Unravelling the genetic diversity and population structure of common walnut in the Iranian Plateau

BACKGROUND

Common walnut (Juglans regia L.) has a long cultivation history, given its highly valuable wood and rich nutritious nuts. The Iranian Plateau has been considered as one of the last glaciation refugia and a centre of origin and domestication for the common walnut. However, a prerequisite to conserve or utilize the genetic resources of J. regia in the plateau is a comprehensive evaluation of the genetic diversity that is conspicuously lacking. In this regard, we used 31 polymorphic simple sequence repeat (SSR) markers to delineate the genetic variation and population structure of 508 J. regia individuals among 27 populations from the Iranian Plateau.

RESULTS

The SSR markers expressed a high level of genetic diversity (H_O = 0.438, and H_E = 0.437). Genetic differentiation among the populations was moderate (F_ST = 0.124), and genetic variation within the populations (79%) significantly surpassed among populations (21%). The gene flow (N_m = 1.840) may have remarkably influenced the population genetic structure of J. regia, which can be attributed to anthropological activities and wind dispersal of pollen. The STRUCTURE analysis divided the 27 populations into two main clusters. Comparing the neighbor-joining and principal coordinate analysis dendrograms and the Bayesian STRUCTURE analysis revealed the general agreement between the population subdivisions and the genetic relationships among the populations. However, a few geographically close populations dispersed into different clusters. Further, the low genetic diversity of the Sulaymaniyah (SMR) population of Iraq necessitates urgent conservation by propagation and seedling management or tissue culture methods; additionally, we recommend the indispensable preservation of the Gonabad (RGR) and Arak (AKR) populations in Iran.

CONCLUSIONS

These results reflected consistent high geographical affinity of the accession across the plateau. Our findings suggest that gene flow is a driving factor influencing the genetic structure of J. regia populations, whereas ecological and geological variables did not act as strong barriers. Moreover, the data reported herein provide new insights into the population structure of J. regia germplasm, which will help conserve genetic resources for the future, hence improving walnut breeding programs' efficiency.

Dataset on estimate of intra-specific genetic variability of African yam bean (Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms.) based on rbcL gene marker

African yam bean (Sphenostylis stenocarpa (Hochst. ex A. Rich.) Harms.) (Fabaceae) is a versatile crop of nutritional, nutraceutical, and pharmacological value widely grown for its edible seeds and underground tubers. Its high-quality protein, rich mineral elements, and low cholesterol make it a suitable source of food for age groups. However, the crop is still under-exploited and constrained by factors such as intra-specific incompatibility, low yields, indeterminate growth pattern and long gestation period, hard-to-cook (HTC) seeds, and the presence of antinutritional factors (ANFs). To efficiently utilize its genetic resources for improvement and utilization, it is necessary to understand the crop's sequence information and select promising accessions for molecular hybridization trials and conservation purposes. A total of 24 accessions of AYB were collected from the Genetic Resources center of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria, and subjected to PCR amplification and Sanger sequencing. The dataset determines genetic relatedness among the twenty-four accessions of AYB. The data consist of partial rbcL gene sequences (24), estimates of intra-specific genetic diversity, the maximum likelihood of transition/transversion bias, and evolutionary relationships based on the UPMGA clustering method. The data identified 13 variables (segregating sites) as SNPs, 5 haplotypes, and codon usage of the species that can be explored further to advance the genetic utilization of AYB.

Cryopreserved-pollen viability is regulated by NO-induced programmed cell death

After cryopreservation, the NO content in pollen increased, inducing programmed cell death as a key reason for reduced viability. Low recovery of biomaterials after cryopreservation is a bottleneck that limits the application of this technology. At present, the mechanism of viability decline after cryopreservation is not fully understood. In this study, the effects of nitric oxide (NO) on programmed cell death (PCD) and its relationship with viability were investigated, using Paeonia lactiflora 'Fen Yu Nu' pollen with significantly decreased viability after cryopreservation. The results showed that: the activity of caspase-3-like and caspase-9-like protease and the apoptosis rate of pollen cells were significantly increased, the expression level of the promoting PCD (pro-PCD) genes was up-regulated, while the expression level of the inhibiting PCD (anti-PCD) genes was down-regulated after preservation in liquid nitrogen (LN); the NO content in pollen cells increased significantly after LN exposure. The correlation analysis showed that NO was significantly correlated with pollen viability and all indicators of PCD. The addition of a NO carrier SNP after LN storage reduced pollen viability, increased endogenous NO content, decreased mitochondrial membrane potential level, activated caspase-3-like and caspase-9-like protease in pollen cells, and increased cell apoptosis rate. The expression levels of pro-PCD genes PDCD2 and ATG8CL were significantly up-regulated, while the expression levels of anti-PCD genes DAD1, BI-1 and LSD1 were significantly down-regulated. The addition of NO scavenger c-PTIO improved pollen viability, and produced the opposite effect of sodium nitroferricyanide (III) dihydrate (SNP), but did not change the mitochondrial membrane potential. These results suggest that NO induced PCD during the cryopreservation of pollen, which was one of the reasons for the significant decrease of pollen viability after cryopreservation.

