Molecular characterization and genetic diversity of Prunus rootstocks

Twenty microsatellite primer pairs, previously developed in peach, were used to characterize and to explore genetic relationships among 44 clones, representing three groups of rootstocks defined as: (1) Peach-based rootstocks (Prunus dulcis × P. persica, P. persica × P. davidiana); (2) Myrobalan-Marianna plums (P. cerasifera and interspecific hybrids having P. cerasifera as a parent); and (3) Slow growing plums (P. insititia, P. domestica, and P. domestica × P. spinosa). Eighteen SSR markers, from the 20 initially used, were able to amplify polymorphic products for the Peach-based rootstocks and 13 common markers gave also polymorphism for the Myrobalan-Marianna and Slow growing plums groups. The Dice coefficient of similarity was calculated between all pairs of accessions and their genetic similarity represented by a principal coordinate analysis. The genetic diversity detected among the 44 clones studied divided them in three groups, which are in agreement with their current taxonomic classification and their morphological characteristics. A set of three microsatellites (BPPCT001, CPPCT022 and UDP98-407) can distinguish between all the clones analyzed. The analysis within groups reveal another two sets of three SSR to distinguish between the clones from the Peach based rootstocks and the Myrobalan-Marianna plums, respectively, and only a single SSR is needed to distinguish within the clones from the Slow growing plums group. These results demonstrate the high potential of the SSR analysis for peach rootstock identification and studies of diversity in Prunus species.     

Evaluation of the effectiveness of soil-applied plant derivatives of Meliaceae species on nitrogen availability to peach trees

We assessed the effect of soil-applied derivatives of melia (Melia azedarach L.) and neem (Azadirachta indica A. Juss) on nitrogen (N) soil availability, root uptake and peach (Prunus persica L.) growth. First we evaluated the effectiveness of experimentally prepared amendments made with fresh ground melia leaves or commercial neem cake incorporated into the soil as nitrification inhibitors, then we evaluated the effect of fresh ground melia fruits and neem cake on growth and N root uptake of potted peach trees, and on soil microbial respiration. Soil-applied fresh ground melia leaves at 10 and 20 g kg⁻¹ of soil as well as commercial neem cake (10 g kg⁻¹) were ineffective in decreasing the level of mineral N after soil application of urea-N as a source of mineral N, rather they increased soil concentration of nitric N and ammonium N. The incorporation into the soil of fresh ground melia fruits (at 20 and 40 g kg⁻¹) and neem cake (at 10 and 20 g kg⁻¹) increased N concentration in leaves of GF677 peach × almond (Prunus amygdalus) hybrid rootstock alone or grafted with one-year-old variety Rome Star peach trees. An increase in microbial respiration, leaf green color and plant biomass compared to the control trees were also observed. The Meliaceae derivatives did not affect, in the short term (7 days), N root uptake efficiency, as demonstrated by the use of stable isotope ¹⁵N, rather they promoted in the long term an increase of soil N availability, N leaf concentration and plant growth.     

Use of ISSR,SRAP, and RAPD markers to assess genetic diversity in Turkish melons

The genetic relationships among 63 melon (Cucumis melo L.) genotypes collected from various regions of Turkey were determined by comparing their molecular ISSR, SRAP, and RAPD markers with those of 19 foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Total 162 polymorphic markers (69, 18, and 75 obtained from ISSR, SRAP, and RAPD primers, respectively) were used to define the genetic similarity among the melon genotypes by dendrogram or two and three dimensional scalings. The average similarity (SM coefficient) between any two pairs of accessions examined as estimated by molecular variation was 0.73 ± 0.48. Within-group genetic similarities ranged between 0.46 and 0.96. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Southeastern Anatolian genotypes were distinctly apart from group inodorus and group cantalupensis (sweet) genotypes. This reinforced the position of Turkey in the secondary genetic diversity center of melon. The genetic diversity among Turkish genotypes (H = 0.28 and I = 0.42) was only a little less than that of the world accessions (H = 0.30 and I = 0.45). On the other hand, the percentage of polymorphic loci among Turkish melon genotypes (90.7%) was even higher than that of the world accessions (87.6%).     

