Wheat Sequences Research Articles

Effect of long term fertilization and manuring on soil quality and productivity under sorghum (Sorghum bicolor)-wheat (Triticum aestivum) sequence in Inceptisol

A permanent field experiment is continued since 1984-85 at Research Farm, AICRP on Cropping Systems Research Unit, Akola, Maharashtra with a view to find out effect of integrated nutrient management on soil quality and productivity of sorghum [Sorghum bicolor (L.) Moench] -wheat (Triticum aestivum L.) crop sequence. The long term impact of organic, inorganic and integrated nutrient management practices on soil quality and productivity were studied after 27th cycle (2010-11). The treatments comprised different levels of recommended dose of fertilizers (RDF), viz. 50, 75 and 100% and RDF in combination with farmyard manure, wheat straw, leucaena loppings and the farmer's practice. The results indicated that, application of 50% RDF + 50% N through FYM recorded highest sorghum (24.58 q/ha) and wheat (26.23 q/ha) grain yield as well as sorghum grain equivalent yield (61 q/ha). The uptake of N, P, K and S by sorghum (83.98, 23.14, 98.67 and 18.60 kg/ha) and wheat (96.17, 18.79, 74.69 and 13.53 kg/ha) was maximum with the integrated nutrient management. The improvement in soil fertility status was observed under the same treatment with concomitant increase in sustainability yield index (0.494) and soil quality index (2.33). The overall increase in the soil quality index (1.98-2.33) was recorded under INM, whereas only chemical fertilizers caused considerable decrease in the SQI (1.19-1.87). The hydraulic conductivity contributed substantially in governing sorghum yield (63.09%) and wheat yield (98.75%). The soil organic carbon contributed substantially in sorghum yield (29.01%). The parameters like hydraulic conductivity (94.7%), OC (5.14%) and DHA (0.07%) contributed in SQI.

Effects of Biomethanated Spentwash on Soil Properties, Nutrient Availability, Uptake, and Yield of Soybean–Wheat Sequence on Inceptisol

The research aimed to study the effect of presown application of primary biomethanated spentwash (PBSW) on soil properties, nutrient availability, uptake and yield of soybean–wheat sequence on Inceptisol. The field experiment with randomised block design was initiated during 2007–8 and present observation was recorded during 2009–10 and 2010–11.The five treatments were, recommended dose (RD) of NPK (T1), 100% RD of N through PBSW without (T2) and with P chemical fertilizer (T3), 50 and 25% RD of N through PBSW + remaining N and P through chemical fertilizers (T4,T5), respectively. The results revealed that the soil physical properties and microbial populations were improved in T2 and T3. The lowest soil pH and pHs were observed in T2. The soil electrical conductivity, organic carbon, exchangeable sodium percentage and sodium adsorption ratio of soil extracts and available K were increased with the increase in PBSW as compared to RD-NPK. The soil available N and P were decreased as PBSW increased at all the soil depths. The greatest yields and total N,P,K uptake of soybean and wheat were observed in T5.

Prospecting plant growth promoting bacteria and cyanobacteria as options for enrichment of macro- and micronutrients in grains in rice–wheat cropping sequence

AbstractThe influence of plant growth promoting bacteria (PGPB) and cyanobacteria, alone and in combination, was investigated on micronutrient enrichment and yield in rice–wheat sequence, over a period of two years. Analysis of variance (ANOVA) in both crops indicated significant differences in soil dehydrogenase activity and micronutrient enrichment in grains (Fe, Zn in rice, and Cu, Mn in wheat). The combined inoculation of Anabaena oscillarioides CR3, Brevundimonas diminuta PR7, and Ochrobactrum anthropi PR10 (T6) significantly increased nitrogen, phosphorus, and potassium (NPK) content and improved rice yield by 21.2%, as compared to the application of recommended dose of NPK fertilizers (T2). The treatment T5 (Providencia sp. PR3 + B. diminuta PR7 + O. anthropi PR10) recorded an enhancement of 13–16% in Fe, Zn, Cu, and Mn concentrations, respectively, in rice grains. In wheat, Providencia sp. PW5 (T6) recorded the highest yield (5.23 Mg ha−1) and significantly higher enrichment of Fe and Cu (44–45%) ...