Cryopreservation of margay (Leopardus wiedii) spermatozoa: Effects of different extenders and frozen protocols

Sperm cryopreservation offers many benefits to wild felids conservation programs. However, the implementation of these programs is limited by the different responses of each species to the cryopreservation protocols and extenders used, requiring the formulation of species-specific protocols. For this purpose, semen samples from 6 margays (Leopardus wiedii) were submitted to 2 cryopreservation protocols: 1) manual freezing (cooling rate of - 0.33 °C/min at 5 °C/180 min and freezing rate with two steps - 9 °C/min for 2 min and -19.1 °C/min for 2 min) and 2) automatic freezing machine (cooling rate of - 0.25 °C/min at 5 °C/120 min and freezing rate with one step -20 °C/min for 8.3 min) using 2 commercial extenders, an egg yolk-based (Test Yolk Buffer; TYB) and an egg yolk-free extender (AndroMed; MED). Post-thawed sperm quality was assessed at 3 time points (immediately after thawing and 1 and 2 h post-thawed) by sperm motility index (SMI), plasma membrane and acrosomal integrity, and mitochondrial membrane potential (MMP). Regarding SMI, TYB yielded superior results (29.4 ± 3.5%) compared to MED (11.2 ± 2.8%; p < 0.002) immediately after thawing until 2 h after thawing (TYB 3.9 ± 1.7% and MED 0.0 ± 0.0%; p < 0.05). Furthermore, the automated freezing method provided higher motility compared to the manual freezing procedure immediately post-thaw (25.08 ± 3.66% and 15.78 ± 3.29%, respectively) and 1 h post-thaw (13.71 ± 2.56% and 6.03 ± 1.97%, respectively; p < 0.05). The percentage of intact acrosomes and plasma membranes and the percentage of sperm with high MMP were superior for TYB when compared to MED regardless of cryopreservation protocol (p < 0.05). Conversely, the interaction between cryopreservation protocols and extenders was observed for MMP where TYB exhibits better results compared to MED (p < 0.05) in both procedures, but it was higher in automated procedures. For MED, no changes were found in MMP between procedures. Considering only TYB, samples showed higher MMP when submitted to an automated procedure (p < 0.05). In conclusion, the slow cooling rates with shorter time of exposure to glycerol contributed to minimize cryodamage in the Margays' sperm. Moreover, results indicated that association between TYB and automatic freezing machine ensured the minimal quality of spermatozoa after thawing required for further use in in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI).

Structural aspects of cypsela and seed development of Trichocline catharinensis (Cabrera): a Brazilian endemic species

This is the first study to describe in a timescale morphohistological and ultrastructural characteristics of fruit (cypsela) and seed development in Trichocline catharinensis, which was completed 21 days after anthesis (DAA). At anthesis, we identified an ovary with three differentiated regions, including the inner epidermis, inner part, and outer epidermis. The mature ovule showed an integument with the outer epidermis, integumentary parenchyma, and endothelium. Cells around the endothelium form the periendothelial zone with thick cell walls that showed Periodic acid-Schiff (PAS)-positive reaction. The periendothelial zone and endothelium showed degradation of the cells during embryogenesis. The main stages of embryo development from fecundation through mature seed were identified. The ripe cypsela showed the pericarp (exocarp), seed coat (exotesta), and remaining endosperm surrounding the embryo. Mature embryos were straight with shoot apical meristem (SAM), and root apical meristem (RAM) was separated by the hypocotyl. Light microscopy (LM) and transmission electron microscopy (TEM) analyses indicate cells with characteristics of meristem cells, as well as proteins and lipid bodies and mitochondria with few cristae in cotyledon cells. Our findings provide insight into taxonomic and physiological studies by detailing cypsela and seed ontogenesis from an endemic and vulnerable Asteraceae from southern Brazil. This study is also a starting point for establishing the biological criteria for seed harvesting and future studies of seed physiology and conservation of plant genetic resource.

