Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers

 Inter-simple sequence repeat polymorphic DNA (ISSR) was evaluated for its applicability as a genetic marker system in wheat. PCR was carried out with primers that annealed to simple sequence repeats. The resultant products were subjected to agarose-gel electrophoresis, and the banding patterns were compared among six wheat accessions containing diploid, tetraploid, and hexaploid members. Out of 100 examined, 33 primers produced distinguishable as well as polymorphic bands in each of the six accessions. Although most of the primers that gave distinct bands (30 primers out of 33) contained dinucleotide repeats, each of the primers with tri-, tetra-, and penta-nucleotide motifs also yielded discrete bands. Primers based on (AC)_n repeats gave the most polymorphic bands. In total, 224 polymorphic bands were found in the comparison between Einkorn wheats whereas, on the average, 120 polymorphic bands were detected between common wheats. ISSR primers produced several times more information than RAPD markers. The extent of band polymorphism was similar to that of RFLP markers, and greater than that of RAPDs. The genetic relationships of wheat accessions estimated by the polymorphism of ISSR markers were identical with those inferred by RFLP and RAPD markers, indicating the reliability of ISSR markers for estimation of genotypes. These polymorphic bands are potential candidates as novel markers for use in linkage-map construction in wheat. The characteristic features of ISSR markers, i.e. polymorphism, generation of information and ease of handling, suggest their applicability to the analysis of genotypes as well as to the construction of PCR-based genome maps of wheats. Received: 15 September 1996 / Accepted: 25 October 1996     

Physical map of chloroplast DNA in sugi,Cryptomeria japonica

Summary To investigate the evolution of conifer species, we constructed a physical map of the chloroplast DNA of sugi, Cryptomeria japonica, with four restriction endonucleases, PstI, SalI, SacI and XhoI. The chloroplast genome of C. japonica was found to be a circular molecule with a total size of approximately 133 kb. This molecule lacked an inverted repeat. Twenty genes were localized on the physical map of C. japonica cpDNA by Southern hybridization. The chloroplast genome structure of C. japonica showed considerable rearrangements of the standard genome type found in vascular plants and differed markedly from that of tobacco. The difference was explicable by one deletion and five inversions. The chloroplast genome of C. japonica differed too from that of the genus Pinus which also lacks one of the inverted repeats. The results indicate that the conifer group originated monophyletically from an ancient lineage, and diverged independently after loss of an inverted repeat structure.     

Nitrogen nutrition of Douglas-fir (Pseudotsuga menziesii) on strongly acid sandy soil

Through ionic balance calculations, the effect of different sources and levels of nitrogen on nutrient uptake by Douglas-fir was studied. With ammonium as the sole source of N, growth of the plant was very poor. Increasing the levels of ammonium supply strongly decreased the surplus of total inorganic cations (C) over total inorganic anions (A). This decrease in C-A value, corresponding to the level of carboxylates in the plant, implies that in the long term the plant will run out of carboxylates and will then no longer be able to eliminate protons in the cytoplasm, produced during assimilation of ammonium. This can lead to internal acidification of the plant, toxic concentrations of free ammonium and an unbalanced amino acid composition. Values for the ratio of net carboxylate production and organic nitrogen production were in the same range as commonly found for other species. This did not support the theory of a conifer-specific ionic balance regulation as posed by others.     

Transfer conductance in second growth Douglas-fir (Pseudotsuga menziesii (Mirb.)Franco) canopies

