Soybean Sequence Research Articles

Changes in soil phosphorus (P) fractions and P bioavailability after 10 years of continuous P fertilization

Phosphorus fertilization modify soil P fractions differing in availability, but little is known about bioavailability of these pools for the crops when increasing P fertilizer rates in the medium term. Our objectives were to evaluate: i) changes in Bray-1 P content (extracted with 0,03 M NH4F and 0,1 M HCl) and soil P fractions as estimated by physical (Cambardella and Elliot method, POM-P) and chemical fractionation (Hedley method), ii) the relationship between these fractions and P bioavailability quantified in a test crop, and iii) the interaction with sulfur (S) fertilization after 10 years of continuous P and S fertilization. Soil samples were taken after 10 years in an experiment that followed a maize - full season-soybean - double-cropped wheat /soybean sequence that received P and S fertilization when cereals were sown. Treatments consisted of a factorial combination of three P rates (0, 20, and 40 kg P ha−1) and four S rates (0, 12, 24, and 36 kg S ha−1) applied to cereals from 2000 to 2010. After that, a maize used as a test crop was sown and P uptake was considered as bioavailable P. Soil samples were taken before sowing the test crop, and P in soil was fractionated chemically by the Hedley method and physically by wet sieving. After 10 years, when P fertilizer was not applied, soil Bray-1 P decreased 50 % respect to the initial P values, and increased up to 2.3 times when evaluating the highest P fertilizer rate. P fertilization did not change in POM-P. P soil labile (NaHCO3-Pi) and moderately labile (NaOH- Pi and HCl 1 M- Pi) inorganic fractions increased 83 %, 50 %, and 22 % in response to P addition, representing an increase of 4.2, 4.9, and 4.5 mg kg−1 of these fractions per 100 kg of applied P. Likewise, these fractions were related with P uptake in the maize test crop with 1.6, 1.5, and 1 kg of P uptake ha−1 in mg kg−1 increase in each of these fractions, respectively. Then, these fractions may be responsible for the legacy-P after 10 years of continuous fertilization in a Luvic Phaeozem of the Pampas region.

Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development

Glutathione S-transferases are a multifunctional protein superfamily that is involved in diverse plant functions such as defense mechanisms, signaling, stress response, secondary metabolism, and plant growth and development. Although the banana whole-genome sequence is available, the distribution of GST genes on banana chromosomes, their subcellular localization, gene structure, their evolutionary relation with each other, conserved motifs, and their roles in banana are still unknown. A total of 62 full-length GST genes with the canonical thioredoxin fold have been identified belonging to nine GST classes, namely tau, phi, theta, zeta, lambda, DHAR, EF1G, GHR, and TCHQD. The 62 GST genes were distributed into 11 banana chromosomes. All the MaGSTs were majorly localized in the cytoplasm. Gene architecture showed the conservation of exon numbers in individual GST classes. Multiple Em for Motif Elicitation analyses revealed few class-specific motifs and many motifs were found in all the GST classes. Multiple sequence alignment of banana GST amino acid sequences with rice, Arabidopsis, and soybean sequences revealed the Ser and Cys as conserved catalytic residues. Gene duplication analyses showed the tandem duplication as a driving force for GST gene family expansion in banana. Cis-regulatory element analysis showed the dominance of light-responsive element followed by stress- and hormone-responsive elements. Expression profiling analyses were also done by RNA-seq data. It was observed that MaGSTs are involved in various stages of fruit development. MaGSTU1 was highly upregulated. The comprehensive and organized studies of MaGST gene family provide groundwork for further functional analysis of MaGST genes in banana at molecular level and further for plant breeding approaches.

