5S ribosomal gene variation in the soybean and its progenitor

Summary The soybean, Glycine max and its wild progenitor, Glycine soja, have been surveyed for repeat length variation for the nuclearly encoded 5S ribosomal RNA genes. There is little variation among the 33 accessions assayed, with a common repeat length of 345 bases being typical of both taxa. A 334 base size variant was encountered in individuals from two populations of G. soja from China. The low level of variability is in marked contrast to the variation observed within and between the species of the perennial subgenus Glycine.     

The genomic relationship between Glycine max (L.) Merr. and G. soja Sieb. and Zucc. as revealed by pachytene chromosome analysis

Summary This study was conducted with the objective of determining the genomic relationship between cultivated soybean (Glycine max) and wild soybean (G. soja) of the subgenus Soja, genus Glycine. Observations on cross-ability rate, hybrid viability, meiotic chromosome pairing, and pollen fertility in F ₁ hybrids of G. max × G. soja and reciprocals elucidated that both species hybridized readily and set mature putative hybrid pods, generated vigorous F₁ plants, had a majority of sporocytes that showed 18II + 1IV chromosome association at diakinesis and metaphase I, and had a pollen fertility that ranged from 49.2% to 53.3%. A quadrivalent was often associated with the nucleolus, suggesting that one of the chromosomes involved in the interchange is a satellited chromosome. Thus, G. max and G. soja genetic stocks used in this study have been differentiated by a reciprocal translocation. Pachytene analysis of F₁ hybrids helped construct chromosome maps based on chromosome length and euchromatin and heterochromatin distribution. Chromosomes were numbered in descending order of 1–20. Pachytene chromosomes in soybean showed heterochromatin distribution on either side of the centromeres. Pachytene analysis revealed small structural differences for chromosomes 6 and 11 which were not detected at diakinesis and metaphase I. This study suggests that G. max and G. soja carry similar genomes and validates the previously assigned genome symbol GG.Research supported in part by the Illinois Agricultural Experiment Station and U.S. Department of Agriculture Competitive Research Grant (85-CRCR-1-1616)     

Marker chromosomes commonly observed in the genus Glycine

Summary Soybean [Glycine max (L.) Merr.] chromosomes were analyzed using the chromosome image analyzing system, CHIAS, and seven groups, including subgroups, were identified based on morphological characteristics. Two pairs of chromosomes were conspicuous in their morphological traits. One pair of chromosomes, which had the largest arm ratio among all the chromosomes, was commonly observed in the species in all three subgenera of the genus Glycine. These chromosomes also displayed a unique pattern after N-banding and were detected as marker chromosomes. G. soja, which is considered to be the ancestor of G. max, has two types of marker chromosomes. The lines that carry the same type as G. max may be the ancestors of G. max among the lines of G. soja. The morphological differences of the marker chromosomes within the species in the subgenus Soja are discussed in relation to the domestication process of soybean.     

Nucleotide diversity patterns of three divergent soybean populations: evidences for population‐dependent linkage disequilibrium and taxonomic status of Glycine gracilis

The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high‐resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high‐diversity single‐copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r² = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r² ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.     

Seed bank persistence of clonal weeds in contrasting habitats: implications for control

The ability of weeds to form a seed bank is important for their population dynamics and management because it provides a refuge enabling reinvasion after established target plants have died. However, knowledge of the differential seed behaviour of individual species over multiple years and varying environmental conditions is surprisingly rare but necessary for effective control of diverse weed populations. We established a seed burial experiment in alpine habitats differing in management regime (i.e., forest, hay meadow and pasture) to determine whether seeds of the unpalatable perennial weeds, Veratrum album (white hellebore) and Gentiana lutea (yellow gentian) were able to delay germination and remain viable over 3 years. Our study shows that both species formed a short-term persistent seed bank; in the third-year, the soil seed banks of both species were nearly depleted, having declined to <5% of their original size. Both species had strikingly different germination strategies: G. lutea seeds mainly germinated in their first-year, whilst the majority of V. album seeds germinated in their second-year. The fraction of dormant G. lutea seeds increased with seed age, indicating that seeds remained viable after forgoing germination in the previous year. Habitat-specific differences in seed germination increased with seed age, with germination fractions being lowest in moist hay meadows. This suggests that the negative effects of anoxic conditions became more pronounced as seeds aged in hay meadows. Conversely, seed dormancy was equal among habitats. The absence of a long-term persistent seed bank has important implications for the management of both nuisance and endangered-plant populations. In the case of V. album and G. lutea, re-colonization of habitats from the seed bank is unlikely after established plants have been removed.     