The retrospect and prospect of the applications of biotechnology in Phoenix dactylifera L

Date palm (Phoenix dactylifera L.) is one of the most important fruit trees that contribute a major part to the economy of Middle East and North African countries. It is quintessentially called "tree of life" owing to its resilience to adverse climatic conditions, along with manifold nutritional-cum-medicinal attributes that comes from its fruits and other plant parts. Being a tree with such immense utility, it has gained substantial attention of tree breeders for its genetic advancement via in vitro biotechnological interventions. Herein, an extensive review of biotechnological research advances in date palm has been consolidated as one of the major research achievements during the past two decades. This article compares the different biotechnological techniques used in this species such as: tissue and organ culture, bioreactor-mediated large-scale propagation, cell suspension culture, embryogenic culture, protoplast culture, conservation (for short- and long-term) of germplasms, in vitro mutagenesis, in vitro selection against biotic and abiotic stresses, secondary metabolite production in vitro, and genetic transformation. This review provides an insight on crop improvement and breeding programs for improved yield and quality fruits; besides, it would undeniably facilitate the tissue culture-based research on date palm for accelerated propagation and enhanced production of quality planting materials, along with conservation and exchange of germplasms, and genetic engineering. In addition, the unexplored research methodologies and major bottlenecks identified in this review should be contemplated on in near future.

In Vitro Propagation and Conservation of Withania somnifera (Dunal) L

Plant tissue culture offers several techniques for rapid clonal propagation, germplasm conservation, regeneration of genetically manipulated superior clones, production of phyto-constituents, and ex vitro conservation of valuable phytodiversity. An improved and efficient micropropagation protocol for Withania somnifera (L.), a drug-producing medicinal plant, using juvenile explants (nodal explants) has been developed. Highest multiplication and subsequent elongation of shoots is observed on MS medium containing BA and NAA. The regenerated microshoots roots best on ½ MS medium containing NAA, established in earthen pots containing garden soil and are maintained in the greenhouse with 95 % survival rate. Genetic uniformity of micropropagated plants is confirmed by PCR-based DNA fingerprinting techniques, viz., RAPD and ISSR. No variation is observed in DNA fingerprinting patterns among the micropropagated plants, which are similar to that of the donor plant illustrating their genetic uniformity.

Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation

Background

The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia.

Results

In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity.

Conclusion

The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0505-7) contains supplementary material, which is available to authorized users.

The inheritance of wheat grain longevity: a comparison between induced and natural ageing

Seed longevity is an important trait for both ex situ genebanks and the seed industry. It is partially determined by genetic factors, but is also dependent on the environmental conditions experienced by the mother plant during seed maturation, as well as those imposed during the post-harvest and storage periods. For practical reasons, the variation in longevity has repeatedly been analysed by treating fresh seed to various induced ageing protocols, but the extent to which these procedures mimic the natural ageing process remains debatable. Here, a comparison was attempted between the wheat genomic regions identified by biparental mapping as harbouring determinants of viability loss identified in grain which had been either aged artificially or had been stored long term. Only one locus proved to be shared, but even here, the parental origin of the positive allele differed. Correlation analysis revealed no relationship between various induced ageing treatments and long-term storage.

Somatic Embryogenesis in Araucaria angustifolia (Bertol.) Kuntze (Araucariaceae)

This chapter deals with the features of somatic embryogenesis (SE) in Araucaria angustifolia, an endangered and native conifer from south Brazil. In this species SE includes the induction and proliferation of embryogenic cultures composed of pro-embryogenic masses (PEMs), which precede somatic embryos development. A. angustifolia SE model encompasses induction, proliferation, pre-maturation, and maturation steps. Double-staining with acetocarmine and Evan's blue is useful to evaluate the embryonic somatic structures. In this chapter we describe A. angustifolia SE protocols and analyzes morphological features in the different SE developmental stages.

Tissue culture and associated biotechnological interventions for the improvement of coconut (Cocos nucifera L.): a review

The present review discusses not only advances in coconut tissue culture and associated biotechnological interventions but also future research directions toward the resilience of this important palm crop. Coconut (Cocos nucifera L.) is commonly known as the 'tree of life'. Every component of the palm can be used to produce items of value and many can be converted into industrial products. Coconut cultivation faces a number of acute problems that reduce its productivity and competitiveness. These problems include various biotic and abiotic challenges as well as an unstable market for its traditional oil-based products. Around 10 million small-holder farmers cultivate coconut palms worldwide on c. 12 million hectares of land, and many more people own a few coconut palms that contribute to their livelihoods. Inefficiency in the production of seedlings for replanting remains an issue; however, tissue culture and other biotechnological interventions are expected to provide pragmatic solutions. Over the past 60 years, much research has been directed towards developing and improving protocols for (i) embryo culture; (ii) clonal propagation via somatic embryogenesis; (iii) homozygote production via anther culture; (iv) germplasm conservation via cryopreservation; and (v) genetic transformation. Recently other advances have revealed possible new ways to improve these protocols. Although effective embryo culture and cryopreservation are now possible, the limited frequency of conversion of somatic embryos to ex vitro seedlings still prevents the large-scale clonal propagation of coconut. This review illustrates how our knowledge of tissue culture and associated biotechnological interventions in coconut has so far developed. Further improvement of protocols and their application to a wider range of germplasm will continue to open up new horizons for the collection, conservation, breeding and productivity of coconut.