The internal conductance from intercellular spaces to the sites of carboxylation (g_i) has only been measured in a few tree species and not in conifers, despite the fact it may impose a large limitation on photosynthesis. The present study provides the first estimates of g_i for a coniferous species, and examines variation in g_i with height and its relationships to anatomical, biochemical and physiological traits. Measurements were made on upper and lower canopy current‐year needles of 50‐year‐old Douglas‐fir (Pseudotsuga menziesii (Mirb.) Franco). Needle thickness and specific leaf area decreased by 30% from the top to bottom of the canopy. These anatomical/morphological changes were accompanied by modest variation in allocation of N to chlorophyll and the chlorophyll a/b ratio. Allocation of N to Rubisco did not vary with height, but the ratio of Rubisco to chlorophyll did owing to the aforementioned changes in allocation to chlorophyll. The value of g_i was estimated in one tree from concurrent measurements of carbon isotope discrimination and net photosynthesis. To examine the variation in g_i among trees a second independent method based on day respiration and the difference between the chloroplastic and intercellular photocompensation points (photocompensation point method) was used. Estimates of g_i obtained by the two methods agreed well with values varying between 0.14 and 0.20 mol m^?2 s^?1. It is estimated that g_i limits photosynthesis by approximately 20% as compared to an approximately 30% stomatal limitation (under well‐watered conditions). The value of g_i scaled approximately with maximum rates of photosynthesis, which were significantly greater in upper canopy needles. Nevertheless, g_i did not vary significantly with canopy height, owing to greater variability in g_i than photosynthesis.     

A linkage map for sugi (Cryptomeria japonica) based on RFLP,RAPD, and isozyme loci

A linkage map for sugi was constructed on the basis of restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and isozyme loci using a three-generation pedigree prepared for genetic analysis of heartwood color. A total of 128 RFLP (123 cDNA and 5 genomic probes), 33 RAPD, 2 isozyme, and 1 morphological (dwarf) loci segregated in 73 progeny. Of the 164 segregating loci, 145 loci were distributed in 20 linkage groups. Of these loci, 91 with confirmed map positions were assigned to 13 linkage groups, covering a total of 887.3 cM. A clustering of markers with distorted segregation was observed in 6 linkage groups. In the four clusters, distortions with a reduction in the number of homozygotes from one parent only were found.Abbreviations MAS marker-assisted selection - PAGE polyacrylamide gel electrophoresis - QTL quantitative traits of loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism This work was supported by a Grant-in-Aid from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated Research Program for the Use of Biotechnological Procedures for Plant Breeding) and by a Grant-in-Aid from the Ministry of Education, Science and Culture of Japan (Cooperative Research, no. 04304017)     

Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta

Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders  genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (N_a), observed heterozygosity (H_o), expected heterozygosity (H_e), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01035-w.     

Enrichment of cadmium-mediated antibiotic-resistant bacteria in a Douglas-fir (Pseudotsuga menziesii) litter microcosm.

A set of Douglas-fir needle litter microcosms was amended with cadmium, acid, a combination of both, or neither. After 2 weeks of incubation, bacterial colony counts were made of litter homogenates inoculated onto agar media containing an antibiotic (streptomycin, chloromycetin, ampicillin, or gentamicin), cadmium, both, or neither. In all microcosms bacterial abundance was similar but the quality was very dissimiliar. Cadmium-treated microcosms had populations enriched for cadmium and gentamicin resistance and streptomycin and chloramphenicol sensitivity. Acid amendment had no consistent effect on the microcosm populations except that which could be attributed to the cadmium treatment amendment alone.     

Enrichment of cadmium-mediated antibiotic-resistant bacteria in a Douglas-fir (Pseudotsuga menziesii) litter microcosm.

A set of Douglas-fir needle litter microcosms was amended with cadmium, acid, a combination of both, or neither. After 2 weeks of incubation, bacterial colony counts were made of litter homogenates inoculated onto agar media containing an antibiotic (streptomycin, chloromycetin, ampicillin, or gentamicin), cadmium, both, or neither. In all microcosms bacterial abundance was similar but the quality was very dissimiliar. Cadmium-treated microcosms had populations enriched for cadmium and gentamicin resistance and streptomycin and chloramphenicol sensitivity. Acid amendment had no consistent effect on the microcosm populations except that which could be attributed to the cadmium treatment amendment alone.     

