Polymerase chain reaction detect polymorphisms and trait association in soybean

Five sets of synthetic oligonucleotide (20-to 24-mers containing no intenal repeats) primers of known gene sequences [yellow lupin nodule specific (hydroxyl) proline-rich protein, pearl millet alcohol dehydrogenase, Pisum sativum heat shock proteins, Drosophila homeobox, and tRNA] were used to differentiate 73 soybean accessions, including 56 Glycine max (L.) Merr. and 17 G. soja Zucc. & Sieb. The amplified genetic markers revealed polymorphic bands for most genotypes studied. The χ²-analyses of the results showed that several fragments produced with these gene primers were associated non-randomly with resistance to Phytophothora, maturity, seed size, flower colour, seed coat colour, seed hilum colour, growth type, and leaf shape. These markers appear to be valuable for differentiation of G. max and G. soja species and genotypes within these species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Investigations of proliferative and senescent callus of soybean

Different explant sources from several Giycine max (L.) Merr. cultivars and several G. soja F. J. Herm Plant Introductions were tested for calluas production. Embryo axis explants produced callus most readily; hence, they were selected for media response studies and microscopic evaluation. Two callus types, proliferative and senescing, were identified and characterized by light and scanning electron microscopy (SEM). Proliferative callus was composed of chloroplast-containing cells interspersed with colorless meristematic areas, while senescing callus contained mostly large, vacuolate cells without chloroplasts. In SEM preparations a furry, layered, mucilaginous coating was seen on the outer surface of the senescing callus, while proliferative callus cells had uncoated, smooth or wrinkled surfaces. The mucilage contained glucose and galactose.     

基于大豆胞囊线虫病抗性候选基因的SNP位点遗传变异分析

以我国363份栽培和野生大豆资源为材料, 对大豆胞囊线虫抗性候选基因(rhg1和Rhg4)的SNP位点(8个)进行遗传变异分析, 以期阐明野生和栽培大豆间遗传多样性及连锁不平衡水平差异。结果表明, 与野生大豆相比, 代表我国栽培大豆总体资源多样性的微核心种质及其补充材料的连锁不平衡水平较高(R²值为0.216)。在栽培大豆群体内, 基因内和基因间分别有100％和16.6％的SNP位点对连锁不平衡显著, 形成两个基因特异的连锁不平衡区间(Block)。在所有供试材料中共检测到单倍型46个, 野生大豆的单倍型数目(27)少于栽培大豆(31), 但单倍型多样性(0.916)稍高于栽培大豆(0.816)。单倍型大多数(67.4％)为群体所特有(31个), 其中15个为野生大豆特有单倍型。野生大豆的两个主要优势单倍型(Hap_10和Hap_11)在栽培大豆中的发生频率也明显下降, 推测野生大豆向栽培大豆进化过程中, 一方面形成了新的单倍型, 另一方面因为瓶颈效应部分单倍型的频率降低甚至消失。     

野生大豆与栽培大豆种子差异蛋白质组学研究

运用蛋白质组学方法比较研究3个野生大豆(Glycinesoja)和3个栽培大豆(Glycinemax)的种子贮藏蛋白差异情况.结果发现,在考马斯亮蓝染色的双向电泳pH4～7的胶上,经过PDQuest图像分析软件平均可检测到550个左右的蛋白质点.进一步分析发现,表达量变化2.5倍以上的点有10个,其中大部分蛋白质仅在栽培大豆中检测到.对这10个蛋白质点进行了胶内酶解,用基质辅助激光解析电离飞行时间质谱测定均得到了肽质量指纹图谱.搜索大豆UniGene库和NCBI库共鉴定出5个蛋白质,主要是与大豆抗性、抗营养以及种子萌发相关的蛋白质,包括大豆血凝素,种子成熟蛋白PM24,糖结合蛋白,胰蛋白酶抑制剂p20以及成熟多肽.对这些蛋白质可能的作用进行了讨论.     