Impact of Cropping System Diversification on Vegetative and Reproductive Characteristics of Waterhemp (Amaranthus tuberculatus)

Corn- and soybean-dominated cropping systems create and maintain a favorable environment for summer annual weeds whose emergence and growth phenology are similar to these annual summer crops. Cropping system diversification can be an effective approach for controlling noxious weeds without increasing reliance on chemical herbicides. Diversification may be especially important for managing waterhemp, a dioecious, summer annual weed that is becoming increasingly prevalent in the US Corn Belt due to its life history characteristics and herbicide resistance profile. Compared to corn and soybean, alfalfa and oat emerge and establish earlier and are thus more competitive with warm-season weeds like waterhemp. Knowledge of vegetative and reproductive characteristics in a range of crop environments can be valuable for planning weed management strategies. However, most of the relevant characteristics for a population dynamics model were available in corn and soybean monocultures. We examined the relationship between waterhemp's aboveground mass and fecundity under four crop species' presence within three crop rotation systems: a 2-year sequence of corn and soybean; a 3-year sequence of corn, soybean, and oat intercropped with red clover; and a 4-year sequence of corn, soybean, oat intercropped with alfalfa, and alfalfa. All the rotation systems were treated with conventional or reduced rates of herbicides. We established eighteen linear equations to predict waterhemp's fecundity from dried aboveground mass in each crop and associated crop management program since measuring the latter allows for quicker estimation of fecundity compared to counting seeds on each individual plant. Rotation system and crop phase within rotation system had significant effects on all the response variables but weed control regime on some. The sex ratios at maturity were slightly female-biased in oat and alfalfa. Mature waterhemp plants were larger in corn and soybean than in oat and alfalfa. Oat and alfalfa were planted earlier than corn and soybean and successfully competed for resources against waterhemp despite the absence of herbicide or interrow cultivation. Frequent hay cuts in alfalfa served as physical weed control and contributed to suppressing waterhemp and other weeds substantially.

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Characteristics and phylogeny of DREB gene subfamily in soybeans [Glycine max (L.) Meril

Dehydration responsive element binding proteins (DREB) are transcription factors linked to cis-acting elements of the promoter region, which regulate plant gene expression in response to abiotic stress. In this study, 69 DREB gene sequences of soybean from NCBI belonging to 18 GmDREB (Glycine max DREB) genes of 1 to 8 copies distributed on 17 chromosomes were identified in which GmDREB3 has 8 copies and the rest consisted of 1 to 4 ones. The motif PTPEMAARAYDVAALALKGPSARLNFPEL containing 11 points associated with the promoter of functional genes existed in 4 main types with the most popular one RGRRWKERRWT found in 13/18 DREB proteins was regarded as the popular AP2 domain of DREB protein. The phylogenetic tree based on the nucleotide sequences of GmDREB genes and the amino acid sequences of the AP2 domain expresses the evolution and relationship of the DREB subfamily in soybean. This study provides comprehensive information about the DREB subfamily, which formed the basis for experimental analyses to clarify the function of some members of this subfamily.

Microbial Community Dynamics of Soybean (Glycine max) Is Affected by Cropping Sequence.

The microbial composition of the rhizosphere soil could be an important determinant of crop yield, pathogen resistance, and other beneficial attributes in plants. However, little is known about the impact of cropping sequences on microbial community dynamics, especially in economically important species like soybean. Using 2-year crop sequences of corn-soybean, canola-soybean, and soybean-soybean, we investigated how crops from the previous growing season influenced the structure of the microbiome in both the bulk soil and soybean rhizosphere. A combination of marker-based Illumina sequencing and bioinformatics analyses was used to show that bacterial species richness and evenness in the soybean rhizosphere soil were similar following canola and soybean compared to a previous corn sequence. However, fungal species richness and evenness remained unaffected by crop sequence. In addition, bacterial and fungal species diversity in both the bulk and soybean rhizosphere soil were not influenced by crop sequence. Lastly, the corn-soybean sequence significantly differed in the relative abundance of certain bacterial and fungal classes in both the soybean rhizosphere and bulk soil. While canola-soybean and a continuous soybean sequence did not, suggesting that a preceding corn sequence may reduce the occurrence of overall bacterial and fungal community members. For the present study, crop sequence impacts bacterial diversity and richness in both the bulk soil and soybean rhizosphere soil whereas fungal diversity and richness are resilient to crop sequence practices. Together, these findings could help drive decision making for annual crop and soil management practices.