Long-term effects of managed grass competition and two pruning methods on growth and yield of peach trees

Ground cover competition and tree training strongly affect development of newly planted peach trees and eventual productivity of peach orchards. This experiment characterized the long-term interactive effects of three levels of competition and two pruning criteria on yield, fruit size, and marketable yield efficiency. Trees of two cultivars (’Jersey Dawn’, JD, and ‘Redskin’, RS, on Lovell) of peach (Prunuspersica (L.) Batsch) were planted in an orchard in 1993 and grown for 14 years in a vegetation free area (VFA) width of 0.6 or 2.4 m. A separate group of trees that were in the 2.4 m VFA had grass seeded beneath them in 1998 to obtain 0 m VFA. All trees were pruned to maintain canopy size with wide-angled scaffold limbs and intense pruning (IP) or upright branch form with reduced pruning (RP). In general, RS had greater yield than JD and yield was greatest in the 2.4 m VFA with RP and least in the 0.6 m VFA with IP. Cumulative marketable (≥6.35 cm) and average annual total yield of both cultivars was similar for RP trees in 0 m VFA and IP trees in 2.4 m VFA's although more of the fruit were in the largest size class (>6.98 cm) in the IP trees. Reduced pruning increased crop load. Fruit weight decreased with increased crop load more in RS than JD and this response was similar for all VFA's within each cultivar. Grass competition tended to reduce both the number and weight of fruit per tree but the average weight of individual marketable fruit was reduced only in the 0.6 m VFA of RS. Tree size was reduced by grass competition and pruning times measured from 1995 to 2000 were less in RP than IP. Consequently, marketable yield efficiency of marketable fruit (grams fruit ≥6.35 cm/cm² trunk cross-sectional area, TCSA) measured from 2004 to 2007 was generally greater in trees with RP than IP and in the 0.6 than the 0 and 2.4 m VFA. The results indicate that persistent competition will reduce total annual yield per tree but with reduced pruning the concomitant increased crop load can help maintain marketable yield.     

Genetic diversity and population structure of an endangered Orchid (Dendrobium loddigesii Rolfe) from China revealed by SRAP markers

Dendrobium loddigesii Rolfe is an endangered perennial herb with ornamental and medicinal value. Due to habitat deterioration and human over-exploitation, it has suffered a significant decline in abundance. Determining the level of genetic diversity and pattern of population genetic structure of this species would be helpful for its conservation and management. In this paper, sequence-related amplified polymorphism (SRAP) markers were applied to assess the level and pattern of genetic diversity in seven populations of D. loddigesii. Seventeen SRAP primer combinations generated a total of 231 clear amplification bands encompassing 187 (80.95%) polymorphic bands. A high level of genetic diversity was detected (PPB = 80.52%, H = 0.2743, I = 0.4113) at the species level. There was a moderate genetic differentiation (G_st = 0.304) among populations. Two main clusters were detected by cluster analysis using the unweighted pair-group method with arithmetic average (UPGMA). Mantel test revealed that no significant positive correlation was found between genetic distances and geographic distances (r = 0.2302; P > 0.05). Recommendations for conservation of the endangered species resources are proposed.     

Use of ISSR markers to assess genetic diversity of African edible seeded Citrullus lanatus landraces

We used the twenty primers to evaluate the genetic variability of 80 individuals belonging to four accessions of edible seeded Citrullus lanatus originated from Côte d’Ivoire. Edible seeded C. lanatus, named “egusi” or “pistachio”, had a great importance in nutrition in West Africa. Nevertheless, due to its neglected status no study to our knowledge has been devoted to its genetic variability using DNA markers. The twenty ISSR primers generated 258 bands among which 252 were polymorphic (97.67%). On the whole, the bands generated revealed three types of profile sharply distinct from each other with minor differences within each type. One profile (P1) was most frequent with 65 individuals. Three accessions (NI084, NI127 and NI145) generated the three types of profile and had medium values of genetic diversity (GD = 0.246–0.275, respectively). On the opposite, the accession NI076 only contained individuals of the most represented type of profile (P1) and had the lowest genetic diversity (GD = 0.055 ± 0.017). The pairwise genetic distance between the 80 individuals varied from 0 to 0.61. The Factorial Component Analysis and the dendrogram clearly separated the 80 individuals into three clusters corresponding to the three types of profile. The results showed that clusters were well separated from each other whereas accessions were not. Our results suggest that high number of individuals should be taken into account for sampling missions and conservation strategies because accessions were not well differentiated from each other. Local agricultural practices consisting of frequent seeds exchanges between farmers and the conservation of harvested seeds for next year culture could be one explanation.     

