76.07%). Analysis of molecular variance revealed also significant differentiation among all populations (ΦST = 0.245) and among populations within bioclimates (ΦSC = 0.233), even at a low scale space. The UPGMA and the PCoA analyses showed that most populations clustered independently to bioclimate or geographical distance indicating that genetic differentiation mainly occurs at local space scale due to genetic drift.

CONCLUSIONS

The in-situ conservation of the species should be maintained on natural populations as a forest genetic resources. Moreover, ex-situ conservation should involve the selection of genotypes with extensive collection of seeds and cuttings from different populations of the target area.

Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau

Elymus sibiricus L. is a perennial allotetraploid belonging to Triticeae of Poaceae, Elymus L., as the type species of genus Elymus L. The existing geographical distribution pattern and genetic spatial structure of E. sibiricus on Qinghai-Tibetan Plateau (QTP) are not yet clear. In this study, population genetic structure and demography history of 216 individuals from 44 E. sibiricus populations on QTP were studied used specific-locus amplified fragment sequencing (SLAF-seq). The result of genetic diversity showed that there was no single genetic diversity center was observed across all E. sibiricus populations. The results of genetic variation showed that 44 populations were clearly divided into the following three groups: Qinghai Plateau (Group I), South Tibet (Group II), and Hengduan Mountains (Group III). From the three analyses of AMOVA, Mantel test and Treemix, strong genetic differentiation across all populations and low genetic differentiation among populations within three groups. Molecular dating indicated that E. sibiricus diverged at 16.08 Ma (during the early Miocene) can be linked to the Himalayan Motion stage of QTP uplift. It is speculated that the reasons affecting the current phylogeographical pattern are as follows: (1) The environmental changes due to the uplift of the QTP; (2) The geographic distance between the populations (Groups I and III are close in geographic distance, and gene flow are frequent); (3) Geographical barriers (the Tanggula and Bayangela Mountains between Groups I and II). This study provides new evidence and historical perspective to the future exploration of the evolution and geographic distribution pattern of Elymus L.

The Diversity of Melia azedarach L. from China Based on Transcriptome-Developed SSR Marker

Melia azedarach L. is a native tree species that can be used in a comprehensive way and is widely distributed in all provinces south of the Yellow River in China. Genetic diversity analysis of different M. azedarach germplasm sources is an important basic work for the selection, evaluation, and genetic improvement of M. azedarach germplasm resources. In this study, 100 pairs of SSR primers were designed and synthesized based on M. azedarach transcriptome data, and 16 pairs of reliable SSR primers were finally selected. The developed primers were used to analyze the genetic diversity of M. azedarach from 15 sources in 10 provinces in East, Central, and South China. The results showed that the frequency of the M. azedarach transcriptome SSR loci was high, and the distribution density was high. There were 15 sources of M. azedarach genetic diversity at a moderate level, and genetic variation was mainly present within the sources. The present study further enriches the existing SSR marker database of the M. azedarach family and can provide a reference for genetic diversity analysis and molecularly assisted breeding of M. azedarach plants at the genomic level.

Genetic Structure of Native Blue Honeysuckle Populations in the Western and Eastern Eurasian Ranges

Blue honeysuckle (Lonicera caerulea L.) is a promising berry crop producing edible early-ripening berries with a valuable chemical composition. We evaluated the genetic diversity of native L. caerulea populations from the western (Baltic states) and eastern (the Russian Far East and Japan) edges of the Eurasian range using inter-simple sequence repeat (ISSR) and chloroplast DNA (psbA-trnH and trnL-trnF) markers. The genetic relationships of populations and genotypes were analyzed using principal coordinate and cluster analyses (neighbor joining and Bayesian clustering). Sampling was carried out in two disjunct areas of this circumpolar species and the analyses showed clustering of individuals and populations according to geographic origin. The analysis of genetic structure based on ISSR markers showed that the studied populations of L. caerulea were highly differentiated. However, sequence analysis of two chloroplast DNA (cpDNA) regions revealed no phylogeographic structure among the populations. We also found that the eastern populations of blue honeysuckle had significantly greater genetic diversity parameters than the populations from the Baltic region. This finding correlates with the endangered status of blue honeysuckle in the Baltic states.