SNP Markers Discovery in Soybean with Use of Degenerate Oligolucleotide Primed PCR

There are several strategies that can be applied in SNP discovery, as for example the locus-specific amplification of target genome regions （Primmer et al., 2002; Van et al., 2004） or simultaneous assembly of anonymous sequences which are the product of whole genome shotgun sequencing （Webber and Myers, 1997） or reduced representation shotgun sequencing （Altshuler et al., 2000）. The majority of these methods are highly cost-prohibitive, however, and there is a necessity for development of new strategies that would be more suitable for small and medium-scale laboratories.     

Effects of inbreeding on nodal root system morphology and architecture of white clover (<Emphasis Type="Italic">Trifolium repens</Emphasis> L.)

Plants of white clover (Trifolium repens L.) cultivar Crau, a self-fertile Crau genotype, and nine generations of inbred progeny were raised in sand culture in a glasshouse experiment. Digital images of the root systems were made and root morphological characteristics were determined on all the plants. Root architectural parameters were measured on the Crau parent and the S₁, S₄, S₆, and S₉ inbred lines. The clover roots became shorter and thicker with inbreeding but the number of root tips per plant was unchanged. Root architecture (branching pattern) was largely unaffected by inbreeding. It is concluded that inbreeding white clover will lead to shorter, thicker roots, and reduced nutrient uptake efficiency compared with the parent clover. The degree to which these deleterious traits are overcome during the development of F₁ hybrids needs to be determined.     

The inheritance of chemical phenotype in <Emphasis Type="Italic">Cannabis sativa</Emphasis> L. (III): variation in cannabichromene proportion

The mechanism that controls the proportion of cannabichromene (CBC), a potential pharmaceutical, in the cannabinoid fraction of Cannabis sativa L. is explored. As with tetrahydrocannabinol (THC) and cannabidiol (CBD), CBC is an enzymatic conversion product of the precursor cannabigerol (CBG). CBC is reported to dominate the cannabinoid fraction of juveniles and to decline with maturation. This ontogeny was confirmed in inbred lines with different mature chemotypes. A consistent CBC presence was found in early leaves from a diverse clone collection, suggesting that CBC synthase is encoded by a fixed locus. Morphological variants possessing a ‘prolonged juvenile chemotype’ (PJC), a substantial proportion of CBC persisting up to maturity, are presented. PJC is associated with a reduced presence of floral bracts, bracteoles, and capitate-stalked trichomes. Genetic factors causing these features were independent of the allelic chemotype locus B that was previously postulated and regulates THC and CBD synthesis and CBG accumulation. In contrast to previously described Cannabis chemotypes, the cannabinoid composition of PJCs showed plasticity in that reduced light levels increased the CBC proportion. The ability of PJC plants to enable the production of pharmaceutical raw material with high CBC purity is demonstrated.     

Production of mutants with high cold tolerance in spring canola (<Emphasis Type="Italic">Brassica napus</Emphasis>)

A major factor affecting spring canola (Brassica napus) production in Canada is killing frosts during seedling development in the spring and seed maturation in the fall. The objective of this study was to explore the possibility of producing spring canola lines with mutations that have altered biochemical pathways that increase cold tolerance. The approach was to generate UV point mutations in cultured microspores followed by chemical in vitro selection of individual mutant microspores or embryos resulting in measurable alterations to various biochemical pathways with elevated levels of key defense signaling molecules such as, salicylic acid (SA), p-Fluoro-d,l-Phenyl Alanine (FPA), and jasmonic acid (JA). In addition, since proline (Pro) is known to protect plant tissues in the cold-induced osmotic stress pathway, mutants that overproduce Pro were selected in vitro by using three Pro analogues: hydroxyproline (HP), azetidine-2-carboxylate (A2C); and, 3,4-dehydro-d,l-proline (DP). Of the 329 in vitro selected mutant embryos produced, 74 were identified with significant cold tolerance compared to their donor parents through indoor freezer tests at −6°C, and 19 had better winter field survival than winter canola checks. All chemically selected mutant doubled haploids with increased cold tolerance compared well with parent lines for all seed quality and agronomic parameters. Development of increased frost tolerant cultivars should allow for spring canola to be produced in western Canada without compromising seed quality.     