Genetic diversity of Dianthus accessions as assessed using two molecular marker systems (SRAPs and ISSRs) and morphological traits

Dianthus chinensis, Dianthus barbatus and Dianthus superbus are members of the Caryophyllaceae and are grown widely as ornamental plants. Information about relative genetic relationships can facilitate breeding programs. Here, we have compared two polymerase chain reaction (PCR)-based systems (sequence-related amplified polymorphisms (SRAPs) and inter-simple sequence repeats (ISSRs)) and morpological trait measurements for their relative effectiveness in estimating the genetic diversity found between 22 Chinese pink (D. chinensis) inbred-lines, one accession of D. barbatus and one accession of D. superbus. Interspecific differences were readily detected but the markers were less reliable in distinguishing the accessions according to their region of origin or in separating the wild species from the cultivars. Morphological traits were found to be the least effective genetic markers. The relative effectiveness of the three systems as markers for genetic diversity was concluded to be SRAP > ISSR > morphological traits, but the combined data from ISSR + SRAP analyses was superior to all three. The information generated by the SRAP marker system correlated more closely with morphological variability than did the ISSR marker system. The morphological markers of plant height/crown size ratio, lower leaf length, ovary shape index and calyx length showed strong correlations with the genetic diversity index (GD_ij, PPB(II) and PSB) as generated by the percentage of polymorphic bands and percentage of special bands of the PCR-based markers.     

Comparative analysis of genetic diversity in Indian bitter gourd (Momordica charantia L.) using RAPD and ISSR markers for developing crop improvement strategies

A genetic analysis of 38 diverse Indian bitter gourd (Momordicacharantia var. charantia, and var. muricata) accessions was performed using 29 RAPD and 15 ISSR markers. RAPD primers yielded 208 amplicons of which 76 (36.5%) were polymorphic providing an average of 2.6 amplicons per primer. RAPD amplicons per primer ranged from 3 (OPE-19, OPW-09) to 15 (OPW-05), and varied in size from 200 bp to 3000 bp. Fifteen ISSR primers provided a total of 125 bands of which 94 (74.7%) were polymorphic. Polymorphic ISSR markers ranged from 0 (UBC-841) to 12 (UBC-890) providing a mean of 6.3 amplicons per primer that ranged in size from 150 bp to 2700 bp. Nevertheless, the concordance among bitter gourd accession groupings after cluster analysis was relatively high (r = 0.77), indicating that RAPD- and ISSR-based diversity assessments in this germplasm array were generally consistent. The M.charantia var. charantia (domesticated) and var. muricata (wild, free-living) accessions examined were genetically distinct, and these differences provided for the development of strategies for genetic analyses and crop improvement in this species.     

Genetic diversity in mainland and island populations of the endangered Pancratium maritimum L. (Amaryllidaceae) in Tunisia

Tunisian Pancratium maritimum L. populations are at present endangered and represented by scattered individuals as a result of coastal habitat destruction caused by urbanization and overharvesting for its significant ornamental interest. Nineteen populations growing in mainland and island habitats were sampled for allozyme diversity to assess their genetic diversity and structuration using seven isozymes revealed by starch gel electrophoresis. The species exhibited relatively high levels of genetic diversity (the mean A_p = 1.37, P = 37.4%, and H_e = 0.100), indicates a preferentially outcrossing mating system.     