No-till surface runoff and soil losses in southern Brazil

No-till is widely used to control soil erosion in agricultural areas in Brazil and is currently practiced on about 30Mha. However, studies have shown that no-till is not as efficient in controlling surface runoff losses as it is in reducing soil loss. The objective of this study is to evaluate soil and surface runoff losses on small and large plots with differing slope lengths, cropping sequences and tillage systems in southern Brazil. Surface runoff and soil losses under natural rainfall erosion plots (3.5×11m, 3.5×22m, 50×100m, and 100×100m) were evaluated in two experiments in a well-drained Oxisol (>60% clay) with 9% and 7% slopes, respectively. The experiment extended over 14 years comparing 4 different soil management systems: (a) bare soil plots with slope length 22m; (b) bare soil plots with slope length 11m; (c) sequence of wheat (Triticum aestivum)/soybean [Glycine max (L.) Merr] with disk plow+lighter off-set disk-harrow (DP+LD); and (d) sequence of wheat/soybean under no-till (NT). In another experiment using large field plots, three soil tillage regimens (DP+LD; heavy off-set disk-harrow+lighter off-set disk-harrow (HD+LD), and NT) were compared over the course of a 5-yr. crop sequence of black oats (Avena estrigosa)/soybean-black oats/corn (Zea mays L.)-wheat/soybean- black oats/soybean -blue lupine (Lupinus angustifolium)/corn. Results for both experiments show that, when compared with conventional soil tillage (DP+LD or HD+LD), soil losses for NT were >70% lower. However, the benefit of reduced surface runoff losses was less evident, suggesting the need to implement additional practices to control surface runoff to avoid transport of pollutants to waterways.

Characterization and sequence diversity of the Gsp-1 gene in diploid species of the Aegilops genus

Several studies have suggested a minor role in determining grain endosperm texture for the Gsp-1 gene, although appears related with the synthesis of the arabinogalactan-peptide. The current study evaluated the allelic variability of Gsp-1 genes in five diploid species of the Aegilops genus along with the molecular characterization of the main allelic variants found in each species and their phylogenetic relationships with the polyploid wheats. There was a high level of polymorphism in Gsp-1 genes – up to 19 alleles were obtained, of which 11 were novel. The processing of Gsp-1 amino acid sequences led to two main domains: AGP (arabinogalactan peptide) and GSP-1 (grain softness protein). Several substitutions were detected in both domains with respect to the bread wheat sequences, which could modify grain hardness. The sequences obtained showed relationship with the Gsp-B1 and Gsp-D1 genes of common wheat. These results showed that diploid Aegilops species are a rich resource of novel genetic variability for the Gsp-1 gene, whose hypothetical functionality should be tested in the genetic pool of modern wheat, valuing as the true role of these genes in grain hardness and their effective role as source of the AGP, a non-starch polysaccharide with health properties.

Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.)

Georgia plays an important role in wheat formation. In the past, the Zanduri population of Georgia was a set of diploid—Triticum monococcum var. hornemanii (2n = 14) (Gvatsa Zanduri), tetraploid Triticum timopheevii (2n = 28) (Chelta Zanduri) and hexaploid Triticum zhukovskyi Men. et Er. (2n = 42). It is a Zanduri puzzle that wild T. araraticum was not found in Georgia, though cultivated T. timopheevii was only detected here. Next-generation sequencing technologies, which have been developed in recent years, enable the determination of complete nucleotide sequences of both chloroplast and mitochondrial DNA of many higher plants, including wheat. The genetic structure of Zanduri wheat is more accurately inferred by the complete sequences of chloroplast DNA. In the present investigation, the complete sequences of three Zanduri wheats (T. timopheevii, T. zhukovskyi, and T. monococcum var. hornemanii) and wild T. araraticum are presented. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. In comparison to T. araraticum, there are 12 SNPs, a 25 bp inversion in the ccsA-ndhD intergenic sequence, and a 38-bp inversion in the intergenic sequence rbcL-rpl23 pseudogene identified in T. timopheevii and T. zhukovskyi. In addition, a 24 bp repeat of trnG-trnI intergenic sequence is present as a double copy in T. araraticum, whereas in T. timopheevii and T. zhukovskyi, it is present as a triple copy. Unlike T. araraticum, T. timopheevii and T. zhukovskyi have a 6 bp repeat in the gene ndhH, which results in a dipeptide duplication in the corresponding protein. Gvatsa Zanduri (T. monococcum var. hornemanii) chloroplast DNA slightly differs from other einkorn chloroplast DNA. In comparison to T. monococcum, four SNPs can be identified in T. monococcum (Gvatsa Zanduri), two in gene matK and one in gene ndhD. The sequenced chloroplast DNA molecules were compared to other Triticum and Aegilops species, and a phylogenetic tree was constructed. T. araraticum, T. timopheevii and T. zhukovskyi chloroplast DNA showed the closest phylogenetic relationship with the chloroplast DNA of Ae. speltoides. The most significant difference was in the 114-bp deletion within the gene ndhH in the Timopheevi species.