Identification and in-silico characterization of Serpin genes in legumes genomes

Serine protease inhibitors (serpins) are a unique family of protease inhibitor containing mobile reactive center loop. The availability of genome sequences of pigeonpea, soybean, commanbean, cowpea, mungbean and adzuki bean provided an opportunity to search for the serpin genes. A total of seven serpin genes were identified in the above legume genomes. Phylogenetic analysis of legume serpins, devided them into two major clades (Clade-I:VanSerpin, VraSerpin, VunSerpin, PvuSerpin and clade-II: GmaSerpin1, GmaSerpin2 and CcaSerpin) based on conserved reactive center (P2-P1’), domains and exon-intron boundary in the gene structure. The common reactive center of all the seven serpins indicated their ability to target cognate proteases and play an important role in response to insects, fungal pathogens and also the drought.

An electrochemical DNA biosensor fabricated from graphene decorated with graphitic nanospheres

Graphene decorated with graphitic nanospheres functionalized with pyrene butyric acid (PBA) is used for the first time to fabricate a DNA biosensor. The electrode was formed by attaching a DNA probe onto PBA, which had been stacked onto a graphene material decorated with graphene nanospheres (GNSs). The nanomaterial was drop-coated onto a carbon screen-printed electrode (SPE) to create the GNS-PBA modified electrode (GNS-PBA/SPE). A simple method was used to produce GNS by annealing graphene oxide (GO) solution at high temperature. Field emission scanning electron micrographs confirmed the presence of a spherical shape of GNS with a diameter range of 40–80 nm. A stable and uniform PBA-modified GNS (GNS-PBA) was obtained with a facile ultrasonication step. Thus allowing aminated DNA probes of genetically modified (GM) soybean to be attached to the nanomaterials to form the DNA biosensor. The GNS-PBA/SPE exhibited excellent electrical conductivity via cyclic voltammetry (CV) and differential pulse voltammetry (DPV) tests using potassium ferricyanide (K3[Fe(CN)6]) as the electroactive probe. By employing an anthraquinone monosulfonic acid (AQMS) redox intercalator as the DNA hybridization indicator, the biosensor response was evaluated using the DPV electrochemical method. A good linear relationship between AQMS oxidation peak current and target DNA concentrations from 1.0 × 10−16 to 1.0 × 10−8 M with a limit of detection (LOD) of less than 1.0 × 10−16 M was obtained. Selectivity experiments revealed that the voltammetric GM DNA biosensor could discriminate complementary sequences of GM soybean from non-complementary sequences and hence good recoveries were obtained for real GM soybean sample analysis. The main advantage of using GNS is an improvement of the DNA biosensor analytical performance.

The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants.

Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes. Promoter analysis showed that these 15 genes were rich in ABRE, MYB and MYC cis-acting elements which were reported to be involved in abiotic stress responses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that 15 GmbZIP genes could be induced by drought and salt stress. GmbZIP2 was significantly upregulated under stress conditions and thus was selected for further study. Subcellular localization analysis revealed that the GmbZIP2 protein was located in the cell nucleus. qRT-PCR results show that GmbZIP2 can be induced by multiple stresses. The overexpression of GmbZIP2 in Arabidopsis and soybean hairy roots could improve plant resistance to drought and salt stresses. The result of differential expression gene analysis shows that the overexpression of GmbZIP2 in soybean hairy roots could enhance the expression of the stress responsive genes GmMYB48, GmWD40, GmDHN15, GmGST1 and GmLEA. These results indicate that soybean bZIPs played pivotal roles in plant resistance to abiotic stresses.

