Genetic relatedness of Portuguese almond cultivars assessed by RAPD and ISSR markers

Plant height variation and genetic diversity between Prunus ledebouriana (Schlecht.) YY Yao and Prunus tenella Batsch based on using SSR markers in East Kazakhstan

Background

Genetic differences between isolated endemic populations of plant species and those with widely known twin species are relevant for conserving the biological diversity of our planet's flora. Prunus ledebouriana (Schlecht.) YY Yao is an endangered and endemic species of shrub almond from central Asia. Few studies have explored this species, which is closely related and morphologically similar to the well-known Prunus tenella Batsch. In this article, we present a comparative analysis of studies of three P. ledebouriana populations and one close population of P. tenella in Eastern Kazakhstan in order to determine the particular geographic mutual replacement of the two species.

Methods

The populations were collected from different ecological niches, including one steppe population near Ust-Kamenogorsk (P. tenella) and three populations (P. ledebouriana) in the mountainous area. Estimation of plant height using a t-test suggested a statistically significant difference between the populations and the two species (P < 0.0001). DNA simple sequence repeat (SSR) markers were applied to study the two species' genetic diversity and population structure.

Results

A total of 19 polymorphic SSR loci were analyzed, and the results showed that the population collected in mountainous areas had a lower variation level than steppe populations. The highest level of Nei's genetic diversity index was demonstrated in the 4-UK population (0.622) of P. tenella. The lowest was recorded in population 3-KA (0.461) of P. ledebouriana, collected at the highest altitude of the four populations (2,086 meters above sea level). The total genetic variation of P. ledebouriana was distributed 73% within populations and 27% between populations. STRUCTURE results showed that two morphologically similar species diverged starting at step K = 3, with limited population mixing. The results confirmed the morphological and genetic differences between P. tenella and P. ledebouriana and described the level of genetic variation for P. ledebouriana. The study's results proved that the steppe zone and mountain altitude factor between P. tenella and isolated mountain samples of P. ledebouriana.

Genetic Stability, Phenolic, Flavonoid, Ferulic Acid Contents, and Antioxidant Activity of Micropropagated Lycium schweinfurthii Plants

Lycium schweinfurthii is a Mediterranean wild shrub rich in plant secondary metabolites. In vitro propagation of this plant may support the production of valuable dietary supplements for humanity, introduction of it to the world market, and opportunities for further studies. The presented study aimed to introduce an efficient and reproducible protocol for in vitro micropropagation of L. schweinfurthii and assess the genetic stability of micropropagated plants (MiPs) as well as to estimate phenolic, flavonoid, ferulic acid contents, and the antioxidant activity in leaves of micropropagated plants. Two DNA-based techniques, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR), and one biochemical technique, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), were used to assess the genetic stability in MiPs. Spectrophotometric analysis was performed to estimate total phenolic and flavonoid contents and antioxidant activity of MiPs leaves, while ferulic acid content was estimated using high-performance thin-layer chromatography (HPTLC). Sufficient shoot proliferation was achieved at MS (Murashige and Skoog) medium supplemented with 0.4 mg L^-1 kinetin and rooted successfully on half-strength MS medium fortified with 0.4 mg L^-1 Indole-3-butyric acid (IBA). The Jaccard's similarity coefficients detected in MiPs reached 52%, 55%, and 82% in the RAPD, ISSR, and SDS-PAGE analyses, respectively. In the dried leaves of MiPs, the phenolic, flavonoid, and ferulic acid contents of 11.53 mg gallic acid equivalent, 12.99 mg catechin equivalent, and 45.52 mg were estimated per gram, respectively. However, an IC₅₀ of 0.43, and 1.99 mg mL^-1 of MiP dried leaves' methanolic extract was required to scavenge half of the DPPH, and ABTS free radicals, respectively. The study presented a successful protocol for in vitro propagation of a valued promising plant source of phenolic compounds.

High-resolution magic angle spinning nuclear magnetic resonance (HR-MAS-NMR) as quick and direct insight of almonds

Almonds are the tasty seeds of Prunus dulcis plants globally appreciated for the pleasant palatability and remarkable nutritional value, therefore it is very spread as snack and as basic ingredient of the confectionery products. The HR-MAS-NMR is a simple spectroscopy able to directly and quickly explore the chemical composition of powdered seed samples dispersed in D₂O. ¹H spectra witness the remarkable presence of triglyceride fatty esters together with sucrose; other minor water soluble metabolites are also detectable. This very rough approach is effectively providing chemical profiles featuring almond samples. In this analysis we were able to statistically distinguish the "Avola" almonds from other marketed products submitted to the same analysis. This is just a first investigation based on the main compounds but it might pave the way toward the quantitative evaluation of many other compounds in the almond therefore implementing the HR-MAS-NMR knowledge of these precious seeds.