Shoot multiplication from mature trees of Douglas-fir (Pseudotsuga menziesii) and sugar pine (Pinus lambertiana)

Opening of apical and axillary buds of mature Douglas-fir and sugar pine trees was obtained on a newly formulated basal medium (DCR) without growth regulators. Elongation of buds was observed on 1/2 strength DCR with 0.3% activated charcoal (DCR-1). In sugar pine, multiple shoots were obtained when explants on DCR with 0.5 mg/1 BAP for 5–6 weeks were transferred to DCR-1 medium. On subculture, axillary buds again developed when shoots were cultured on DCR with 0.2 mg/1 BAP for Douglas-fir and 0.5 mg/1 BAP for sugar pine. These buds were again elongated on DCR-1 medium. By subculturing 7–10 shoots of Douglas-fir and 2–3 shoots of sugar pine, over 100 shoots can be obtained in a year.Abbreviations BAP N⁶-benzylaminopurine - KN kinetin - NAA -naphthalene acetic acid - IAA Indole-3-acetic acid - MS Murashige-Skoog medium - WPM woody-plant medium     

Detection and seasonal expression pattern of a pathogenesis-related protein (PR-10) in Douglas-fir (Pseudotsuga menziesii) tissues

Previously, a PR-10 protein Pin m III was described in western white pine. In this study, primers based on cDNA of Pin m III were utilized to obtain the genomic sequence of a Pin m III homologue – Pse m I – in Douglas-fir. A comparative analysis of a deduced amino acid sequence of Pin m III and Pse m I genes indicated about 80% similarity between the two protein sequences, and a consensus 20 amino acid sequence located around the p-loop sequence was used to synthesize a peptide of 20 amino acids. An antibody to this synthetic peptide was able to detect the Pse m I protein in Douglas-fir. The anti- Pse m I antibody was used in a western immunoblot to monitor seasonal variation of the Pse m I in Douglas-fir needles and its level was shown to increase with overwintering of Douglas-fir seedlings. However, unlike the Pin m III, there is no indication that the Pse m I is associated with frost hardiness. Analysis of infected Douglas-fir roots showed a possible trend to up-regulation of Pse m I by pathogens such as the laminated root rot fungus, Phellinus weirii . The expression of Pse m I protein in Douglas-fir seedlings is very low compared to the expression of Pin m III protein in western white pine seedlings. In addition, a light-harvesting complex I protein, PSI-F, was identified in Douglas-fir by N-terminal amino acid sequencing.     

Linkage mapping and genome length in eastern white pine (Pinus strobus L.)

 Haploid linkage analysis of eastern white pine, Pinus strobus L., was carried out using mainly RAPD markers and microsatellite, or simple-sequence-repeat, markers. Ninety one loci mapped to 12 linkage groups of three or more markers. The resulting framework genome map, the first for a soft pine species, contained 69 markers. The map covered 58% of the estimated genome length of 2071 cM(K), with a 95% confidence interval of 1828–2242 cM(K). A systematic comparison of linkage data from eastern white pine, longleaf pine (P. palustris Mill.) and maritime pine (P. pinaster Ait.), gave genome-length estimates for all three species very close to either 2000 cM(K) or 2600 cM(H), depending on whether the Kosambi(K) or Haldane(H) map functions, respectively, were employed. Differences among previous pine genome-length estimates were attributed to the divergent criteria used in the methods of estimation, and indicate the need for the adoption of uniform criteria when performing genome-length estimates. Current data suggest that members of the two pine subgenera, which diverged during the late Mesozoic era, have highly conserved rates of recombination. Received: 5 January 1997/Accepted: 24 January 1997     

Metabolite profiling of Douglas-fir (Pseudotsuga menziesii) field trials reveals strong environmental and weak genetic variation

The primary objective of this study was to assess metabolomics for its capacity to discern biological variation among 10 full-sib families of a Douglas-fir tree breeding population, replicated on two sites. The differential accumulation of small metabolites in developing xylem was examined through metabolite profiles (139 metabolites common to 181 individual trees) generated by gas chromatography mass spectrometry and a series of statistical analyses that incorporated family, site, and tree growth and quantitative phenotypic wood traits (wood density, microfibril angle, wood chemistry and fiber morphology). Multivariate discriminant, canonical discriminant and factor analyses and broad-sense heritabilities revealed that metabolic and phenotypic traits alike were strongly related to site, while similar associations relating to genetic (family) structure were weak in comparison. Canonical correlation analysis subsequently identified correlations between specific phenotypic traits (i.e. tree growth, fibre morphology and wood chemistry) and metabolic traits (i.e. carbohydrate and lignin biosynthetic metabolites), demonstrating a coherent relationship between genetics, metabolism, environmental and phenotypic expression in wood-forming tissue. The association between cambial metabolites and tree phenotype, as revealed by metabolite profiling, demonstrates the value of metabolomics for systems biology approaches to understanding tree growth and secondary cell wall biosynthesis in plants.     