RFLP analysis of soybean seed protein and oil content

Summary The objectives of this study were to present an expanded soybean RFLP map and to identify quantitative trait loci (QTL) in soybean [Glycine max (L.) Merr.] for seed protein and oil content. The study population was formed from a cross between a G. max experimental line (A81-356022) and a G. soja Sieb. and Zucc. plant introduction (PI 468916). A total of 252 markers was mapped in the population, forming 31 linkage groups. Protein and oil content were measured on seed harvested from a replicated trial of 60 F₂-derived lines in the F₃ generation (F₂₃ lines). Each F₂₃ line was genotyped with 243 RFLP, five isozyme, one storage protein, and three morphological markers. Significant (P<0.01) associations were found between the segregation of markers and seed protein and oil content. Segregation of individual markers explained up to 43% of the total variation for specific traits. All G. max alleles at significant loci for oil content were associated with greater oil content than G. soja alleles. All G. soja alleles at significant loci for protein content were associated with greater protein content than G. max alleles.     

Inheritance of polymorphic markers generated by DNA amplification fingerprinting and their use as genetic markers in soybean

DNA amplification fingerprinting (DAF) using a high primer-to-template ratio and single, very short arbitrary primers, was used to generate amplified fragment length polymorphic markers (AFLP) in soybean (Glycine max (L.) Merr.). The inheritance of AFLPs was studied using a cross between the ancestral Glycine soja PI468.397 and Glycine max (L.) Merr. line nts382, F1 and F2 progeny. The amplification reaction was carried out with soybean genomic DNA and 8 base long oligounucleotide primers. Silver-stained 5% polyacrylamide gels containing 7 M urea detected from 11 to 28 DAF products with primers of varying GC content (ranging from 50 to 100% GC). Depending on their intensity, AFLPs were classified into three classes. DAF profiles were reproducible for different DNA extractions and gels. Forty AFLPs were detected by 26 primers when comparing G. soja and G. max. Most AFLPs were inherited as dominant Mendelian markers in F1 and F2 populations. However, abnormal inheritance occured with about 25% of polymorphisms. One marker was inherited as a maternal marker, presumably originating from organelle DNA while another showed apparent paternal inheritance. To confirm the nuclear origin and utility of dominant Mendelian markers, three DAF polymorphisms were mapped using a F11 mapping population of recombinant inbred lines from soybean cultivars Minsoy × Noir 1. The study showed that DAF-generated polymorphic markers occur frequently and reliably, that they are inherited as Mendelian dominant loci and that they can be used in genome mapping.     

QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields

The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple‐site field trial. Generally, the fitness of the F₁ hybrids and hybrid derivatives from self‐pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F₂ progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self‐pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.     

Study of the biosafety of genetically modified soybean in the center of its origin and diversity in the Far East of the Russian Federation

Wild soybean (Glycine soja Sieb. and Zucc.) is the nearest relative of cultivated soybean (G. max (L.) Merr.). Study of the population genetic structure of wild-growing relatives of genetically modified (GM) plants in the centers of their origin is one of the main procedures before introduction of GM crops in these areas. We studied the genetic variability of nine wild-growing soya populations of Primorskii krai using RAPD analysis. The level of genetic variability of G. soja was considerably higher than that of G. max. We analyzed phylogenetic relationships in the genus Glycine subgenus Soja using RAPD markers. Our data confirm the validity of allocation to G. gracilis of the rank of species.     

Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis

Amplified fragment length polymorphism (AFLP) analysis is a PCR-based technique capable of detecting more than 50 independent loci in a single PCR reaction. The objectives of the present study were to: (1) assess the extent of AFLP variation in cultivated (Gycine max L. Merr.) and wild soybean (G. soja Siebold & Zucc.), (2) determine genetic relationships among soybean accessions using AFLP data, and (3) evaluate the usefulness of AFLPs as genetic markers. Fifteen AFLP primer pairs detected a total of 759 AFLP fragments in a sample of 23 accessions of wild and cultivated soybean, with an average of 51 fragments produced per primer pair per accession. Two-hundred and seventy four fragments (36% of the total observed) were polymorphic, among which 127 (17%) were polymorphic in G. max and 237 (31%) were polymorphic in G. soja. F₂ segregation analysis of six AFLP fragments indicated that they segregate as stable Mendelian loci. The number of polymorphic loci detected per AFLP primer pair in a sample of 23 accessions ranged from 9 to 27. The AFLP phenotypic diversity values were greater in wild than in cultivated soybean. Cluster and principal component analyses using AFLP data clearly separated G. max and G. soja accessions. Within the G. max group, adapted soybean cultivars were tightly clustered, illustrating the relatively low genetic diversity present in cultivated soybean. AFLP analysis of four soybean near-isogenic lines (NILs) identified three AFLP markers putatively linked to a virus resistance gene from two sources. The capacity of AFLP analysis to detect thousands of independent genetic loci with minimal cost and time requirements makes them an ideal marker for a wide array of genetic investigations.     