DNA profiling and genetic diversity of Korean soybean (<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merrill) landraces by SSR markers

Approximately 7,000 accessions of Korean soybean (Glycine max (L.) Merrill) landraces, largely composed of three collections, the Korea Atomic Energy Research Institute’s soybean (KAS), the Korean Crop Experiment Station’s soybean (KLS) and the Korean Agricultural Development and Technology Center’s soybean (KADTC) collections, have been conserved at the Rural Development Administration (RDA) genebank in Korea. The accessions within collections were classified based on their traditional uses such as sauce soybean (SA), sprouted soybean (SP), soybean for cooking with rice (SCR), and OTHERS. A total of 2,758 accessions of Korean soybean landraces were used to profile and to evaluate genetic structure using six SSR loci. A total of 110 alleles were revealed by at the six SSR loci. The number of alleles per SSR locus ranged from 9 to 39 in Satt187 and Satt_074, respectively. The number of alleles ranged from 87 in the KADTC collection to 96 in the KLS collection, and from 63 in the SCR group to 95 in the SP group. Nei’s average genetic diversity ranged from 0.68 to 0.70 across three collections, and 0.64 to 0.69 across the usage groups. The average between-group differentiation (G _st) was 0.9 among collections, and 4.1 among the usage groups. The similar average diversity among three collections implies that the genetic background of the three collections was quite similar or that there were a large number of duplicate accessions in three collections. The selection from the four groups classified based upon usage may be a useful way to select accessions for developing a Korean soybean landrace core collection at the RDA genebank. DNA profile information of accessions will provide indications of redundancies or omissions and aid in managing the soybean collection held at the RDA genebank. The information on diversity analysis could help to enlarge the genetic diversity of materials in breeding programs and could be used to develop a core collection.     

Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)

Here we characterized eight novel polymorphic SSR markers, developed from an enriched genomic library of garlic (Allium sativum L.). These SSRs produced a total of 64 alleles across 90 garlic accessions, with an average of 8 alleles per locus. Values for observed (H_O) and expected (H_E) heterozygosity ranged from 0.16 to 0.77 (mean = 0.44) and from 0.22 to 0.86 (mean = 0.65), respectively. Six loci deviated significantly (P < 0.05) from Hardy–Weinberg equilibrium (HWE). The averages of gene diversity and PIC values were 0.65 and 0.62, respectively. The mean genetic similarity coefficient was 0.4380, indicating that among garlic accessions existed wide genetic variation. Based on 64 alleles obtained by 8 SSRs, a phenogram was constructed to understand the relationships among the 90 accessions. These newly developed SSRs should prove very useful tools for genotypes identification, assessment of genetic diversity and population structure in garlic.     

Effects of AMF inoculation on growth of Panax ginseng C.A. Meyer seedlings and on soil structures in mycorrhizosphere

We aimed to investigate the effects of inoculating Panax ginseng C.A. Meyer seedlings with arbuscular mycorrhizal fungi (AMF) by examining the root colonization, plant nutrition uptake, growth characteristics, and soil aggregation of P. ginseng seedlings inoculated at the time of transplantation. At 16 weeks, the AMF spore density per 30 g of fresh mycorrhizosphere in seedlings inoculated with AMF (AMF+ seedlings) was 256.8 and that in seedlings not inoculated with AMF (AMF− seedlings) was 186.3, respectively. The colonization rate of AMF in the lateral roots of AMF+ seedlings was approximately 19% higher than that in the lateral roots of AMF− seedlings. The patterns of AMF colonization in ginseng roots were similar to those of the Paris-type mycorrhizal association. Plant growth characteristics, such as plant height, root length, leaf area, number of lateral roots, fresh weight of shoots and roots, and chlorophyll content, were significantly enhanced in AMF+ seedlings compared to AMF− seedlings. The macronutrient content (P, K, and Ca) and micronutrient content (Cu, Fe, and Zn) of both shoots and roots were also significantly higher in AMF+ seedlings compared to AMF− seedlings. Furthermore, glomalin content and soil aggregation were significantly enhanced in AMF inoculated areas. Our results indicate that AMF inoculation may enhance the growth of ginseng seedlings by improving the uptake of mineral nutrients and the soil structure in mycorrhizosphere.     