Wide genetic diversity of Rosa damascena Mill. germplasm in Iran as revealed by RAPD analysis

The genetic relationships among 41 Rosa damascena accessions from various cultivation areas of Iran and one accession from Bulgaria were analyzed using 31 RAPD (Randomly Amplified Polymorphic DNA) primers. Each primer exhibited 3–12 banding patterns for a total of 343 scorable and 184 polymorphic bands. The combination of 11 primers was found optimal for discrimination of 42 accessions with very low values of cumulative confusion probability (9.7 × 10⁻⁵); indicating that only one pair from over 10,000 distinct pairs of accessions would be indistinguishable. Unweighted pair group method cluster analysis based on similarity values revealed 10 groups at the distance of 0.85. The Bulgarian genotype grouped with the majority of the Iranian genotypes in a main cluster. Results of molecular variance analysis (AMOVA) indicated that the major proportion (65.7%) of the total genetic variation was within collecting provinces rather than between them. The wide genetic variation seen for R. damascena in Iran indicates that Iran is a center of genetic diversity for this species and that there is a promising future for the breeding.     

Development of novel chloroplast microsatellite markers for Dendrobium officinale, and cross-amplification in other Dendrobium species (Orchidaceae)

Nine pairs of polymorphic chloroplast microsatellite primers were developed for Dendrobium officinale Kimura et Migo, an endangered herb. Levels of polymorphism were tested across a total of 55 individuals from four natural populations (12–15 individuals per population). Allele numbers varied from two to four per locus, while the number of haplotypes ranged from four to six per population. Transferability of the nine polymorphic chloroplast microsatellite primers was checked on an additional set of 51 Dendrobium individuals (belonging to 17 different species). Three markers could be transferable to all the species tested, while the remaining six markers successfully cross-amplified in most species tested. Moreover, polymorphism of the nine chloroplast microsatellite primers was tested across Dendrobium moniliforme (L.) Sw. and Dendrobium loddigesii Rolfe. All of them were polymorphic in D. moniliforme, while seven of which were polymorphic in D. loddigesii. These polymorphic chloroplast microsatellite primers developed for D. officinale will be a useful tool for the study of genetic diversity, population genetic structure, evolution of D. officinale and establishment of effective conservation strategies.     

Molecular polymorphism of cytoplasmic DNA in Ficus carica L.: Insights from non-coding regions of chloroplast DNA

The trnL (UAA) intron and the intergenic spacer between the 3′ exon of trnL (UAA) and trnF (GAA) sequences were used as genetic markers for differentiating Ficus carica cultivars and establishing refined genetic relationships. The study was based on 20 fig cultivars, collected from south and centre of Tunisia. Since, the intron was thought to be more variable among close relatives than is the chloroplast spacer. The size of these non-coding regions varied from 554 to 589 and from 989 to 1022 bases pairs for the intron and the combined sequences correspondingly. The average of GC content was 33.9% and 34.6% in the intron and the combined intron and spacer respectively. High values of A + T contents were detected in both data sets and may explain the high proportions of transversions founded. The observed variation pattern of plastid DNA provides evidence of an important genetic diversity. The overall transition/transversion bias (R) was 0.202 in the intron and 0.27 in the combined regions. The RI index of 0.592 indicates that these combined sequences have clearly more homoplasy then the intron (RI = 0.705) and spacer (RI = 0.777) sequences separately. Phylogenetic trees were generated based on maximum parsimony (MP) and neighbor-joining (NJ) analysis of the chloroplast sequences data. Results proved that a typically continuous genetic diversity characterizes the local fig germplasm. In fact, relationships inferred from the cpDNA analysis suggest several clades, which do not show geographical or tree sex correspondence. Although the level of apparent diversity is considerable, we may conclude that non-coding regions of chloroplast genome provide a new and practical opportunity to evaluate genetic diversity and to discriminate fig cultivars. Revealed cytoplasmic DNA markers are reliable to elaborate a molecular data base to conduct management and breeding programs on local fig germplasm.     

Genetic diversity and population's structure in Tunisian strawberry tree (Arbutus unedo L.)