Effects of forest fire ash on germination and early growth of four pinus species

Fire modifies the germination of seeds of numerous species. One of the fire factors that cause these modifications is the ash. This study analysed the germination of seeds of Pinus sylvestris L., Pinus nigra Arn. Pinus radiata D. Don and Pinus pinaster Aiton, subjected to different ash treatments, and the development of seedlings that grew in these conditions for 14 weeks. We obtained the ash by completely burning leaves and small twigs from the most abundant woody species in populations of pines. The ash treatments applied were as follows: Control (without ash), Low (half of the amount registered in a fire), Medium (equal to the amount registered in a fire) and High (double the amount registered in a fire). Germination took place on paper inside Petri dishes and in soil, and growth was only analysed for the plants that grew in the soil. For all species, and especially P. nigra, germination rate decreased as the amount of ash applied increased. The negative effects of the ash were more apparent following treatments in Petri dishes than in the soil. In the dishes, the average germination time varies little between the four species of pine. In soil, the average germination time is more prolonged, and only some differences were observed between treatments in P. sylvestris and P. nigra. In these species the high treatment significantly increased the average germination time. We found a greater sensitivity of P. sylvestris and P. nigra to the addition of ash, showing a higher seedling mortality rate. However, it appears that seedling development (length and weight) was not affected in any of the species through the addition of ash. These tests allow us to deduce that, in P. sylvestris, P. nigra, P. radiata and P. pinaster, the ash produced by forest fires has an inhibiting effect on germination and little effect on the development of seedlings in the first months of life. This revised version was published online in June 2006 with corrections to the Cover Date.     

Estimating susceptibility of biological control agents to pesticides: influence of life history strategies and population structure

In this study we examined the influences that differing life history strategies and population structures at the time of pesticide exposure have on population susceptibility to pesticides. We used life table data and a matrix projection model to incorporate combinations of mortality (lethal effect) and reductions in fecundity (sublethal effect) into estimates of intrinsic population growth rates (r) for a predator, the seven-spot lady beetle, Coccinella septempunctata L., and its prey, the pea aphid, Acyrthosiphon pisum Harris, and an aphid parasitoid, Diaeretiella rapae (M’Intosh). All three species exhibited differences in key life history variables. The aphid had the highest r and shortest generation time, the ladybeetle had the lowest r and longest generation, while the parasitoid exhibited intermediate life history characteristics. When the model was run with populations started as neonates (aphids) or eggs (lady beetle, parasitoid) for each species, ladybeetle populations were much more susceptible than either aphid or parasitoid populations 30 days after simulated exposure to a pesticide. For example, 50% mortality and a 50% reduction in fecundity resulted in a population headed toward extinction (negative r) for the ladybeetle while the parasitoid population grew exponentially (positive r) even after sustaining 70% mortality and a 70% reduction in fecundity. The aphid species maintained exponential growth after sustaining 80% mortality and an 80% reduction in fecundity. Thus, differences in life history variables accounted for the greater susceptibility of the ladybeetle to a pesticide than its aphid prey or the parasitoid over a set time interval. These differences in susceptibility were greatly reduced when the model was run starting with a mixed age/stage population (the stable age distribution) for each species indicating that population structure at the time of pesticide exposure plays a critical role in population susceptibility. These results suggest that life history attributes as well as population structure at the time of pesticide exposure both play a major role in population susceptibility to pesticides, highlighting the need to explicitly consider differences in life history variables among species when calculating compatibility of pesticides and biological control agents as well as the population structure of beneficial species at the time of pesticide application.     