Reducing nitrous oxide emissions from a maize‐wheat sequence by decreasing soil nitrate concentration: effects of split application of pig slurry and dicyandiamide

SummaryPig slurry (PS) is a valuable nitrogen (N) source for agricultural crops but the simultaneous supply of readily decomposable carbon and mineral N can result in large soil nitrous oxide (N2O) emissions. Our objective was to determine the individual and combined effects of split PS application and addition of a nitrification inhibitor (dicyandiamide, DCD) on N2O emissions and soil mineral N concentration in southern Brazil. Soil N2O fluxes were measured from November 2010 to November 2011 from a maize (Zea mays L.)‐wheat (Triticum aestivum L.) sequence under various fertilizer treatments: no‐N control, PS applied in a single pre‐plant dose with or without DCD, PS split‐applied with or without DCD, and urea split‐applied. Cumulative N2O emissions increased linearly (R2 = 0.73) with increasing soil nitrate (NO3−) exposure, indicating that management practices aimed at reducing soil NO3− concentrations can decrease soil N2O emissions. In total for the two crops, splitting PS reduced N2O emission factors (EF) by 33%, whereas the addition of DCD reduced EF by 60 and 41% when PS was applied in single and split doses, respectively. However, splitting PS or adding DCD failed to reduce N2O losses more than a single pre‐plant PS application in maize where background soil NO3− concentrations were large. The addition of DCD to PS applied as a single pre‐plant dose resulted in the largest reduction in soil N2O emissions, whereas splitting PS with and without DCD resulted in significantly smaller abatements. Consequently, we concluded that adding DCD to PS in a single pre‐plant application is a better option than splitting PS applications for reducing soil N2O emissions in no‐till cereal cropping systems in southern Brazil.

Dynamic crop sequencing in Western Australian cropping systems

During the last two decades in Western Australia, the traditional mixed farming system has been increasingly displaced by intensive crop sequences dominated by wheat. Intensive wheat sequences are usually maintained by using suitable breaks, including pasture, fallow, or alternative cereal, oilseed and legume crops, to control weeds and disease, or maintain the supply of nitrogen to crops. New cereal fungicide options may also assist to maintain intensive cereal systems by suppressing soilborne cereal diseases. To guide the successful diversification of intensive cereal systems, we evaluated the effect of a 2-year experimental matrix of 10 different sequence options. Wheat in the sequence was treated with the fluquinconazole fungicide Jockey (wheat + J) to control soilborne pathogens, or with the usual seed dressing of flutriafol fungicide (wheat – J), used for control of bunts and smuts only. The sequences were wheat + J, wheat – J, barley, grain oats, oaten hay, canola, lupin, field pea, oat–vetch green manure, bare fallow) in which all treatment combinations were grown in year 2 following the same 10 treatments in year 1. In year 3, wheat + J was grown across the entire area as the test crop. In year 2, grain yields of all crops were reduced when crops were grown on their own residues, including wheat (22% reduction), canola (46%), lupin (40%) and field pea (51%). Wheat + J significantly outyielded wheat – J by 300 kg ha–1 in year 1 (14% increase) and 535 kg ha–1 in year 2 (26% increase). Wheat + J was more responsive to break crops than wheat – J in both year 1 and year 2. Break crops sown in year 1, such as canola, fallow, field pea, lupin and oaten hay, continued to have a positive effect on year 3 wheat + J yields. This study has highlighted the importance of break crops to following cereal crops, and provided an example in which a seed-dressing fungicide fluquinconazole in the presence of low levels of disease consistently improved wheat yields.

How much do sod-based rotations reduce nitrate leaching in a cereal cropping system?