Production of interspecific hybrids between commercial cultivars of the eggplant (Solanum melongena L.) and its wild relative S. torvum

Interspecific hybrids between cultivars of eggplant (Solanum melongena L.) and its wild relative S. torvum, which has disease resistance and desirable traits for crop improvement, were obtained by cross-hybridization and embryo rescue. Twenty-one hybrid progenies were obtained and examined based on morphological traits, RAPD and ISSR markers. Five of them were confirmed to be true interspecific hybrids. Eighteen and 14 bands from 7 RAPD and 14 ISSR primers, respectively, were polymorphic and present in all five hybrid seedlings and their parents. The morphological characteristics of leaf margin, inflorescence type and spine positions of the five seedlings were intermediate to the parents. These interspecific hybrids had low pollen viability, probably due to abnormal meiosis.

Supervised chemical pattern recognition in almond ( Prunus dulcis ) Portuguese PDO cultivars: PCA- and LDA-based triennial study

Almonds harvested in three years in Trás-os-Montes (Portugal) were characterized to find differences among Protected Designation of Origin (PDO) Amêndoa Douro and commercial non-PDO cultivars. Nutritional parameters, fiber (neutral and acid detergent fibers, acid detergent lignin, and cellulose), fatty acids, triacylglycerols (TAG), and tocopherols were evaluated. Fat was the major component, followed by carbohydrates, protein, and moisture. Fatty acids were mostly detected as monounsaturated and polyunsaturated forms, with relevance of oleic and linoleic acids. Accordingly, 1,2,3-trioleoylglycerol and 1,2-dioleoyl-3-linoleoylglycerol were the major TAG. α-Tocopherol was the leading tocopherol. To verify statistical differences among PDO and non-PDO cultivars independent of the harvest year, data were analyzed through an analysis of variance, a principal component analysis, and a linear discriminant analysis (LDA). These differences identified classification parameters, providing an important tool for authenticity purposes. The best results were achieved with TAG analysis coupled with LDA, which proved its effectiveness to discriminate almond cultivars.

Functional characterization of two almond C-repeat-binding factors involved in cold response

Low temperature plays a crucial role in seasonal development of woody plants and may directly impact crop production, more particularly in temperate fruit trees. Given its high genetic variability and adaptability to different climatic conditions, almond (Prunus dulcis Mill.) is an interesting model to understand the mechanisms regulating low temperature sensing in fruit trees. In this paper, we report the cloning and characterization of two genes (PdCBF1 and PdCBF2) belonging to the C-repeat-binding factor (CBF) family of transcription factors. Southern blotting analysis showed that this family is composed of at least five members. In almond shoots propagated in vitro, transcription of these genes was rapidly induced by low temperature, suggesting an involvement in cold acclimation. Transactivation assays showed that PdCBF1 and PdCBF2 could bind to dehydration responsive element/C-repeat containing sequences, as activators of gene expression. In addition, induction of both PdCBFs by cold was higher towards the end of the day, which agreed with the expression pattern of PdDehydrin1, a predicted CBF target gene. Furthermore, PdCBF1 and PdCBF2 were also transiently induced by abscisic acid and drought treatments. Considering the bin mapping analysis that correlated PdCBFs and PdDHN1 (respectively in linkage groups 5 and 7) with two different quantitative trait locicontrolling blooming time, it is relevant to perform further association studies that may validate their effect on this trait.

Comparison of RAPD and ISSR markers for assessment of genetic diversity among endangered rare Dalbergia oliveri (Fabaceae) genotypes in Vietnam

Dalbergia oliveri is a leguminous tree of the Fabaceae family. This species is popular and valuable in Vietnam and is currently listed on the Vietnam Red List and on the IUCN Red List as endangered. Two PCR techniques using RAPD and inter-simple sequence repeat (ISSR) markers were used to make a comparative analysis of genetic diversity in this species. Fifty-six polymorphic primers (29 RAPD and 27 ISSR) were used. The RAPD primers produced 63 bands across 35 genotypes, of which 24 were polymorphic. The number of amplified bands varied from one to four, with a size range from 250 to 1400 bp. The percentage polymorphism ranged from 0 to 75. Amplification of genomic DNA of the 35 genotypes, using ISSR analysis, yielded 104 fragments, of which 63 were polymorphic. The number of amplified fragments using ISSR primers ranged from one to nine and varied in size from 250 to 1500 bp. The percentage polymorphism ranged from 0 to 100. ISSR markers were relatively more efficient than RAPDs. The mental test between two Jaccard's similarity matrices gave r ≥0.802, showing good fit correlation between ISSRs and RAPDs. Clustering of isolates remained more or less the same for RAPDs compared to combined RAPD and ISSR data. The similarity coefficient ranged from 0.785 to 1.000, 0.698 to 0.956 and 0.752 to 0.964 with RAPD, ISSR, and the combined RAPD-ISSR dendrogram, respectively.