Long-term cropping systems management influences soil strength and nutrient cycling

Elucidating complex interactions of cover crops and crop residues on soil physicochemical properties is critical to sustaining soil productivity long-term. Our objective was to compare soil strength and chemistry (physiochemical), cover crop residue composition, and soil compaction following 15-years of cropping system implementation under non-tillage. Main effects were cropping sequences of soybean (Glycine max L.), corn (Zea mays L.), and cotton (Gossypium hirsutum L.), grown on a Loring silt loam, and sequences of corn and soybean on a Maury silt loam. Split-block treatments consisted of winter wheat (Triticum aestivum L.), Austrian winter pea (Pisum sativum L. sativum var. arvense) and hairy vetch (Vicia villosa Roth) cover crops, as well as poultry litter, and a fallow control. Soil physicochemical characteristics were evaluated at surface (0–15 cm) and sub-surface (15–30 cm) depths. Overall, soil physicochemical parameters were more affected by long-term cover crops and poultry litter in surface layers, whereas crop rotations impacted soil chemistry at sub-surface layers. High-nitrogen (N) containing cover crops had more desirable composition for soil biota (less recalcitrant), whereas corn had the highest soil carbon (C), N, and C:N ratio, likely owing to the greatest amount of residue being produced under this cropping sequence. Whole profile (0–1.2 m) assessment of soil compaction indicates: continuous cotton > continuous soybean > corn-soybean > continuous corn > corn-cotton, likely owing to greater planting and spraying traffic throughout the cotton production cycle. Study results help identify cropping system management effects on soil physicochemical properties under no-tillage and such data are needed for quantifying soil quality per soil conservation management.

Agronomic and economic tradeoffs between alternative cover crop and organic soybean sequences

AbstractOrganic grain producers are interested in reducing tillage to conserve soil and decrease labor and fuel costs. We examined agronomic and economic tradeoffs associated with alternative strategies for reducing tillage frequency and intensity in a cover crop–soybean (Glycine max L. Merr.) sequence within a corn (Zea mays L.)–soybean–spelt (Triticum spelta L.) organic cropping system experiment in Pennsylvania. Tillage-based soybean production preceded by a cover crop mixture of annual ryegrass (Lolium perenne L. ssp. multiflorum), orchardgrass (Dactylis glomerata L.) and forage radish (Raphanus sativus L.) interseeded into corn grain (Z. mays L.) was compared with reduced-tillage soybean production preceded by roller-crimped cereal rye (Secale cereale L.) that was sown after corn silage. Total aboveground weed biomass did not differ between soybean production strategies. Each strategy, however, was characterized by high inter-annual variability in weed abundance. Tillage-based soybean production marginally increased grain yield by 0.28 Mg ha−1 compared with reduced-tillage soybean. A path model of soybean yield indicated that soybean stand establishment and weed biomass were primary drivers of yield, but soybean production strategy had a measurable effect on yields due to factors other than within-season weed–crop competition. Cumulative tillage frequency and intensity were quantified for each cover crop—sequence using the Soil Tillage Intensity Rating (STIR) index. The reduced-tillage soybean sequence resulted in 50% less soil disturbance compared to tillage-based soybean sequence across study years. Finally, enterprise budget comparisons showed that the reduced-tillage soybean sequence resulted in lower input costs than the tillage-based soybean sequence but was approximately $114 ha−1 less profitable because of lower average yields.

Crop Rotations and Poultry Litter Affect Dynamic Soil Chemical Properties and Soil Biota Long Term.

Dynamic soil chemical interactions with conservation agricultural practices and soil biota are largely unknown. Therefore, this study aims to quantify long-term (12-yr) impacts of cover crops, poultry litter, crop rotations, no-tillage, and their interactions on dynamic soil properties and to determine their relationships with nutrient cycling, crop yield, and soil biodiversity (soil microbial and earthworm communities). Main effects were 13 different cropping sequences of soybean [ (L.) Merr.], corn ( L.), and cotton ( L.) at the Research and Education Center at Milan, TN, and eight sequences of corn and soybean at the Middle Tennessee Research and Education Center, Spring Hill, TN. Sequences were repeated in 4-yr phases from 2002 to 2014. Split-block cover crop treatments consisted of winter wheat ( L.), hairy vetch ( Roth), poultry litter, and a fallow control. Soil C and nutrient fluxes were calculated at surface (0-5 cm) and subsurface (5-15 cm) layers during Years 0, 2, 4, 8, and 12. After 12 yr, weighted means (0-15 cm) of soil pH, P, K, Ca, Mg, total N, and C were greater under poultry litter-amended soils compared with cover crops ( < 0.05). In addition, continuous corn sequences resulted in greater soil K, N, and C concentrations than soybean-soybean-corn-corn rotations ( < 0.05). Poultry litter treatments were positively correlated with greater soil fertility levels, as well as higher crop yield and soil biodiversity. These results underscore linkages between manure additions and cropping sequences, within the nutrient cycling, soil health, and crop production continuum.

