Assessment of genetic diversity in the endangered populations of Breonadia salicina (Rubiaceae) growing in the kingdom of Saudi Arabia using inter-simple sequence repeat markers

Genetic diversity and population structure of Euscaphis japonica, a monotypic species

Background

Understanding plant genetic diversity is important for effective conservation and utilization of genetic resources. Euscaphis japonica (Thunb.) Dippel, is a monotypic species with high phenotypic diversity, narrow distribution, and small population size. In this study, we estimated the genetic diversity and population structure of E. japonica using nine natural populations and inter-simple sequence repeat (ISSR) markers. Our results could provide a theoretical reference for future conservation and utilization of E. japonica.

Results

We obtained a total of 122 DNA bands, of which 121 (99.18%) were polymorphic. The average number of effective alleles (Ne = 1.4975), Nei’s gene diversity index (H = 0.3016), and Shannon’s information index (I = 0.4630) revealed that E. japonica possessed a high level of genetic diversity. We observed that E. japonica consisted of both deciduous and evergreen populations. UPGMA tree showed that the evergreen and deciduous E. japonica form a sister group. There is little genetic differentiation among geographic populations based on STRUCTURE analysis. The Dice’s similarity coefficient between the deciduous and evergreen populations was low, and the Fst value was high, indicating that these two types of groups have high degree of differentiation.

Conclusion

Rich genetic diversity has been found in E. japonica, deciduous E. japonica and evergreen E. japonica populations, and genetic variation mainly exists within the population. The low-frequency gene exchange between deciduous and evergreen populations may be the result of the differentiation of deciduous and evergreen populations. We suggest that in-situ protection, seed collection, and vegetative propagation could be the methods for maintenance and conservation of E. japonica populations.

ISSR Characterization and Quantification of Purpurin and Alizarin in Rubia cordifolia L. Populations from India

Rubia cordifolia L., is an industrially viable medicinal crop and is widely exploited for the therapeutic potential of its bioactive metabolite, purpurin. The present investigation aimed to explore the chemotypic and molecular variability in seven wild populations of R. cordifolia from South Eastern Ghats region of India. Thirty-eight individuals were assessed for molecular fingerprinting (ISSR markers) and densitometric quantification of purpurin and alizarin. The populations of Yelagiri Hills and Shervaroy Hills contained the highest levels of alizarin (0.115 and 0.093%, respectively) while Pachamalai and Kolli Hills revealed the highest purpurin content (0.284 and 0.280%, respectively). Genetic diversity was generally higher in the same populations that produced higher metabolite content, with the exception of Pachamalai, suggesting a highly prioritized conservation concern. The study revealed a Nei's total gene diversity at species level of 0.266 and of 0.187 at population level, with an average population genetic differentiation of 0.28. No clear genetic or chemical structure was retrieved between the studied populations, with individuals from different locations clustering together, and no significant correlation was obtained between metabolites and genetic diversity or between these and the populations' geographic distances.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Genetic diversity and population structure of Haloxylon salicornicum moq. in Kuwait by ISSR markers

Haloxylon salicornicum moq. Bunge ex Boiss (Rimth) is one of the native plants of Kuwait, extensively depleting through the anthropogenic activities. It is important to conserve Haloxylon community in Kuwait as it can tolerate extreme adverse conditions of drought and salinity to be potentially used in the desert and urban revegetation and greenery national programs. Therefore, a set of 16 inter simple sequence repeat (ISSR) markers were used to assess genetic diversity and population structure of 108 genotypes from six locations in Kuwait. The ISSR primers produced 195 unambiguous and reproducible bands out of which 167 bands were polymorphic (86.5%) with a mean PIC value of 0.31. The overall average values of Nei’s gene diversity (h') and Shannon’s diversity index (I) were 0.254 and 0.375, respectively. Results of AMOVA revealed high genetic variations within populations (77.8%) and low among populations (22%). The values of Fixation index (F_ST = 0.22; P = 0.0), Genetic differentiation (G_{ST =} 0.262; G’_ST = 0.327; D = 0.335 and Gene flow (N_M = 0.880) were indicative of heterozygous populations. The results of STRUCTURE and split decomposition analysis suggested that the Rimth accessions of Kuwait can be grouped into five and six subpopulations, respectively. Principal coordinate analysis (PCoA) grouped them into three clusters. The pairwise Nei’s genetic distances (D_S) among populations demonstrated a narrow range from 0.047 to 0.187 (Scale-0.0 to 1.0). The Mantel’s test revealed a weak correlation (r²- 0.188; P-0.013) between the genetic distance and geographic distances. Our results suggest that the narrowly distributed Haloxylon community in Kuwait demonstrated a high genetic diversity within the populations however the overall population structure was weak.