Assessment of genetic diversity and relatedness among Tunisian almond germplasm using SSR markers

Genetic diversity of 50 Tunisian almond (Prunus dulcis Mill.) genotypes and their relationships to European and American cultivars were studied. In total 82 genotypes were analyzed using ten genomic SSRs. A total of 159 alleles were scored and their sizes ranged from 116 to 227 bp. The number of alleles per locus varied from 12 to 23 with an average of 15.9 alleles per locus. Mean expected and observed heterozygosities were 0.86 and 0.68, respectively. The total value for the probability of identity was 4 × 10(-13) . All SSRs were polymorphic and they were able all together to distinguish unambiguously the 82 genotypes. The Dice similarity coefficient was calculated for all pair wise and was used to construct an UPGMA dendrogram. The results demonstrated that the genetic diversity within local almond cultivars was important, with clear geographic divergence between the northern and the southern Tunisian cultivars. The usefulness of SSR markers for almond fingerprinting, detection of synonyms and homonyms and evaluation of the genetic diversity in the Tunisian almond germplasm was also discussed. The results confirm the potential value of genetic diversity preservation for future breeding programs.

Antioxidant potential of chestnut (Castanea sativa L.) and almond (Prunus dulcis L.) by-products

The antioxidant properties of almond green husks (Cvs. Duro Italiano, Ferraduel, Ferranhês, Ferrastar and Orelha de Mula), chestnut skins and chestnut leaves (Cvs. Aveleira, Boa Ventura, Judia and Longal) were evaluated through several chemical and biochemical assays in order to provide a novel strategy to stimulate the application of waste products as new suppliers of useful bioactive compounds, namely antioxidants. All the assayed by-products revealed good antioxidant properties, with very low EC(50) values (lower than 380 μg/mL), particularly for lipid peroxidation inhibition (lower than 140 μg/mL). The total phenols and flavonoids contents were also determined. The correlation between these bioactive compounds and DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity, reducing power, inhibition of β-carotene bleaching and inhibition of lipid peroxidation in pig brain tissue through formation of thiobarbituric acid reactive substances, was also obtained. Although, all the assayed by-products proved to have a high potential of application in new antioxidants formulations, chestnut skins and leaves demonstrated better results.

Optimizing the efficiency of the touchdown technique for detecting inter-simple sequence repeat markers in corn (Zea mays)

We evaluated the efficiency of the touchdown method to determine the ideal PCR conditions for distinct inter-simple sequence repeat primers for processing DNA from common corn, popcorn, sweet corn, and a Tripsacum-maize hybrid. Genomic DNA was extracted from eight accessions of corn: two of the dent type, one Tripsacum-maize hybrid, one sweet corn, one flint-type corn, and three popcorn. Fifteen inter-simple sequence repeat primers were used: (CT)(8)RC, (CT)(8)TG, (GA)(8)T, (GA)(8)YC, (CTC)(5)RC, (GTC)(6), (GA)(6)CC, (GT)(6)CC, (CAC)(3)GC, (AG)(8)YT, (AC)(8)T, (AC)(8)YG, (CT)(8)RG, (GGAT)(3)GA, and (GAA)(6)AA. The annealing temperature and the melting temperature for each primer were estimated using a formula for RW Genes products, or we used the temperatures indicated by the manufacturer (Invitrogen). The touchdown method was then applied to each primer, varying the number of final cycles (10 or 12) and the decrease in temperature (0.5 degrees or 1.0 degrees C intervals). The gels were compared, considering the revelation quality, band sharpness and the number of bands visualized. The touchdown-PCR method was more efficient for band amplification for most of the primers, especially at higher annealing temperatures. This type of system is useful for reducing the resources, time and effort needed for optimizing temperature conditions for a group of representative primers.