Genome-wide analysis and expression profiling of respiratory burst oxidase homologue gene family in Glycine max

Plant respiratory burst oxidase homologs (Rbohs) are key enzymes that catalyze the generation of reactive oxygen species (ROS) in plants. There is a diverse family of Rboh genes in different plants, mediated a multiplicity of physiological functions. However, there have been limited reports on the characterization of Rboh gene family in soybean. In the present study, seventeen GmRboh genes were identified from the whole-genome sequence of soybean, and these proteins were phylogenetically clustered into five distance subgroups. Comprehensive expression profile analysis provided insights into the soybean-specific functional divergence among members of the Rboh gene family. The expressions patterns of GmRboh genes under biotic/abiotic stress were evaluated based on global gene expression tools and qRT-PCR analysis, and the 'hotspot' genes for development and stress responses were identified. Some duplicate genes were partially redundant, while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. At last, applying diphenylene iodonium (DPI), a classical NADPH oxidase inhibitor, significantly reduced ROS accumulation in soybean roots under abiotic stress, and also influenced the expression of GmRboh genes. Taken together, our results provided a good reference for further functional characterization analysis of members of the Rboh genes in soybean.

Novel method for in situ investigation into graphene quantum dots effects on the adsorption of nitrated polycyclic aromatic hydrocarbons by crop leaf surfaces

Nitrated polycyclic aromatic hydrocarbons (NPAHs) are PAH derivatives with more toxic effects to ecosystem, and the partitioning of NPAHs in crop system constitutes the potential exposure to human health through the dietary pathway. In the present study, a novel method for in situ detection of 9-nitroanthracene (9-NAnt) and 3-nitrofluoranthene (3-NFla) adsorbed onto the leaf surfaces of living soybean and maize seedlings was established based on the fiber-optic fluorimetry combined with graphene quantum dots (GQDs) as a fluorescent probe. The detection limits for the in situ quantification of the two adsorbed NPAHs ranged from 0.8 to 1.6 ng/spot (spot represents determination unit, 0.28 cm2 per spot). Using the novel method, the effects of GQDs on the adsorption of individual 9-NAnt and 3-NFla by the living soybean and maize leaf surfaces were in situ investigated. The presence of GQDs altered the adsorption mechanism from the sole film diffusion to the combination of film diffusion and intra-particle diffusion, and shortened the time required to achieving adsorption equilibrium by 15.8–21.7%. Significant inter-species and inter-chemical variability existed in terms of the equilibrated adsorption capacity (qe) with the sequence of soybean > maize and 3-NFla > 9-NAnt. The occurrence of GQDs enlarged the qe values of 9-NAnt and 3-NFla by 22.8% versus 28.7% for soybean, and 16.2% versus 20.3% for maize, respectively, which was largely attributed to GQDs-induced expansion to the surface area for adsorbing NPHAs and the stronger electrostatic interaction between the -NO2 of NPAH molecules and the functional groups (e.g., -COOH, -OH) of GQDs outer surfaces. And, the varied enhancement degrees in the order of 3-NFla > 9-NAnt might be explained by the steric effects that resulted in the easier accessibility of -NO2 of 3-NFla to the outer surface of GQDs. Summarily, the GQDs increased the retention of NPAHs on crop leaf surfaces, potentially threatening the crop security.