Importance of genetic characterization and conservation of plant genetic resources: The breeding system and genetic diversity of wild soybean (Glycine soja)

Abstract Plant genetic resources play an important role in the improvement of cultivated plants. To characterize and evaluate the ecological and reproductive features of wild soybean ( Glycine soja Sieb. et Zucc.), which is the most probable ancestor of cultivated soybean ( G. max (L) Merr.), the breeding system and genetic diversity of G. soja were investigated. The extent of natural cross-pollination of G. soja was estimated in four populations along the Omono River in Akita Prefecture, Japan by examining allozyme variation. Although it has been previously believed that G. soja is autogamous, as is cultivated soybean, the mean multilocus outcrossing rate ( t m) estimate was 13%. These values are much higher than the outcrossing rate previously reported for both G. soja and G. max . Frequent visits by honeybees and carpenter bees to flowers were also observed, which supported this conjecture. Furthermore, to evaluate the genetic variation of G. soja as a genetic resource, the genetic structure of 447 populations over Japan were analyzed. Wild soybean populations had a higher degree of variation of isozyme loci. The G ST coefficient of gene differentian values among the sites within the district were particularly high, revealing that the isozyme genotype was greatly different among site populations and homogeneous within the sites. The genetic differentiation among nine districts was observed in the allele frequencies of a few loci, indicating that geographic isolation in the wild soybean population was effectively created through the distance between the districts. The difference in the allele frequency among the districts may be produced under genetic drift. Finally, the importance of the preservation of natural plant populations and the habitats of wild progenitors (i.e. the in situ conservation of plant genetic resources) was emphasized.     

栽培大豆和野生大豆耐盐性及离子效应的比较

以国际上常用的耐盐大豆（Glycine max L.)品种Lee68为对照,在发芽期和苗期两个阶段,利用发芽指数、指害指数和耐盐系数等指标对一年生具盐腺野生大豆（Glycine soja L.)和部分栽培大豆（Glycine max L.)及某些野生大豆品系或品种的耐盐性进行了比较,讨论了耐盐指标的可行性。从离子效应方面比较了Na^ 和Cl^-对大豆发芽率的影响,并对具盐腺野生大豆的耐盐机理进行了初步分析。结果表明,大豆品种的耐盐性在发芽期和苗期无一致相关性。轻度等渗胁迫下,Na^ 对种子发芽率的抑制作用大于Cl^-,而重度等渗胁迫下则相反。通过减少由根系吸收的Na^ 、Cl^-向叶片的运输,维持叶片中较高含量的K^ ,减轻盐离子毒害,可能是具盐腺野生大事耐盐的主要生理机制之一。     

A recessive soybean cyst nematode allele for incompatibility with soybean PI 88287

The objective of this research was to characterise the degree of dominance of a soybean cyst nematode (Heterodera glycines) allele for incompatibility which interacts with a recessive soybean (Glycine max) allele for incompatibility to prevent the formation of cysts. Crosses of inbred nematode populations were made and the F, and F, populations evaluated for the numbers of cysts they could produce on several soybean lines. The nematode gene for avirulence interacts with the one recessive gene for resistance in soybean line PI 88287 and also appears to be recessive. This is the first example of a recessive-recessive gene-for-gene interaction; genes for avirulence and resistance are usually dominant. The difficulties of doing definitive genetic studies with cyst nematodes are discussed.     

国家基因库野生大豆（Glycine soja）资源最近十年考察与研究

总结了国家种质库最近10年野生大豆搜集进展和研究概况。我国野生大豆资源在1979-1982年间搜集并保存在国家基因库的为5939份;1996-2000年搜集了600份;2001-2010最近10年补充搜集了全国17个省(市、区)、318个县(市、旗)、930个乡镇(农场)。其中新搜集县市178个,共收集典型野生大豆资源1979份,野生大豆收集样品新增资源33.3%。     

The effect of methionine, ethylene and polyamine catabolic intermediates on polyamine accumulation in detached soybean leaves