Nitrogen is essential to improving agricultural production systems, explaining why the contamination of groundwater by this nutrient is widespread. The aim of this paper was to describe data collected over 9 years on estimated leaching levels using a simple computation procedure and measurements of soil water content and water balance, nitrate concentrations in drainage water and meteorological data, and to assess the impacts of the duration of the grassland phase and the level of nitrogen fertilization on grassland on the drainage water quality. The study was carried out at a site of the Long-term Environmental Research Observation and Experimentation facility (SOERE) for Environmental Research- Agro-ecosystems, Biogeochemical Cycles and Biodiversity, run by the INRA experimental unit of Lusignan. The experimental treatments were sequences of maize, wheat and barley with different grassland rotational periods (a pure arable crop rotation; three or six years of grassland receiving high-level nitrogen applications; six years of grassland with a low N application rate and long-term grassland with nitrogen application). The study covered the period from April 2005 to June 2013, during which most drainage occurred in the autumn and early winter. Treatments with the longest duration of grassland exhibited less drainage than those containing a higher proportion of arable crops. The average nitrate concentration was 52.7±38.63mgNO3L−1 under a pure crop rotation, compared to 14.9±14.76mgNO3L−1 under a permanent grassland treatment. There were significant differences (P<0.0001) in cumulative nitrogen leaching between the different cropping systems, ranging from 9 to 37kgNha−1year−1. The introduction of mowed grassland sequences into this arable crop rotation caused a marked reduction in the nitrate levels in groundwater, and the greater the proportion of grassland within the rotation the more markedly was the NO3− concentration reduced, whatever the level of N fertilization during the grassland sequence.

New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.

Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum)

Flow cytometric sorting of individual chromosomes and chromosome-based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow-sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNA(L) (ys) and tRNA(M) (et) species, while the nonrepetitive assembly reveals tRNA(A) (la) species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome-specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome-level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor.

Identification of HSP20 gene family in wheat and barley and their differential expression profiling under heat stress.

Small heat shock proteins (sHSPs) are chaperones that play an important role in various developmental, biotic and abiotic stresses. The sHSP family possess a conserved domain of approximately 80 to 100 amino acids called alpha-crystalline domain (ACD), flanked by N- and C-terminal regions. Search for complete proteomes and expressed sequenced tag (EST) database of wheat and barley using Hidden Markov Model and BLAST algorithm was conducted. Here, we report genome-wide identification and characterization of 27 newly TaHSP20 candidate genes in wheat and 13 HvHSP20 in barley, describing structures, phylogenetic relationships, conserved protein motifs, and expression patterns. The structural analysis highlights that this gene family possesses a conserved ACD region at the C-terminal. Detailed pattern analysis of HSP20 revealed presence of P-G doublet and I/V/L-X-I/V/L motif that helps in oligomerization. Identification of conserved motif sequences of wheat and barley HSP20 strongly supported their identity as sHSP families. This study illustrates for the first time 3D model prediction of full-length wheat HSP20 (TaHSP20) protein and ACD region. Digital expression analysis was also carried out in order to reveal a widespread distribution of the sHSP family genes at various developmental stages of wheat and barley. In addition, five selected transcripts of both wheat and barley were validated for their expression profile under 35 °C and 42°C heat stress conditions. Results indicate up-regulation of all the transcripts under heat stress condition except TaCBM38894 candidate, which showed down-regulation in wheat.

Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors.

Extensive studies have focused on the largest class of disease resistance genes (nucleotide binding site-leucine-rich repeat, NBS-LRR) in various plants. However, no research on the dynamic evolution of these genes in domesticated species and their progenitors has been reported. Recently published genome sequences of bread wheat and its two ancestors provide a good opportunity for comparing NBS-encoding genes between ancestors and their progeny. Over 2000 NBS-encoding genes have been identified in bread wheat, which is the largest number having been reported so far. Compared with other grass species, its two progenitors also contained more NBS-encoding genes, indicating that there was an expansion of these genes in their common ancestor. Interestingly, the inherited relationships of NBS-LRR genes among the bread wheat and its two progenitors were ambiguous and only 3 % single-copy orthologues retained gene order in three-way genome comparisons of the three genomes. Lots of NBS-encoding genes present in the either ancestor could not be found in the bread wheat. These results indicated that NBS-LRR genes in bread wheat might have evolved rapidly through a rapid loss of ancestor genes.