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is largely unknown. Therefore, changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites. Main effects of four different cropping sequences of corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max L.) were rotated in four year phases for 12-yrs at two Tennessee Research and Education Centers in a randomized complete block design with split-block treatments of four winter bio-covers: hairy vetch (Vicia villosa L.), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Using Illumina high-throughput sequencing of 16S rRNA genes, bacterial community composition was determined. Composition, diversity, and relative abundance of specific taxa were correlated per cropping system, bio-cover, and their interaction. We found that i) richness and diversity varied temporally and spatially, coinciding with soil carbon, pH, nutrient levels, and climatic variability; ii) community composition varied by cropping system, with continuous corn, soybean, and the corn-soybean rotation presenting a hybrid of the continuous corn and soybean communities; however, continuous cotton resulted in the most varied assemblage; iii) bio-covers asserted the greatest influence on microbial communities; specifically poultry litter treatments differed from cover crops (all of which received inorganic-N). Consequently, microbial diversity was greatest under nutrient rich bio-covers (poultry litter) and high residue producing, less pesticide-intensive cropping sequences (soybean and corn compared to cotton), suggesting a more dynamic soil ecology under these no-till cropping systems. This suggests that nutrient management (inorganic fertilizers vs. animal manure) and greater crop rotations (within 4-yr phases) may directly drive phylogenetic community structure and subsequent ecosystem services across agricultural landscapes.

Impact of Crop Rotations and Soil Amendments on Long‐Term No‐Tilled Soybean Yield

Core Ideas Poultry litter increased yields by 11% across locations and years when compared to wheat cover crops. Yields in soybean–soybean–corn–cotton rotations during Phase II and corn–corn–soybean–corn during Phase I were greatest. Incorporating corn once within a 4‐yr cropping cycle resulted in 8% greater yields than continuous soybean. Continuous cropping systems without cover crops are often perceived as unsustainable for long‐term yields and soil health. Continuous cropping systems without cover crops are perceived as unsustainable for long‐term yield and soil health. To test this, cropping sequence and cover crop effects on soybean (Glycine max L.) yield were assessed. Main effects were 10 sequences of soybean, corn (Zea mays L.), and cotton (Gossypium hirsutum L.) grown on a Loring silt loam at the Research and Education Center at Milan (RECM), TN, and six cropping sequences of corn and soybean on a Maury silt loam at the Middle Tennessee Research and Education Center (MTREC), Spring Hill, TN. Sequences were repeated in 4‐yr Phases (i.e., I, II, and III) from 2002 to 2013. Split‐block treatments consisted of hairy vetch (Vicia villosa L.), Austrian winter pea (Pisum sativum L. sativum var. arvense), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Continuous soybean yield was equivalent to all rotations (2.6 and 2.7 Mg ha−1, respectively; P = 0.23), however, yield varied per phase (P &lt; 0.001). Specifically, soybean yield in soybean‐soybean‐corn‐cotton during Phase II and corn‐corn‐soybean‐corn during Phase I (4.2 and 4.1 Mg ha−1, respectively) exceeded continuous systems during Phases II and III (P &lt; 0.05). Poultry litter increased yield 11% across locations and years compared to wheat cover crops (P &lt; 0.05). Incorporating corn once within a Phase increased yield 8% relative to continuous soybean, whereas cotton (once or twice) within a rotation had no effect. Consequently, including corn once within a 4‐yr rotation and poultry litter improved soybean yields, albeit no mono‐cropping yield penalties occurred long‐term.

Continuous Corn and Soybean Yield Penalties across Hundreds of Thousands of Fields