A growing interest in the use of the Strawberry tree (Arbutus unedo L., Ericaceae) has been recently reported for industrial, pharmaceutical and chemical fields. However, the bulk material comes from natural populations because of the lack of selection of interesting cultivars. In Tunisia, A. unedo populations are severely destroyed due to deforestation and over-collecting. The species occurs in small scattered populations decreasing progressively in size. Yet, no conservation or improvement programs are attempted to preserve and promote the potential value of this resource. In this work, we assessed the genetic diversity of nine Tunisian populations of A. unedo L. from different bioclimates, using 65 polymorphic RAPD loci. The analysis of the genetic variation within and among populations is primordial to elaborate conservation and improvement programs. A low genetic diversity within a population estimated by both Nei's (He) and Shannon's diversity (H′) indices (0.155 < He < 0.248; 0.229 < H′ < 0.364) was observed due to genetic drift and selfing. At the species level, the amount of the within population variation estimated by Shannon's index (H_POP/H_SP = 0.686) and the molecular variance (80.67%) was higher than that among populations. A moderate genetic differentiation among populations (Φ_ST = 0.193 and G_ST = 0.314) which could be attributed to the long seed distance dispersal was detected. The UPGMA dendrogram based on Φ_ST values showed three clusters each including populations without relationship to bioclimatic or geographical origin indicating that differentiation occurs at a local space scale. The in situ protection measures should be made appropriately according to a population within bioclimates. The ex situ conservation and the selection of genotypes should involve extensive collection of seeds or cuttings from the within populations rather than among them.     

Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers

Eighty-one accessions representing apricot germplasm in Tunisia were collected from different areas of cultivation and fingerprinted using amplified fragment length polymorphism (AFLP) and microsatellites (SSR) markers. A total of 339 polymorphic markers were revealed using 5 AFLP primers combinations and 24 SSR loci. AFLP and SSR markers expressed a high level of polymorphism allowing the distinction of the accessions with an efficiency coefficient of discrimination of 100% for AFLP and 97% for SSR markers. Genetic diversity structure was assessed with AFLPs and SSRs markers separately then with combined matrix data by the help of hierarchical clustering elaborated using Wards method based on Nei and Li (1979) distances. Comparison of the obtained dendrograms revealed a phylogeographic structure into two major groups with significant conservation between the observed subgroups in relation with the geographic origin of the accessions. The relative efficiency of the markers in determining the genetic relationships among apricot accessions has been assessed and a combination of AFLPs and SSRs markers was the most effective. In addition, Mantel test based on genetic distances indicated highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with Pearson correlation values of r = 0.873 and r = 0.692, respectively, revealing the higher efficiency of the combination of both molecular techniques (AFLP and SSR) to estimate the levels of genetic variability among apricot germplasm.     

Aneuploid strawberry (2n = 8x + 2 = 58) was developed from homozygous unreduced gamete (8x) produced by second division restitution in pollen

Unreduced gamete formation is significant in the evolutionary development of complex polyploidy series found in wild strawberry, genus Fragaria (Rosaceae). Also, it is important for genetics and breeding in strawberry plants to elucidate the mechanism of unreduced gamete formation. The objective of this study was to search for ploidy anomalies resulting from artificial diploid × octoploid crosses, and examine the mechanism through which these unreduced gametes were produced. Five everbearing cultivars of Fragaria vesca L. diploid (2n = 2x = 14) were crossed with pollen from six June-bearing cultivars of Fragaria × ananassa Duch., octoploid (2n = 8x = 56). A total of 3000 mature seeds, 100 from each of the 30 parental combinations were sown at 23 °C/20 °C (day/night) under artificial lighting with a 16 h day. The seedlings were transplanted to pots and grown in a greenhouse. Reproductive and morphological observations, flow cytometry analyses, chromosome counts and DNA analyses using CAPS markers were performed to identify the genetic background of the offspring. Most of the seed (79%) did not germinate or died soon after germination. Of the seedlings produced, 7% seemed to be pure F. vesca based on morphological characteristics, flow cytometry analyses and chromosome counts; 14% were pentaploids (2n = 5x = 35), 0.1% were hexaploids (2n = 6x = 42), and 0.03% (one individual) was aneuploid (2n = 8x + 2 = 58). Electrophoresis banding patterns obtained by CAPS marker analysis were heterozygotic in the 8x pollen parent but homozygotic in the aneuploid progeny. Judging from the chromosome counts and the CAPS marker analysis, the aneuploid was the result of a homozygous unreduced pollen grain (8x) crossed with an incomplete chromosome compliment from the egg. Because of the homozygosity, the unreduced male gamete must have been derived from second division restitution (SDR) in the octoploid pollen parent.     