Cloning and comparative analysis of the gene encoding diacylglycerol acyltransferase from wild type and cultivated soybean

Diacylglycerol acyltransferase (DGAT), as an important enzyme in triacylglycerol synthesis, catalyzes the final acylation of the Kennedy pathway. In the present study, the GmDGAT gene was cloned from Glycine max by using AtDGAT as a query to search against the soybean EST database and the rapid amplification of cDNA ends (RACE) method. Allelic genes were also isolated from 13 soybean accessions and the divergence of the deduced amino acid sequences were compared. The comparison reveals that although GmDGAT is a highly conserved protein, several differences of insertion/deletion were identified in the N-terminal region of the GmDGATs from various soybean accessions. In the C-terminal regions, a single amino acid mutation specific to both G. max and G. soja was also found. The GmDGAT genomic sequences were further cloned and the number and size of exons in the DGAT genomic sequence were very similar among different plant species, whereas the introns were more diverged. These results may have significance in elucidating the genetic diversity of the GmDGAT among the soybean subgenus.     

Restriction fragment length polymorphism diversity in soybean

Summary Fifty-eight soybean accessions from the genus Glycine, subgenus Soja, were surveyed with 17 restriction fragment length polymorphism (RFLP) genetic markers to assess the level of molecular diversity and to evaluate the usefulness of previously identified RFLP markers. In general, only low levels of molecular diversity were observed: 2 of the 17 markers exhibited three alleles per locus, whereas all others had only two alleles. Thirty-five percent of the markers had rare alleles present in only 1 or 2 of the 58 accessions. Molecular diversity was least among cultivated soybeans and greatest between accessions of different soybean species such as Glycine max (L.) Merr. and G. soja Sieb. and Zucc. Principal component analysis was useful in reducing the multidimensional genotype data set and identifying genetic relationships.     

Factors controlling postfire seedling establishment in southern California chaparral

Summary This paper discusses the interactions among prefire shrub abundance, soil moisture, and plant and animal species on postfire seedling establishment in mixed chparral in southern California. Postfire germination and survival of seedlings in a stand dominated by a facultative seeder (Adenostoma fasciculatum) and by an obligate seeder (Ceanothus greggii) were monitored for 2 years. Relative to prefire abundance, germination of C. greggii was higher than that of A. fasciculatum. Survival during the first year was also higher in C. greggii than in A. fasciculatum. During the second year, however, mortality of C. greggii was greater than that of A. fasciculatum, mostly due to a psyllid infection. Germination of A. fasciculatum was negatively related to prefire shrub abundance. C. greggii germination was not associated with prefire shrub abundance. Seedling mortality of both species was very strongly related to the depletion of soil moisture the first few months after germination. A. fasciculatum was more sensitive than C. greggii to the drying of the soil, especially in the upper levels. C. greggii seedlings had longer roots, greater root/shoot biomass ratios, higher water potentials, and a later peak in seasonal growth activity compared to A. fasciculatum. Herbs promoted greater survival of A. fasciculatum. Our results indicate that the obligate seeder species, C. greggii, is better adapted to establish seedling in chaparral by producing greater relative germination and greater seedling survival than the facultative seeder species A. fasciculatum. The greater adaptability of C. greggii to the physical environment is counteracted by interspecific interference by plant and animal interactions which tend to favor A. fasciculatum over C. greggii.     

Effects of Soil Burn Severity on Post-Fire Tree Recruitment in Boreal Forest

Fire, which is the dominant disturbance in the boreal forest, creates substantial heterogeneity in soil burn severity at patch and landscape scales. We present results from five field experiments in Yukon Territory, Canada, and Alaska, USA that document the effects of soil burn severity on the germination and establishment of four common boreal trees: Picea glauca, Picea mariana, Pinus contorta subsp. latifolia, and Populus tremuloides. Burn severity had strong positive effects on seed germination and net seedling establishment after 3 years. Growth of transplanted seedlings was also significantly higher on severely burned soils. Our data and a synthesis of the literature indicated a consistent, steep decline in conifer establishment on organic soils at depths greater than 2.5 cm. A meta-analysis of seedling responses found no difference in the magnitude of severity effects on germination versus net establishment. There were, however, significant differences in establishment but not germination responses among deciduous trees, spruce, and pine, suggesting that small-seeded species experience greater mortality on lightly burned, organic soils than large-seeded species. Together, our analyses indicate that variations in burn severity can influence multiple aspects of forest stand structure, by affecting the density and composition of tree seedlings that establish after fire. These effects are predicted to be most important in moderately-drained forest stands, where a high potential variability in soil burn severity is coupled with strong severity effects on tree recruitment.     