Identification of necrophagous fly species using ISSR and SCAR markers

Necrophagous fly is the most common insect evidence collected during a death investigation. We analyzed the DNA polymorphism among the five forensically important fly species, namely, Lucilia sericata, Aldrichina grahami, Chrysomya megacephala, Parasarcophaga crassipalpis and Musca domestica using inter simple sequence repeat (ISSR) method. Nine ISSR primers selected from 18 primers could amplify 105 clear and stable bands, of which 95 bands were polymorphic. Some primers produced completely different band pattern in different species, indicating that they can be used to identify these species. Aiming at obtaining more reliable markers that might be universally used, we started an effort to convert species-specific ISSR fragments into the sequence-characterized amplified region (SCAR) markers that can be used for the molecular diagnosis of the five species.

Development of SSR markers for the phylogenetic analysis of almond trees from China and the Mediterranean region

Expressed sequence tag (EST) derived simple sequence repeats (SSRs, microsatellites) were screened and identified from 3863 almond and 10 185 peach EST sequences, and the spectra of SSRs in the non-redundant EST sequences were investigated after sequence assembly. One hundred seventy-eight (12.07%) almond SSRs and 497 (9.97%) peach SSRs were detected. The EST-SSR occurs every 4.97 kb in almond ESTs and 6.57 kb in peach, and SSRs with di- and trinucleotide repeat motifs are the most abundant in both almond and peach ESTs. Twenty one EST-SSRs were thereafter, developed and used together with 7 genomic SSRs, to study the genetic relationship among 36 almond (P. communis Fritsch.) cultivars from China and the Mediterranean area, as well as 8 accessions of other related species from the genus Prunus. Both EST-derived and genomic SSR markers showed high cross-species transferability in the genus. Out of the 112 polymorphic alleles detected in the 36 cultivated almonds, 28 are specific to Chinese cultivars and 25 to the others. The 44 accessions were clustered into 4 groups in the phylogenetic tree and the 36 almond cultivars formed two distinct subgroups, one containing only Chinese cultivars and one of unknown origin and the other only those originating from the Mediterranean area, indicating that Chinese almond cultivars have a distinct evolutionary history from the Mediterranean almond. Our preliminary results indicated that common almond was more closely related to peach (P. persica (L.) Batsch.) than to the four wild species of almond, (P. mongolica Maxim., P. ledebouriana Schleche, P. tangutica Batal., and P. triloba Lindl.). The implications of these SSR markers for evolutionary analysis and molecular mapping of Prunus species are discussed.

Molecular variation and fingerprinting of Leucadendron cultivars (Proteaceae) by ISSR markers

BACKGROUND AND AIMS

There are more than 80 species of Leucadendron and most are used as cut flowers. Currently, more than 100 cultivars are used by industry and many of them are interspecific hybrids. The origin of most cultivars is unclear and their genetic diversity and relationships have not been studied. This investigation was carried out to evaluate the genetic variation and relationships among 30 Leucadendron cultivars.

METHODS

ISSR markers were applied to determine the genetic variation and to discriminate Leucadendron cultivars. Sixty-four ISSR primers were screened and 25 primers were selected for their ability to produce clear and reproducible patterns of multiple bands.

KEY RESULTS

A total of 584 bands of 305-2400 bp were amplified, of which 97 % were polymorphic. A dendrogram generated using the Unweighted Pair Group Method with Arithmetic Average based on a distance measure of total character difference showed that the Leucadendron cultivars clustered into two main groups. Twenty-four of the 30 cultivars can be unequivocally differentiated, but identical profiles were observed for three cultivar pairs, 'Katie's Blush' and 'Silvan Red', 'Highlights' and 'Maui Sunset', and 'Yellow Crest' and 'Yellow Devil'.

CONCLUSIONS

ISSR profiling is a powerful method for the identification and molecular classification of Leucadendron cultivars. A fingerprinting key was generated based on the banding patterns produced using two ISSR primers (UBC856 and UBC857). In addition cultivar-specific ISSR bands were obtained for 17 of the 30 Leucadendron cultivars tested.

Genetic stability of micropropagated almond plantlets, as assessed by RAPD and ISSR markers

Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD and 10 ISSR primers gave 326 distinct and reproducible band classes, monomorphic across all 22 plantlets analysed. Thus, a total of 7,172 bands were generated, exhibiting homogeneous RAPD and ISSR patterns for the plantlets tested. These results suggest that the culture conditions used for axillary branching proliferation are appropriate for clonal propagation of almond clone VII, as they do not seem to interfere with the integrity of the regenerated plantlets. These results allowed us to establish the use of axillary branching plantlets (mother-plants) as internal controls for the analysis of somaclonal variation of shoots regenerated from other in vitro culture processes performed with clone VII (adventitious regeneration, regeneration from meristem culture, virus sanitation programs and genetic engineering).