Evaluating foliar nitrogen compounds as indicators of nitrogen status in Prunus persica trees

Mobile nitrogen (N) forms may be better N indicators of the N status of trees than total nitrogen (TN) due to their higher sensitivity to increasing N supply. A field experiment was carried out over a 3-year period to compare foliar concentrations of total N (TN), soluble N (SN), chlorophyll (Minolta SPAD readings), NH₄–N and NO₃–N as indicators of soil N availability in nectarine, Prunus persica L. Batsch, cv. ‘Fantasia’ (grafted on ‘Nemaguard’ peach, P. persica × P. davidiana) trees. Young trees were exposed to a range of fertilizer-N application rates. Based on correlation analysis, the best association between leaf N compounds with soil N supply and trunk diameter and/or fruit yield was obtained with TN and chlorophyll SPAD readings. Leaf concentrations of mobile N compounds (NH₄–N and NO₃–N) increased more than any other N compound under high N supply; however, their inconsistency among years and low leaf concentration difficult their use as N indicators. The optimum foliar TN for growth decreased with tree age, 4.4%, 3.6% and 3.3% in non-bearing 1-year-old trees, non-bearing 2-year-old trees and 3.3 fruit-bearing 3-year-old trees. The optimum SPAD readings were 40 in 2-year-old trees and 42 in 3-year-old trees. Stable N compounds (TN and chlorophyll SPAD) could be used to N diagnosis in the zone of N deficiency, and soluble N compounds (NH₄–N and NO₃–N) to diagnoses N excess.     

A comparative analysis of the genetic diversity between inbred lines of Zinnia elegans using morphological traits and RAPD and ISSR markers

Genetic diversity within Zinnia elegans is key to the genetic improvement of this important ornamental species. Here, morphological traits and RAPD and ISSR molecular markers were used to assess levels of polymorphism across 20 inbred lines. Thirty-four morphological traits were scored and also 147 RAPD marker-fragments, as amplified by 12 arbitrary primers, and 128 ISSR marker-fragments as generated by 9 primers. The number of polymorphic loci, the percentage of polymorphic loci, Shannon's Information index (I) and the effective number of alleles (Ne) were calculated from the RAPD data as 100, 68.03%, 0.3559 and 1.4169, respectively. From the ISSR data, these respective statistics were calculated as 97, 76.38%, 0.4013 and 1.4728. Thus, ISSR markers were considered slightly superior to RAPD markers for assessing genetic diversity between the accessions; however, Mantel's test indicated significant correlation (R = 0.733) of the RAPD and ISSR results. By contrast, the morphological matrix showed low correlation with both RAPD and ISSR data matrices (R = 0.3814 and 0.3765, respectively). Cluster analysis showed that groupings of the accessions according to all three methods correlated well with their geographic region of origin, but flower color was not strongly associated with the genetic classification of these inbred lines of Z. elegans.     

Are rhododendron hybrids distinguishable on the basis of morphology and microsatellite polymorphism?

Sequence Tagged Microsatellite Sites (STMSs) and morphological trait markers were used to evaluate 33 rhododendron germplasm for genetic diversity assessment and discrimination power. The average genetic diversity estimates were 0.724 (morphological traits) and 0.174 (STMSs) marker datasets. The Shannon index was higher for morphological traits (1.797) than STMS (0.302). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the two markers, showed that estimated values of relationships given for morphological and STMS were not significantly related (p > 0.05). The dataset from STMS, supported by the total probability of identity (1.13 × 10⁻⁹) and total paternity exclusion probability (0.9999), allowed all accessions to be uniquely identified. In summary, STMS marker proved to be an efficient tool in assessing the genetic variability among old broad leaf rhododendron genotypes. The pattern of variation appeared to be consistent, and it can be used for germplasm conservation and management for restoration of historical genetic resources.