Chemical Fractions of Zinc and Their Contribution toward Its Availability under Long-Term Integrated Nutrient Management in Rice–Wheat Sequence in an Acidic Alfisol

This study was carried out in an ongoing field experiment initiated during the 1991 kharif season (May–October) on an acidic soil in the Western Himalayas of India to evaluate the effect of integrated nutrient supply on transformation of zinc (Zn) into various chemical pools. The continuous use of chemical fertilizers alone for 20 years brought about marked depletion in different pools of Zn compared to buffer plots, while integrated use of organic and chemical fertilizers recorded greater content than chemically treated plots. Nonspecifically adsorbed exchangeable Zn (Zn I) was the most important fraction of Zn contributing to diethylene triamine penta-acetic acid (DTPA)–extractable Zn. Content of DTPA-extractable Zn also increased in soil with integrated application of chemical fertilizers and organics over the years. Residual Zn was the most dominant form of Zn, contributing about 55% to total Zn, whereas nonspecifically adsorbed exchangeable Zn was the most important fraction of Zn contributing to DTPA Zn.

Molecular cloning, phylogenetic analysis, and expression profiling of endoplasmic reticulum molecular chaperone BiP genes from bread wheat (Triticum aestivum L.).

BackgroundThe endoplasmic reticulum chaperone binding protein (BiP) is an important functional protein, which is involved in protein synthesis, folding assembly, and secretion. In order to study the role of BiP in the process of wheat seed development, we cloned three BiP homologous cDNA sequences in bread wheat (Triticum aestivum), completed by rapid amplification of cDNA ends (RACE), and examined the expression of wheat BiP in wheat tissues, particularly the relationship between BiP expression and the subunit types of HMW-GS using near-isogenic lines (NILs) of HMW-GS silencing, and under abiotic stress.ResultsSequence analysis demonstrated that all BiPs contained three highly conserved domains present in plants, animals, and microorganisms, indicating their evolutionary conservation among different biological species. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that TaBiP (Triticum aestivum BiP) expression was not organ-specific, but was predominantly localized to seed endosperm. Furthermore, immunolocalization confirmed that TaBiP was primarily located within the protein bodies (PBs) in wheat endosperm. Three TaBiP genes exhibited significantly down-regulated expression following high molecular weight-glutenin subunit (HMW-GS) silencing. Drought stress induced significantly up-regulated expression of TaBiPs in wheat roots, leaves, and developing grains.ConclusionsThe high conservation of BiP sequences suggests that BiP plays the same role, or has common mechanisms, in the folding and assembly of nascent polypeptides and protein synthesis across species. The expression of TaBiPs in different wheat tissue and under abiotic stress indicated that TaBiP is most abundant in tissues with high secretory activity and with high proportions of cells undergoing division, and that the expression level of BiP is associated with the subunit types of HMW-GS and synthesis. The expression of TaBiPs is developmentally regulated during seed development and early seedling growth, and under various abiotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0260-0) contains supplementary material, which is available to authorized users.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Effects of break crops, and of wheat volunteers growing in break crops or in set-aside or conservation covers, all following crops of winter wheat, on the development of take-all (Gaeumannomyces graminis var. tritici) in succeeding crops of winter wheat.

Experiments on the Rothamsted and Woburn Experimental Farms studied the effects on take-all of different break crops and of set-aside/conservation covers that interrupted sequences of winter wheat. There was no evidence for different effects on take-all of the break crops per se but the presence of volunteers, in crops of oilseed rape, increased the amounts of take-all in the following wheat. Severity of take-all was closely related to the numbers of volunteers in the preceding break crops and covers, and was affected by the date of their destruction. Early destruction of set-aside/conservation covers was usually effective in preventing damaging take-all in the following wheat except, sometimes, when populations of volunteers were very large. The experiments were not designed to test the effects of sowing dates but different amounts of take-all in the first wheats after breaks or covers apparently affected the severity of take-all in the following (second) wheats only where the latter were relatively late sown. In earlier-sown second wheats, take-all was consistently severe and unrelated to the severity of the disease in the preceding (first) wheats. Results from two very simple experiments suggested that substituting set-aside/conservation covers for winter wheat, for 1 year only, did not seriously interfere with the development of take-all disease or with the development or maintenance of take-all decline (TAD). With further research, it might be possible for growers wishing to exploit TAD to incorporate set-aside/conservation covers into their cropping strategies, and especially to avoid the worst effects of the disease on grain yield during the early stages of epidemics.