Effects of post-harvest foliar boron and calcium applications on subsequent season's pollen germination and pollen tube growth of pear (Pyrus pyrifolia)

The primary objective of this study was to evaluate the effects of foliar boron and calcium application after harvest on the quantity and activity of pollen in the ‘Housui’ and ‘Wonwhang’ pears on a subsequent year. Pollen grains of the ‘Housui’ pear were cultured on germination medium, to which had been added boric acid (0, 25, 75, 100, 200, 300, 400, and 500 mg L⁻¹) and calcium nitrate (0, 10, 25, 50, 100, 150, 200, 250, 300, 400, and 500 mg L⁻¹). Boric acid, which was added to the germination media, exerted a significant stimulatory effect on both pollen germination and pollen tube growth, although pollen tube growth was inhibited at higher concentrations than 300 mg L⁻¹. Calcium nitrate addition stimulated pollen germination, except at concentration of 500 mg L⁻¹. However, pollen tube growth was significantly inhibited with increasing concentrations of calcium nitrate. In the orchard experiment, boron and calcium were sprayed at concentrations of 0, 100, 200, 500 or 1000 mg L⁻¹ onto leaves after harvest, respectively. Boron and calcium content in the tissues as well as pollen production and growth were determined after these treatments. The foliar application of boron mainly resulted in an increase of boron concentration in buds. It also induced an increase in the weight of the anther and pollen in the following year. On the other hand, the foliar application of calcium resulted in an increase of calcium concentration mainly in the leaves, but pollen weight was decreased at high concentration treatment in the following year. The germination rate and tube growth of collected pollen were highest in the trees which had received boron treatment at a concentration of 200 mg L⁻¹. In contrast, the germination rate and tube growth of collected pollen were decreased by calcium application at concentrations of 500 and 1000 mg L⁻¹ without significant increase at lower concentrations. Consequently, the accumulation of boron in the developed buds of pear trees subjected to post-harvest foliar boron application generated positive effects on both the quantity and quality of pollen in the following year.     

Effects of ethylene,abscisic acid and auxin on fruit abscission in water dropwort (Oenanthe stolonifera DC.)

Fruit abscission in water dropwort (Oenanthe stolonifera DC.) was investigated by measuring fruit removal force (FRF) affected by fruit ages and plant hormones. FRF decreased rapidly 30 days after anthesis (DAA). Ethylene evolution increased rapidly at 35 DAA and ABA concentration increased gradually after 20 DAA. ACC and ethephon decreased the FRF of fruit explants and the promoting effect of ACC was delayed by silver thiosulphate and cycloheximide, but not by norbornadiene and actinomycin D. ABA enhanced fruit abscission without increasing ethylene evolution. However, the observation that CoCl₂ delayed abscission induced by ABA indicates possible involvement of ethylene in the ABA effect. Treatment with NAA, fenoprop and IAA had no effect on 30 DAA fruit explants, but IAA delayed abscission of 25 DAA explants. This suggests that the effect of auxins may differ with fruit age when used as control agents.     

Upscaling as ecological information transfer: a simple framework with application to Arctic ecosystem carbon exchange

Transferring ecological information across scale often involves spatial aggregation, which alters information content and may bias estimates if the scaling process is nonlinear. Here, a potential solution, the preservation of the information content of fine-scale measurements, is highlighted using modeled net ecosystem exchange (NEE) of an Arctic tundra landscape as an example. The variance of aggregated normalized difference vegetation index (NDVI), measured from an airborne platform, decreased linearly with log(scale), resulting in a linear relationship between log(scale) and the scale-wise modeled NEE estimate. Preserving three units of information, the mean, variance and skewness of fine-scale NDVI observations, resulted in upscaled NEE estimates that deviated less than 4% from the fine-scale estimate. Preserving only the mean and variance resulted in nearly 23% NEE bias, and preserving only the mean resulted in larger error and a change in sign from CO₂ sink to source. Compressing NDVI maps by 70–75% using wavelet thresholding with the Haar and Coiflet basis functions resulted in 13% NEE bias across the study domain. Applying unique scale-dependent transfer functions between NDVI and leaf area index (LAI) decreased, but did not remove, bias in modeled flux in a smaller expanse using handheld NDVI observations. Quantifying the parameters of statistical distributions to preserve ecological information reduces bias when upscaling and makes possible spatial data assimilation to further reduce errors in estimates of ecological processes across scale.