Population structure and genotypic variation of Crataegus pontica inferred by molecular markers

Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

Phytochemical diversity of the essential oils of Mexican Oregano (Lippia graveolens Kunth) populations along an Edapho-climatic gradient

Mexican oregano (Lippia graveolens) is an important aromatic plant, mainly used as flavoring and usually harvested from non-cultivated populations. Mexican oregano essential oil showed important variation in the essential-oil yield and composition. The composition of the essential oils extracted by hydrodistillation from 14 wild populations of L. graveolens growing along an edaphoclimatic gradient was evaluated. Characterization of the oils by GC-FID and GC/MS analyses allowed the identification of 70 components, which accounted for 89-99% of the total oil composition. Principal component and hierarchical cluster analyses divided the essential oils into three distinct groups with contrasting oil compositions, viz., two phenolic chemotypes, with either carvacrol (C) or thymol (T) as dominant compounds (contents >75% of the total oil composition), and a non-phenolic chemotype (S) dominated by oxygenated sesquiterpenes. While Chemotype C was associated with semi-arid climate and shallower and rockier soils, Chemotype T was found for plants growing under less arid conditions and in deeper soils. The plants showing Chemotype S were more abundant in subhumid climate. High-oil-yield individuals (>3%) were identified, which additionally presented high percentages of either carvacrol or thymol; these individuals are of interest, as they could be used as parental material for scientific and commercial breeding programs.

Cryopreservation of in vitro-grown shoot-tips of hop (Humulus lupulus L.) using encapsulation/dehydration

 A cryopreservation procedure using encapsulation/dehydration was established for shoot-tips obtained from in vitro-grown shoots of hop. After dissection, shoot-tips were encapsulated in medium with alginate and 0.5 M sucrose. Optimal conditions consisted of preculture for 2 days in solid medium with 0.75 M sucrose, or in increasing sucrose concentrations, desiccation for 4 h with silicagel in a flow cabinet (16% water content) followed by rapid freezing and slow thawing. Shoot recovery after freezing 60 min in liquid nitrogen was around 80%. No phenotypical changes were observed in the recovered plants from cryopreserved shoot-tips growing in the field.

Cryopreservation and storage of embryogenic callus cultures of several Citrus species and cultivars

Nucellus-derived embryogenic callus cultures of Salustiana sweet orange were subjected to cryoconservation assays. Cryoprotection with 10%(vol/vol) dimethylsulfoxide, freezing by slow cooling and thawing by fast warming was suitable to recover viable growing cultures and whole plants through embryogenesis. Evaluation of liquid phase R ₁ and solid phase R ₂ cooling rates using a programmable freezing unit indicated that 100% of embryogenic cultures survived when frozen using a range of cooling rates (R ₁ not above 0.5°C min^-1 and R ₂ not above 1°C min ¹) and thawed by fast warming. Storage up to 2 years in liquid nitrogen did not affect the growth of the cryopreserved cultures and the recovery of whole plants. Cultures of four cultivars of sweet orange (C. sinensis Osb.), three cultivars of grapefruit (C. paradisi Macf.), and one cultivar each of lemon [C. limon (L.) Burm. f.], Cleopatra mandarin (C. reshni Hort. ex Tan.), sour orange (C. aurantium L.) and Mexican lime [C. aurantifolia (Christm.) Swing.] have been successfully cryopreserved. Problems using a viability assessment using fluorescein diacetate staining are discussed.

Germplasm conservation of the tropical forest trees,Cedrela odorata L.,Guazuma crinita Mart., andJacaranda mimosaefolia D. Don., by shoot tip encapsulation in calcium-alginate and storage at 12-25°C

Germplasm conservation of the tropical forest trees,Cedrela odorata L.,Guazuma crinita Mart., andJacaranda mimosaefolia D. Don., at above-freezing temperatures following alginate-bead encapsulation was attempted. Shoot tips excised from in vitro plantlets were encapsulated in calcium-alginate beads and stored on different substrates at 12, 20, and 25 °C. Percent viability when encapsulated shoot tips were stored on substrate containing only water solidified with 1% (wt/vol) agar was 80% after 12 months at 12°C forC. odorata, 90% after 12 months at 25°C forG. crinita, and 70% after 6 months at 20°C forJ. mimosaefolia.