Medicago truncatula f.laxicycla (Leguminosae), a new taxon with loose fruit coiling promoting rapid germination of the fruit-retained seeds

Medicago truncatula is a member ofMedicago sect.Spirocarpos, in which all 34 species have coiled fruit, usually tightly coiled, that permanently retain the seeds. A variant ofM. truncatula from Libya is unique for the species in possessing very loosely coiled fruits, and is here recognized as a new forma,M. truncatula f.laxicycla E. Small. In germination tests of a number of species ofMedicago, the unusual Libyan variant proved to be the only one in which rapid and simultaneous germination of most of the seeds occurred while still within a fruit. The loose coiling of the fruit of the Libyan variety appears to facilitate water entry and seedling escape. Its rapid germination might adapt it to respond quickly to intermittently available moisture, but at the cost of abandoning the strategy of intermittent germination adopted by other populations ofMedicago sect.Spirocarpos.     

黄河口西南侧小岛河河口天然牡蛎礁的牡蛎种群结构

牡蛎礁是生态系统服务价值高、但退化最严重及受关注度最高的海洋生境之一,牡蛎礁修复亦成为国际海洋生态修复的热点。掌握牡蛎自然种群状况及动态变化是评估牡蛎礁修复效果的基础。目前,我国天然牡蛎礁的牡蛎种群状况相关的背景资料较为缺乏。在黄河口西南侧的小岛河河口新发现天然活体牡蛎礁,但该牡蛎礁曾被大规模的商业采捕,亟需推进针对性的保护和修复研究工作。基于2021年11月对该牡蛎礁开展的牡蛎种群生态调查,分析其种类组成、年龄结构及生长特征。结果显示:该牡蛎礁分布有近江牡蛎(Crassostrea ariakensis)和长牡蛎(Crassostrea gigas)。牡蛎礁上以活体牡蛎为主,死亡牡蛎壳体数仅占6.1%-6.7%。活体牡蛎的密度和生物量分别为(2811±778)个/m²和(21.97±30.43)kg/m²,近江牡蛎较多,其密度和生物量分别占比55.7%和76.4%。近江牡蛎和长牡蛎的年龄分别介于0+-4+ 龄和0+-2+ 龄,它们都以壳高介于30-40 mm及壳质量<5 g的0+ 龄个体数量居多(>80%)。近江牡蛎的壳体形态参数均值都高于同龄组长牡蛎的相应值。两种牡蛎壳体均呈负异速增长,不同龄级的壳体延展方向不同。拟合von Bertalanffy生长方程得到,近江牡蛎和长牡蛎的渐近壳高分别为286 mm和173 mm,估算的拐点年龄分别为5.47 龄和2.56 龄,两种牡蛎的生长曲线分布存在极显著差异(P<0.001)。以上结果表明,小岛河河口的天然牡蛎礁的牡蛎自然种群资源较丰富,具有高密度、低龄和低死亡率等特点,有较好的活力和扩张潜力,有利于被采捕后的礁体的恢复。两种牡蛎中,近江牡蛎因其具有较高的生物量和较长的生长年龄,对礁体形成和扩繁可能更为重要。建议对该天然牡蛎礁及牡蛎种群开展周期>3年的原位保护、修复和连续监测计划。     

The role of rhizosphere bacteria in herbicide-mediated increase in Rhizoctonia solani-induced cotton seedling damping-off

A study was carried out to determine the role of rhizosphere-residing bacteria in the observed pendimethalin- and prometryn-mediated increase in cotton seedling damping-off incidence caused by Rhizoctonia solani. Judging from the results, pendimethalin-mediated increase in disease incidence may be due to a decrease in the populations of indigenous cotton root colonizing bacteria in the presence of pendimethalin. Prometryn-mediated increase in disease may be due to a decrease in the populations of indigenous root colonizing bacteria as well as increased susceptibility of cotton seedlings to R. solani infection in the presence of prometryn. Pendimethalin and prometryn neither affected the growth of R. solani nor caused any visible change in seedling physical characteristics.     

Ribosomal gene variation in soybean (Glycine) and its relatives

Summary The genes encoding the 18S25S ribosomal RNA gene repeat in soybean (Glycine max) and its relatives in the genus Glycine are surveyed for variation in repeat length and restriction enzyme site locations. Within the wild species of subgenus Glycine, considerable differences in repeat size occur, with a maximum observed in G. falcata. Repeat length and site polymorphisms occur in several species, but within individual plants only single repeat types are observed. The rDNA of the cultivated soybean and its wild progenitor, G. soja are identical at the level of this study, and no variation is found in over 40 accessions of the two species. Data from rDNA mapping studies are congruent with those of previous biosystematic studies, and in some instances give evidence of divergences not seen with other approaches.