In the present study we determined the effects of methionine, intermediates of polyamine catabolic pathways and inhibitors of either ethylene biosynthetic or polyamine catabolic pathways on polyamine accumulation in soybean leaves. Inhibitors to SAM decarboxylase and spermidine synthase, methylglyloxal-bis-(guanylhy-drazone) and cyclohexylamine, respectively, suggest that methionine may provide aminopropyl groups for the synthesis of polyamine via S-adenosylmethionine (SAM). Results from experiments that utilized a combination of compounds which altered either ethylene or polyamine biosynthesis, namely, aminoethoxyvinyl glycine, CoSO₄, 2,5-norbornadiene, and CuSO₄, suggest the two pathways compete for a common precursor. However, exogenous addition of ethylene (via ethephon treatments) had little or no effect on polyamine biosynthesis. Likewise, polyamine treatments had little or no effect on ethylene biosynthesis. These data suggest that there are few or no inhibitory effects from the end products of one pathway on the synthesis of the other. Data from leaves treated with metabolic intermediates in the catabolic pathway of polyamines and inhibitors of enzymes in the catabolic pathway, i.e. aminoguanidine, hydroxyethyldrazine and gabaculine, suggest that the observed increases in polyamine titers were not due to decreased catabolism of the polyamines. One catabolic intermediate, γ-aminobutyric acid (GABA), elevated putrescine, spermidine and spermine by 12-, 1.4-, and 2-fold, respectively, Ethylene levels decreased (25%) in GABA-treated leaves. This small decrease in ethylene could not account for such large increase in putrescine titers. Further analysis demonstrated that the GABA-mediated polyamine accumulation was inhibited by difluoromethylarginine, an inhibitor of arginine decarboxylase, but not by difluoromethylornithine, an inhibitor of ornithine decarboxylase. These data suggest that GABA directly or indirectly affects the biosynthesis of polyamines via arginine decarboxylase.     

Indirect effects of deer on insect pests and soybean plants

1. White-tailed deer (Odocoileus virginianus Zimmermann) and insect pests negatively affect soybean production; however, little is known about how these herbivores potentially interact to affect soybean yield. Previous studies have shown deer browse on non-crop plants affects insect density and insect-mediated leaf damage, which together reduce plant reproductive output. In soybeans, reproductive output is influenced by direct and indirect interactions of different herbivores.
2. Here, we quantified indirect interactions between two groups of herbivores (mammals and insects) and their effects on soybean growth and yield. We examined responses of insect pest communities along a gradient of deer herbivory (29% to 49% browsed stems) in soybean monocultures.
3. Structural equation models showed that deer browse had direct negative effects on soybean plant height and yield. Deer browse indirectly decreased insect-mediated leaf damage by reducing plant height. Deer browse also indirectly increased pest insect abundance through reductions in plant height. Similarly, deer herbivory had an indirect positive effect on leaf carbon: nitrogen ratios through changes in plant height, thereby decreasing leaf nutrition.
4. These results suggest that pest insect abundance may be greater on soybean plants in areas of higher deer browse, but deer browse may reduce insect herbivory through reduced leaf nutrition.

     

大豆突变新品系部分品质性状的分析

为丰富大豆种质资源,改良大豆品质,对现有的大豆品种进行改良,以获得新的大豆品系。大豆品种高蛋白东农42和高脂肪东农163经NaN3诱变处理后,分别在其M6代品系中取32份和54份材料进行实验,对它们的农艺性状(株高、百粒重等)和部分品质(脂肪、水溶蛋白和碱溶蛋白)进行了分析。结果表明:(1)所有品系的品质性状的变异系数差别较大,说明在后代中进行品质性状筛选是有效的;(2)突变品系内脂肪含量与水溶性蛋白含量呈显著负相关。     

DNA replication and the development of preprophase bands in soybean protoplast cultures