Strongly structured DNA sequences as targets for genosensing: Sensing phase design and coupling to PCR amplification for a highly specific 33-mer gliadin DNA fragment

Electrochemical genosensors are becoming cost-effective miniaturizable alternatives to real-time PCR (RT-PCR) methods for the detection of sequence-specific DNA fragments. We report on the rapid detection of PCR amplicons without the need of purification or strand separation. A challenging target sequence for both PCR amplification and electrochemical detection allowed us to address some difficulties associated to hybridization on electrode surfaces. The target was a highly specific oligonucleotide sequence of wheat encoding the most immunogenic peptide of gliadin that triggers the immune response of celiac disease (CD), the 33-mer. With a sandwich assay format and a rational design of the capture and tagged-signaling probes the problems posed by the strong secondary structure of the target and complementary probes were alleviated. Using a binary self-assembled monolayer and enzymatic amplification, a limit of detection of 0.3nM was obtained. The genosensor did not respond to other gluten-containing cereals such as rye and barley. Coupling to PCR to analyze wheat flour samples required tailoring both the capture and signaling probes. This is the first time that deleterious steric hindrance from long single-stranded regions adjacent to the electrode surface is reported for relatively short amplicons (less than 200bp). The importance of the location of the recognition site within the DNA sequence is discussed. Since the selected gene fragment contains several repetitions of short sequences, a careful optimization of the PCR conditions had to be performed to circumvent the amplification of non-specific fragments from wheat flour.

Soil biological properties as influenced by long-term manuring and fertilization under sorghum (Sorghum bicolor) -wheat (Triticum aestivum) sequence in Vertisols

The effect of long-term manuring and fertilization on soil biological properties was studied under the long term fertilizer experiment on sorghum [Sorghum bicolor (L.) Moench] -wheat (Triticum aestivum L.) sequence conducted on Vertisols. The treatments comprised 50% RDF, 100% RDF, 150% RDF,100% RDF (-S), 100% RDF + 2.5 kg Zn/ ha to wheat crop only, 100% RD of NP, 100% RD of N, 100% RDF + FYM @ 10 tonnes/ha, 100% RDF + S @ 37.5 kg/ ha, FYM @ 10 tonnes/ha, 75% RDF and control. The assessment of soil biological properties at 40 and 70 days after sowing revealed that, significantly highest CO2 evolution was recorded at 70 DAS of sorghum under 100% RDF + FYM @ 10 tonnes/ ha ( 66.82 mg/ 100 kg). Soil microbial biomass carbon was also influenced significantly with the combined application of NPK+FYM (278.9 mg/ kg). The soil enzyme activity, viz. dehydrogenase (55.01 µg TPF/g/24 hr), urease (47.9 mg NH4/kg/ 24 hr) and cellulase (52.23 µg glucose/g/24 hr) were significantly influenced with the application of 100% RDF + FYM @ 10 tonnes/ha. Similarly, the application of 100% RDF + FYM @ 10 tonnes/ha recorded significantly higher grain yield of sorghum.

Site-Specific Trade-offs of Harvesting Cereal Residues as Biofuel Feedstocks in Dryland Annual Cropping Systems of the Pacific Northwest, USA

Cereal residues are considered an important feedstock for future biofuel production. Harvesting residues, however, could lead to serious soil degradation and impaired agroecosystem services. Our objective was to evaluate trade-offs of harvesting wheat and barley residues including impacts on soil erosion and quality, soil organic C (SOC), and nutrient removal. We used agricultural data from 369 geo-referenced points on the 37-ha Washington State University Cook Agronomy Farm combined with model simulations to develop straw harvest scenarios for conventional tillage (CT) and no-tillage (NT) and both 2- and 3-year crop rotations with sequences of wheat, barley, and peas. Site-specific estimates of ethanol production from 2- and 3-year rotation scenarios ranged from 681 to 1,541 L ha−1 yr−1, indicating that both crop rotation and site-specific targeting of residue harvest are important factors. Harvesting straw reduced residue C inputs by 46 % and resulted in levels below that required to maintain SOC under CT. This occurred as a function of both straw harvest and low residue producing crops in rotation. Harvesting straw under CT was predicted to reduce soil quality as Soil Conditioning Indices (SCIs) were negative throughout the field. In contrast, SCIs under NT were positive despite straw harvest. Replacement value of nutrients (N, P, K, S) removed in harvested straw averaged $14.54 Mg−1 dry straw and ranged from $36.04 to $80.30 ha−1, while straw harvesting costs averaged $34.25 Mg−1, and the current (2014) market value of straw is $65 Mg−1. We concluded that substantial trade-offs exist in harvesting straw for biofuel, that trade-offs should be evaluated on a site-specific basis, and that support practices such as crop rotation, reduced tillage, and site-specific nutrient management need to be considered if residue harvest is to be sustainable.