Application of random amplified polymorphic DNA and inter-simple sequence repeat markers in the genus Crataegus

Hawthorn ( Crataegus spp.) has a long history as an ornamental and a source of medicine. We report the use of random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers to determine genetic relationships in the genus Crataegus . Twenty-eight accessions, including eight species ( Crataegus pinnatifida , Crataegus bretschneideri , Crataegus maximowiczii , Crataegus kansuensis , Crataegus altaica , Crataegus songarica , Crataegus dahurica and Crataegus sanguinea ) and two botanical varieties ( C. pinnatifida var. major and C. maximowiczii var. ninganensis ) were analysed. Twelve RAPD primers reproducibly and strongly amplified 128 fragments of which 116 were polymorphic; similarly, 13 ISSR primers generated 127 products of which 119 were polymorphic. Dendrograms based on unweighted pair group method with arithmetic average analysis were constructed from both the RAPD and the ISSR data. Similarity coefficient based on RAPD and ISSR markers ranged from 0.22 to 0.98 and 0.23 to 0.98, respectively. The range in similarity coefficient indicated that the genus has a high level of genetic diversity. The Mantel test on the similarity matrices produced by RAPD and ISSR markers gave r  = 0.86, showing high correlation between RAPD and ISSR markers in their ability to detect genetic relationships between Crataegus accessions. RAPD and ISSR appear to be reliable methods for the analysis of genetic relationships among hawthorns.     

Genotyping of Ganoderma species by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis

Species of Ganoderma are used in traditional medicines. An improved random amplified polymorphic DNA (RAPD) analysis, where the RAMP time is prolonged, has been used to characterize the genetic variation in some well known species of Ganoderma. The DNA materials were collected from ten Ganoderma strains, amplified with randomly selected 24 RAPD primers and evaluated by agarose gel electrophoresis. A cluster dendrogram was constructed for genetic analysis on the basis of amplification results. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 316 bands were found with 93% polymorphism. There was a significant genetic distance between the different strains of Ganoderma, with an index of similarity coefficient in the range of 0.52–0.74. The inter-simple sequence repeat (ISSR) analysis of the Ganoderma DNA samples showed similar trend results to the RAPD analysis with 0.49–0.81 similarity coefficients. This study reports the high level of genetic differences between different species or strains of a single species of Ganoderma and confirms the significance of the improved RAPD method in genetic characterization of organisms. Therefore, the improved RAPD combined with ISSR techniques might be used for the genetic characterization of organisms.     

Inheritance of restriction fragment length polymorphisms and random amplified polymorphic DNAs in coastal Douglas-fir

A total of 225 new genetic loci [151 restriction fragment length polymorphisms (RFLP) and 74 random amplified polymorphic DNAs (RAPD)] in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] have been identified using a three-generation outbred pedigree. The Mendelian inheritance of 16 RFLP loci and 29 RAPD loci was demonstrated based on single-locus segregation in a sample of F₂ progeny. One RFLP locus, PtIFG2025, showed segregation distortion. Probe pPtIFG2025 is a loblolly pine cDNA probe encoding for rbcS. The 16 RFLP loci and 23 allozyme loci were also assayed in a sample of 16 Douglas-fir seed-orchard clones. Allelism was determined at 11 of the 16 RFLP loci. RFLPs were able to detect slightly more variation (4.0 alleles per locus) than allozymes (3.1 alleles per locus). The inheritance of an additional 80 RAPD loci was determined based on haploid segregation analysis of megagametophytes from parent tree 013-1. Once 200–300 markers are identified and placed on a genetic map, quantitative trait loci affecting bud phenology will be mapped.     

Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.)