Nuclear DNA replication and the development of preprophase bands (PPBs) are two chronologically close processes during the higher plant cell cycle. However, it is not clear whether occurrence of PPBs is coupled with DNA replication. A soybean protoplast culture with a high frequency of PPBs was used to study the relationship between the two processes when treated with aphidicolin, a potent and specific inhibitor of eukaryotic DNA polymerase-α. When DNA replication was partially inhibited by 10 mg l^-1 aphidicolin, both the percentage of cells with PPBs and the mitotic index (MI) decreased in absolute terms, but there were proportionately more PPBs than mitoses. Since PPBs change in appearance as they develop, they were divided into categories of early (interphase associated) and late (prophase associated). The increased PPB/MI ratio was associated with an increased proportion of early stage PPBs relative to late stage PPBs. When DNA replication was completely blocked by 50 mg l^-1 aphidicolin, both MI and the percentage of cells with PPBs were close to zero. These results suggest that development of PPBs was to a large extent coupled DNA replication. We propose that the increased PPB/MI ratio at 10 mg l^-1 aphidicolin was due to a linkage between the duration of interphase and the time period in which early stage PPBs are visible. The increased duration of early PPBs partially compensates for the reduced number of nuclei reaching the stage of PPB initiation. Furthermore, in cultures containing aphidicolin, the percentage of PPBs with simultaneous perinuclear fluorescence (PNF, accumulation of microtubules on nuclear envelope) was reduced and whenever PNF was prominent and dense on the nuclear envelope the nucleus showed chromatin condensation. These observations indicated that the transition from PPB to PNF and then to the prophase spindle is closely related to the progress of the nuclear cycle.     

Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections

We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.     

Xylem development and cell wall changes of soybean seedlings grown in space

BACKGROUND AND AIMS: Plants growing in altered gravity conditions encounter changes in vascular development and cell wall deposition. The aim of this study was to investigate xylem anatomy and arrangement of cellulose microfibrils in vessel walls of different organs of soybean seedlings grown in Space. METHODS: Seeds germinated and seedlings grew for 5 d in Space during the Foton-M2 mission. The environmental conditions, other than gravity, of the ground control repeated those experienced in orbit. The seedlings developed in space were compared with those of the control test on the basis of numerous anatomical and ultrastructural parameters such as number of veins, size and shape of vessel lumens, thickness of cell walls and deposition of cellulose microfibrils. KEY RESULTS: Observations made with light, fluorescence and transmission electron microscopy, together with the quantification of the structural features through digital image analysis, showed that the alterations due to microgravity do not occur at the same level in the various organs of soybean seedlings. The modifications induced by microgravity or by the indirect effect of space-flight conditions, became conspicuous only in developing vessels at the ultrastructural level. The results suggested that the orientation of microfibrils and their assembly in developing vessels are perturbed by microgravity at the beginning of wall deposition, while they are still able to orient and arrange in thicker and ordered structures at later stages of secondary wall deposition. CONCLUSIONS: The process of proper cell-wall building, although not prevented, is perturbed in Space at the early stage of development. This would explain the almost unaltered anatomy of mature structures, accompanied by a slower growth observed in seedlings grown in Space than on Earth.     

Comparison of saponin composition and content in wild soybean (Glycine soja Sieb. and Zucc.) before and after germination

Eight wild soybean accessions with different saponin phenotypes were used to examine saponin composition and relative saponin quantity in various tissues of mature seeds and two-week-old seedlings by LC–PDA/MS/MS. Saponin composition and content were varied according to tissues and accessions. The average total saponin concentration in 1?g mature dry seeds of wild soybean was 16.08?±?3.13?μmol. In two-week-old seedlings, produced from 1?g mature seeds, it was 27.94?±?6.52?μmol. Group A saponins were highly concentrated in seed hypocotyl (4.04?±?0.71?μmol). High concentration of DDMP saponins (7.37?±?5.22?μmol) and Sg-6 saponins (2.19?±?0.59?μmol) was found in cotyledonary leaf. In seedlings, the amounts of group A and Sg-6 saponins reduced 2.3- and 1.3-folds, respectively, while DDMP?+?B?+?E saponins increased 2.5-fold than those of mature seeds. Our findings show that the group A and Sg-6 saponins in mature seeds were degraded and/or translocated by germination whereas DDMP saponins were newly synthesized.     