Core Ideas Analysis of 748,374 yield records showed a 4.3% yield penalty for continuous corn. Corn yield penalties were more severe in areas with low moisture and low yields. Continuous soybean showed a 10.3% yield penalty, worse in low‐yielding years. Corn yield penalties grew with up to 3 yr of continuous cropping, but not more. Soybean penalties increased monotonically with number of years continuously cropped. The effects of crop rotations on yields have historically been assessed with field trials, but new datasets offer an opportunity to evaluate these effects using data from commercial farmers’ fields. Here we develop a unique dataset of 748,374 joint observations of field‐level yields, crop histories, and soil and weather conditions across the U.S. Midwest to empirically evaluate crop rotations. For rainfed fields, we found an average continuous corn (Zea mays L.) yield penalty (CCYP) of 4.3% and continuous soybean [Glycine max (L.) Merr.] yield penalty (CSYP) of 10.3% during the 2007 to 2012 growing seasons. The CCYP is greater in locations with low moisture, while the CSYP shows the opposite pattern. Relatedly, irrigation decreases the CCYP but not the CSYP. Both penalties increased with the number of years a field had been continuously cropped, and while the CCYP leveled off after 3 yr in corn, the CSYP showed significant increases out to the (very rare) 5‐yr continuous soybean sequence. An analysis of weather, soil, and planting date interactions with the CCYP and CSYP suggests that timely planting, favorable soil‐climate, and warm early and late‐season minimum temperatures correlate with reductions in the CCYP, while dry conditions and less favorable soil‐climate correlate with reductions in the CSYP. The results of this study not only help refine estimates of rotation effects in commercial fields, but also shed light on the relationships between rotation effects and other factors, thereby offering insight into potential causal mechanisms.

The complete chloroplast genome sequence of semi-wild soybean, Glycine gracilis (Fabales: Fabaceae)

Semi-wild soybean, Glycine gracilis, harbors unique gene resources for the soybean breeding programs, which would help to understand the process of soybean domestication. Here, we sequenced and characterized the complete chloroplast genome sequence of the semi-wild soybean. The genome of G. gracilis has 152,218 bp in length with 35.37% GC content. It contains two inverted repeats blocks of 25,574 bp, separated by the large single-copy block of 83,175 bp and small single-copy block of 17,895 bp. A total of 111 unique genes were annotated, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the ten sequenced Glycine chloroplast genomes revealed that the semi-wild soybean G. gracilis is closer to cultivated soybean G. max than wild soybean G. soja. The newly sequenced complete chloroplast genome of G. gracilis will provide useful resources for the further genetic characterization that would enhance the conservation of this highly endangered species.

Productivity and profitability of upland crop rotations in Northwest Cambodia

The upland cropping region of Northwest Cambodia exhibits limited crop diversity, with maize and cassava dominating rain-fed production systems. Farmers in the Districts of Sala Krau in Pailin Province, and Samlout in Battambang Province, report soil fertility decline in upland cropping systems with associated reduced yields and profitability compared with five years ago. Research was conducted at one site in each of these Districts over a two year period. The purpose of the study was to investigate crop rotations in this system with a focus on better use of soil water throughout the year to increase crop yields and profitability. This included an experiment to investigate increasing cropping intensity from the usual two crops per year to three and evaluate which crop sequences would be feasible. Out of a total 15 crop sequences evaluated, only four were successful in producing viable grain yields. These were the same sequences at both sites and included maize-maize-fallow, maize-maize-sunflower, maize-soybean-fallow and maize-soybean-sunflower. At Pailin, the sequence with the highest overall mean yield (4.3t/ha) and profit was maize-maize-sunflower which returned a gross margin of $USD3700/ha over two years. The sequences with a fallow instead of a third crop produced the lowest financial returns at Pailin. However, in Samlout the maize-fallow was the most profitable sequence with an overall mean yield of 3.0t/ha, returning $1680/ha over two years. The least profitable sequences at Samlout were the two soybean sequences. This study was successful in growing five crops in two years at Pailin, but could not reach the goal of six due to cultivar maturity length. At Samlout four crops over two years were produced, as the pre-monsoon crop was not planted in either year due to lack of sowing rainfall. Seasonal climatic factors had the greatest effect at both field sites on gross margins, which emphasized the importance of matching sowing date to rainfall to make better use of stored soil moisture to optimise yield and profitability. At Pailin, mean seasonal surface soil moisture, hundred seed weight and harvest index also impacted gross margin returns. This research validated the stability of maize in the farming system while sunflower should be further investigated in cropping sequences.

Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants.

High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). Based on this analysis, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nucleotide periodicity in the position of free 5' RNA ends and a bias toward the translational frame. By examining conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice, we found a predominance of 5' termini of RNA degradation intermediates that were separated by a length equal to a ribosome-protected mRNA fragment. Through the analysis of RNA degradome data, we discovered uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, our analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a noncleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.