 Inter-simple sequence repeat (ISSR) amplification was used to analyze microsatellite motif frequency in the rice genome and to evaluate genetic diversity among rice cultivars. A total of 32 primers, containing different simple sequence repeat (SSR) motifs, were tested for amplification on a panel of 59 varieties, representative of the diversity of cultivated rice (Oryza sativa L.). The ISSR analysis provided insights into the organization, frequency and levels of polymorphism of different simple sequence repeats in rice. The more common dinucleotide motifs were more amenable to ISSR analysis than the more infrequent tri-, tetra- and penta-nucleotide motifs. The ISSR results suggested that within the dinucleotide class, the poly(GA) motif was more common than the poly(GT) motif and that the frequency and clustering of specific tri- and tetra-nucleotide simple sequence repeats was variable and motif-specific. Furthermore, trinucleotide ISSR markers were found to be less polymorphic than either dinucleotide or certain tetranucleotide ISSR markers, suggesting which motifs would be better targets for microsatellite marker development. The ISSR amplification pattern was used to group the rice genotypes by cluster analysis. These results were compared to surveys of the same varieties for amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP) and isozyme markers. The ISSR fingerprint could be used to differentiate the genotypes belonging to either Japonica or Indica sub species of cultivated rice and to dissect finer levels of diversity within each subspecies. A higher percentage of polymorphic bands was produced with the ISSR technique than the AFLP method, based on a similar PCR reaction. Therefore, ISSR amplification proved to be a valuable method for determining genetic variability among rice varieties and for rapidly identifying cultivars. This efficient genetic fingerprinting technique would be useful for characterizing the large numbers of rice accessions held in national and international germplasm centers. Received: 25 May 1998 / Accepted: 17 September 1998     

A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags

A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.     

Megagametophytes of Douglas fir (Pseudotsuga menziesii) and hybrid larch (Larix × eurolepis) in culture: Multiplication of neck cells and the formation of binucleate cells

Summary To study the effect of culturing on megagametophytes of Douglas fir (Pseudotsuga menziesii) and hybrid larch (Larix × eurolepis), cones were collected at the time of fertilization and the megagametophytes were removed, then placed on medium. We used a modified Murashige and Skoog medium supplemented with 5% lactose and 10% polyethylene glycol 4000. A variety of cell types proliferated including prothallial, neck, and jacket cells. Some of these multiplying cells showed a binucleate condition. The prothallial cells of the apex divided and expanded. The neck cells formed clusters composed of more cells than normally found in situ; though otherwise they showed ultrastructural similarity to neck cells in situ. These neck cells had large numbers of active Golgi complexes, numerous large and small vacuoles, coated vesicles, smooth vesicles, a well-developed endoplasmic reticulum, and thickened cell walls. These are the first reports of neck cell multiplication and induction of a binucleate state for gymnosperm megagametophyte cells in vitro.     

The effects of cambial age and position within the stem on specific conductivity in Douglas-fir (Pseudotsuga menziesii) sapwood

Specific conductivity (k_s, m²s^-1MPa^-1) describes the permeability of xylem and is determined by all aspects of xylem anatomy that create resistance to the flow of water. Here we test the hypothesis that k_s is a function of radial and vertical position within the stem, rather than solely a function of cambial age (ring number from the pith), by measuring k_s on samples excised from 35-year-old Douglas-fir [Pseudotsuga menziesii var. menziesii (Mirb.) Franco] trees at six heights and two or three radial positions. Sapwood k_s decreased from the cambium to the heartwood boundary, and the difference between outer and inner sapwood increased with height in the tree. Beneath the live crown, inner sapwood had 80-90% the k_s of outer sapwood, but only 55% just 10 m higher in the stem (about 10 nodes down from the tree top). Outer sapwood k_s peaked near the base of the crown and declined toward both the base and top of the stem. These patterns can be explained by two superimposed effects: the effect of cambial age on the dimensions of tracheids as they are produced, and the effect of xylem aging, which may include accumulation of emboli and aspiration of bordered pits. Tracheid lumen diameter and earlywood and latewood density and width, all factors known to vary with cambial age, were measured on different trees of the same age and from the same stand. Lumen diameter increased with cambial age, whereas the proportion of latewood and growth ring density increased after an initial decrease in the first 5 years. Our results suggest that the effect of cambial age on xylem anatomy is not sufficient to explain variation in k_s. Instead, physical position (both vertical and radial) in the stem and cambial age must be considered as determinants of conductivity.