Genetic diversity and population structure of Litsea glutinosa (Lour.) in Central India

Litsea glutinosa (Lour.), one of the most dwindling forest species in central India, is represented by highly fragmented populations that have been drastically reduced for the last 40 years, promulgating government ban on its extraction. For the first time with the help of ISSR markers, we investigated genetic variation and population structure of L. glutinosa in central Indian states. A total of 84 genotypes from 10 populations covering the entire potential pockets of the species in central India were collected. The percentage of polymorphic loci ranged from 44.79% (Rewa) to 94.79% (Marvahi) with a mean value of 70.10%. The sampled populations harbored high level of genetic diversity (mean h = 0.294 and I = 0.424) that was partitioned more within populations (73%) than between populations (27%). Bayesian structure analysis revealed the existence of four admixed genetic pools in L. glutinosa. The unsustainable extraction rather than genetic factor seems to be responsible for population fragmentation and dwindling status of this species. The dioecious nature of the species advocates an in-situ conservation to be the most suited approach for which Chhindwara, Jagdalpur, Balaghat and Jabalpur populations are appropriate.

Genetic diversity and ex situ conservation of Loropetalum subcordatum, an endangered species endemic to China

Background

Loropetalum subcordatum is an endangered species endemic to China that is characterized by narrow distribution, small population size, and delayed fertilization. However, the genetic diversity of the entire extant natural and ex situ populations has not been assessed to date. In this study, we evaluated the genetic diversity and structure of six natural populations and a single ex situ population (the only known ex situ population of L. subcordatum) using sequence-related amplified polymorphism data.

Results

In total, 553 reliable DNA bands, of which 359 (63.28%) were polymorphic, were amplified by polymerase chain reaction with combinations of 15 primers. Low average gene diversity within populations and high genetic differentiation were detected in L. subcordatum. A Mantel test demonstrated that there was a positive correlation between genetic and geographic distances, indicating that significant genetic divergence was likely the result of geographic isolation among natural populations. Furthermore, based on genetic structure patterns, populations of L. subcordatum were divided into three clusters. Group 1 was composed of specimens from Libo, Guizhou Province (GZ) and Huanjiang, Guangxi Zhuang Autonomous Region (GX). Group 2 was composed of Mt. Wuguishan, Guangdong Province (GD). Group 3 was composed of three populations in Hong Kong Special Administrative Region. Additionally, clonal reproduction probably existed in GD population. According to the genetic information analysis and field survey, the ex situ population did not match its source population (GD) in terms of genetics, and its habitat was different from the original natural habitat. We observed that a few individual GD seeds were needed to improve ZS ex situ in the future.

Conclusions

Compared to previous SRAP-based studies of endangered plants, L. subcordatum had extremely low average gene diversity within populations and high genetic differentiation among populations. At present, the unique ex situ population has not been successful due to non-representative samples being taken, a smaller population size, and man-made changes in habitat. Potential strategies are suggested to improve the conservation of this species.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0599-6) contains supplementary material, which is available to authorized users.

Identification and sequencing of Date-SRY Gene: A novel tool for sex determination of date palm (Phoenix dactylifera L.)