Effects of UV-B radiation on soybean yield and seed quality: a 6-year field study

Two soybean [ Glycine max (L.) Merr.] cultivars, Essex and Williams, were grown in the field for 6 consecutive seasons under ambient and supplemental levels of ultravio-Set-B radiation to determine the potential for alterations in yield or seed quality with a reduction in the stratospheric ozone column. The supplemental UV-B fluences simulated a 16 or 25% ozone depletion. The data presented here represent the first field experiment conducted over multiple seasons which assesses the effects of increased UV-B radiation on seed yield. Overall, the cultivar Essex was found to be sensitive to UV-B radiation (yield reductions of 20%) while the cultivar Williams was tolerant. However, the effectiveness of UV-B radiation in altering yield was strongly influenced by the seasonal microclimate, and the 2 cultivars responded differently to these changing factors. Yield was reduced most in Essex during seasons in which water availability was high and was reduced in Williams only when water was severely limiting. The results of these experiments demonstrate the necessity for multiple-year experiments and the need to increase our understanding of the interaction between UV-B radiation and other environmental stresses in order to assess the potential consequences of stratospheric ozone depletion.     

Sensitivity of soybean leaf development to water deficits

Abstract. Drought effects on the final leaf area of individual leaves were hypothesized to depend on the leaf developmental stage at which drought occurred. To evaluate this hypothesis, final leaf area and cell number were measured for soybean ( Glycine max (L.) Merr.) leaves that were at different stages of development when single or cyclical drought treatment was imposed. Leaf emergence rate from the meristem, as depicted by changes in the plastochron index, was not as sensitive as leaf expansion to cyclical droughts. For leaf expansion, small leaves, once they emerged from the meristem, suffered larger decreases in growth than leaves undergoing rapid leaf area expansion. Decreases in final leaf area as a result of a cyclical drought were correlated with decreases in final cell number. Decreases resulting from a single 8-d drought were dependent on the age of the leaf at the time of drought, because small leaves were found to have proportionately larger decreases in final cell number and area than larger leaves. These results indicated that age-dependent leaf responses to drought are based on the relative activity of cell division and expansion at the time stress was imposed.     

Genome-wide identification and characterization of novel microRNAs in seed development of soybean

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA–target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.     

Carbon dioxide concentration at night affects translocation from soybean leaves

Studies have indicated that the concentration of carbon dioxide [CO2] during the dark period may influence plant dry matter accumulation. It is often suggested that these effects on growth result from effects of [CO2] on rates of respiration, but responses of respiration to [CO2] remain controversial, and connections between changes in respiration rate and altered growth rate have not always been clear. The present experiments tested whether translocation, a major consumer of energy from respiration in exporting leaves, was sensitive to [CO2]. Nineteen-day-old soybean plants grown initially at a constant [CO2] of 350 micromol mol(-1) were exposed to three consecutive nights with a [CO2] of 220-1400 micromol mol(-1), with a daytime [CO2] of 350 micromol mol(-1). Change in dry mass of the individual second, third and fourth trifoliate leaves over the 3-d period was determined, along with rates of respiration and photosynthesis of second leaves, measured by net CO2 exchange. Translocation was determined from mass balance for second leaves. Additional experiments were conducted where the [CO2] around individual leaves was controlled separately from that of the rest of the plant. Results indicated that low [CO2] at night increased both respiration and translocation and elevated [CO2] decreased both processes, to similar relative extents. The effect of [CO2] during the dark on the change in leaf mass over 3 d was largest in second leaves, where the change in mass was about 50% greater at 1400 micromol mol(-1) CO2 than at 220 micromol mol(-1) CO2. The response of translocation to [CO2] was localized in individual leaves. Results indicated that effects of [CO2] on net carbon dioxide exchange rate in the dark either caused or reflected a change in a physiologically important process which is known to depend on energy supplied by respiration. Thus, it is unlikely that the observed effects of [CO2] on respiration were artefacts of the measurement process in this case.