Dioecism has always been an issue in many plant species with its numerous disadvantages, especially in woody trees such as date palms. As one of the most important crops in the Middle Eastern countries, researchers are having problems identifying of sex of the plant in its early stages of development. Hence, proper population stands in the male: female ratio for maintenance is almost impossible in the field for better production. In this study, sex determination of date palm (Phoenix dactilyfera L.) were identified in regions of the Y chromosome (Date-SRY) gene, the pivotal gene that initiates sex determination, using a new technique and thus an economically desirable objective, which will significantly impact profits in seed based cultivations. Partial sequences of the Date-SRY were taken and amplified by nested polymerase chain reaction (PCR). According to the results, the exact sex of date palm was identified in all the tested plants, while amplified regions of the Date-SRY gene closely matched with the human and papaya sequences. In addition, a primer pair was designed to amplify the sequences of the SRY-date gene with confidence that it will identify male date palms. These primer sequences include SRY-date Forward 5'- cggccctctaagtatctgtgcgcaacg-3' (SRY-date F) and the SRY-date Reverse 5'- gtttgcacttcgaagcagag-3' (SRY-date R). The complete sequence of the DNA has been registered and deposited in GenBank (BankIt1598036 DPSRY1 KC577225 thenKJ873056).

Photosynthetic, morphological, and reproductive variations in Cypripedium tibeticum in relation to different light regimes in a subalpine forest

Cypripedium tibeticum, a subalpine orchid species, inhabits various habitats of subalpine forests, mainly including the forest edge (FE), forest gap (FG), and understory (UST), which have significantly different light intensities (FE > FG > UST). However, the ecological and physiological influences caused by different light regimes in this species are still poorly understood. In the present study, photosynthetic, morphological, and reproductive characteristics were comprehensively studied in plants of C. tibeticum grown in three types of habitats. The photosynthetic capacities, such as the net photosynthetic rate, light-saturated photosynthesis (Pmax), and dry mass per unit leaf area (LMA), were higher in FE and FG than in UST according to light availability. Compared with FG, the populations in FE and UST suffer from excessively strong and inadequate radiation, respectively, which was further corroborated by the low Fv/Fm in FE and high apparent quantum yield (AQY) in FG. The leaves of the orchids had various proportions of constituents, such as the leaf area, thickness and (or) epidermal hair, to reduce damage from high radiation (including ultraviolet-b radiation) in FE and capture more light in FG and UST. Although the flower rate (FR) was positively correlated to both Pmax and the daily mean PAR, fruit-set only occurred in the populations in FG. The failures in FE and UST might be ascribed to changes in the floral functional structure and low biomass accumulation, respectively. Moreover, analysis of the demographic statistics showed that FG was an advantageous habitat for the orchid. Thus, C. tibeticum reacted to photosynthetic and morphological changes to adapt to different subalpine forest habitats, and neither full (under FE) nor low (UST) illumination was favorable for population expansion. These findings could serve as a guide for the protection and reintroduction of C. tibeticum and emphasize the importance of specific habitats for Cypripedium spp.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

BACKGROUND

Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population's ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population's adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).

METHODS

The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.

RESULTS

SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and Φ PT for SSR (20%) and Φ PT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.

CONCLUSIONS

The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

Molecular Identification of Sex in Phoenix dactylifera Using Inter Simple Sequence Repeat Markers

Early sex identification of Date Palm (Phoenix dactylifera L.) at seedling stage is an economically desirable objective, which will significantly increase the profits of seed based cultivation. The utilization of molecular markers at this stage for early and rapid identification of sex is important due to the lack of morphological markers. In this study, a total of two hundred Inter Simple Sequence Repeat (ISSR) primers were screened among male and female Date palm plants to identify putative sex-specific marker, out of which only two primers (IS_A02 and IS_A71) were found to be associated with sex. The primer IS_A02 produced a unique band of size 390 bp and was found clearly in all female plants, while it was absent in all male plants. Contrary to this, the primer IS_A71 produced a unique band of size 380 bp and was clearly found in all male plants, whereas it was absent in all the female plants. Subsequently, these specific fragments were excised, purified, and sequenced for the development of sequence specific markers further in future for the implementation on dioecious Date Palm for sex determination. These markers are efficient, highly reliable, and reproducible for sex identification at the early stage of seedling.