Agronomy, Volume 6, Issue 1 (March 2016) – 20 articles

The NRT2 transporters mediate High Affinity Nitrate/NitriteTransport (HAN/NiT), which are essential for nitrogen acquisition from these inorganic forms. The NRT2 proteins are encoded by a multigene family in plants, and contain 12 transmembrane-spanning domains. Chlamydomonas reinhardtii has six NRT2, two of which (NRT2.5 and NRT2.4) are located in Chromosome III, in tandem head to tail. cDNAs for these genes were isolated and their sequence revealed that they correspond to half-size NRT2 transporters each containing six transmembrane domains. NRT2.5 has long N- and C- termini sequences without known homology. NRT2.4 also contains long termini sequences but smaller than NRT2.5. Expression of both studied genes occurred at a very low level, slightly in darkness, and was not modified by the N or C source. Silencing of NRT2.4 by specific artificial miRNA resulted in the inhibition of nitrite transport in the absence of other HANNiT (NRT2.1/NAR2) in the cell genetic background. Nitrite transport activity in the Hansenula polymorpha Δynt::URA3 Leu2 mutant was restored by expressing CrNRT2.4. These results indicate that half-size NRT2 transporters are present in photosynthetic organisms and that NRT2.4 is a HANiT. Full article

Rhizoremediation is a bioremediation technique whereby microbial degradation of organic contaminants occurs in the rhizosphere. It is considered to be an effective and affordable “green technology” for remediating soils contaminated with petroleum hydrocarbons. Root exudation of a wide variety of compounds (organic, amino and fatty acids, carbohydrates, vitamins, nucleotides, phenolic compounds, polysaccharides and proteins) provide better nutrient uptake for the rhizosphere microbiome. It is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are carried by conjugative plasmids and transferred among bacteria. Because root exudates can stimulate gene transfer, conjugation in the rhizosphere is higher than in bulk soil. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizosphere microbiome in ways that improve hydrocarbon bioremediation. Full article

Ascochyta blight (AB) caused by Ascochyta rabiei (Pass.) Labr. is an important and widespread disease of chickpea (Cicer arietinum L.) worldwide. The disease is particularly severe under cool and humid weather conditions. Breeding for host resistance is an efficient means to combat this disease. In this paper, attempts have been made to summarize the progress made in identifying resistance sources, genetics and breeding for resistance, and genetic variation among the pathogen population. The search for resistance to AB in chickpea germplasm, breeding lines and land races using various screening methods has been updated. Importance of the genotype × environment (GE) interaction in elucidating the aggressiveness among isolates from different locations and the identification of pathotypes and stable sources of resistance have also been discussed. Current and modern breeding programs for AB resistance based on crossing resistant/multiple resistant and high-yielding cultivars, stability of the breeding lines through multi-location testing and molecular marker-assisted selection method have been discussed. Gene pyramiding and the use of resistant genes present in wild relatives can be useful methods in the future. Identification of additional sources of resistance genes, good characterization of the host–pathogen system, and identification of molecular markers linked to resistance genes are suggested as the key areas for future study. Full article

Rhizodeposition is considered a primary reason for the plant identity effect. However, the detection of distinct rhizosphere bacterial communities (RBC) with different plant species has been variable. The aim of this study was to examine the potential explanations for this variability using three perennial grassland species. In a Kansas field experiment, over two growing seasons, we sampled RBC during the active growth and flowering stages of Agrostis gigantea, Andropogon gerardii and Helianthus maximiliani to: (1) determine the extent of the plant identity effect among these species and if the effect was maintained over time; (2) assess if RBC showed seasonal patterns, corresponding to plant phenology; and (3) examine if soil properties were important for structuring these communities. We found that Helianthus RBC were distinct from those of Agrostis and Andropogon only when Helianthus was flowering. Further, Helianthus RBC exhibited seasonal shifts corresponding to plant phenology. In contrast, Agrostis and Andropogon RBC were similar over time and exhibited gradual non-seasonal changes in compositions. Similar results were observed when accounting for soil properties. Overall, the observance of a plant identity effect depended on the plant species and when RBC were sampled. The seasonality of RBC also depended on the plant species examined. Full article

Soybean is the most produced and consumed oil seed crop worldwide. In 2013, 226 million metric tons were produced in over 70 countries. Organically produced soybean represents less than 0.1% of total world production. In the USA, the certified organic soybean crop was grown on 53 thousand ha or 0.17% of the total soybean acreage in the USA (32 million ha) in 2011. A gradual increase in production of organically grown soybean has occurred since the inception of organic labeling due to increased human consumption of soy products and increased demand for organic soybean meal to produce organic animal products. Production constraints caused by pathogens and insect pests are often similar in organic and non-organic soybean production, but management between the two systems often differs. In general, the non-organic, grain-type soybean crop are genetically modified higher-yielding cultivars, often with disease and pest resistance, and are grown with the use of synthetic pesticides. The higher value of organically produced soybean makes production of the crop an attractive option to some farmers. This article reviews production and uses of organically grown soybean in the USA, potential constraints to production caused by pathogens and insect pests, and management practices used to reduce the impact of these constraints. Full article

Barley is a cereal of primary importance for forage and human nutrition, and is a useful model for wheat. Autophagy genes first described in yeast have been subsequently isolated in mammals and Arabidopsis thaliana. In Arabidopsis and maize it was recently shown that autophagy machinery participates in nitrogen remobilization for grain filling. In rice, autophagy is also important for nitrogen recycling at the vegetative stage. In this study, HvATGs, HvNBR1 and HvATI1 sequences were identified from bacterial artificial chromosome (BAC), complementary DNA (cDNA) and expressed sequence tag (EST) libraries. The gene models were subsequently determined from alignments between genome and transcript sequences. Essential amino acids were identified from the protein sequences in order to estimate their functionality. A total of twenty-four barley HvATG genes, one HvNBR1 gene and one HvATI1 gene were identified. Except for HvATG5, all the genomic sequences found completely matched their cDNA sequences. The HvATG5 gene sequence presents a gap that cannot be sequenced due to its high GC content. The HvATG5 coding DNA sequence (CDS), when over-expressed in the Arabidopsis atg5 mutant, complemented the plant phenotype. The HvATG transcript levels were increased globally by leaf senescence, nitrogen starvation and dark-treatment. The induction of HvATG5 during senescence was mainly observed in the flag leaves, while it remained surprisingly stable in the seedling leaves, irrespective of the leaf age during stress treatment. Full article

Extremes in soil mineral supply alter the metallome of seeds much less than that of their herbage. The underlying mechanisms of mineral homeostasis and the “puzzle of seed filling” are not yet understood. Field crops of wheat, rye, pea, and the mushroom Kuehneromyces mutabilis were established on a set of metalliferous uranium mine soils and alluvial sands. Mineral concentrations in mature plants were determined from roots to seeds (and to fungal basidiospores) by ICP-MS following microwave digestion. The results referred to the concentrations of soil minerals to illustrate regulatory breaks in their flow across the plant sections. Root mineral concentrations fell to a mean of 7.8% in the lower stem of wheat in proportions deviating from those in seeds. Following down- and up-regulations in the flow, the rachis/seed interface configured with cuts in the range of 1.6%–12% (AsPbUZn) and up-regulations in the range of 106%–728% (CuMgMnP) the final grain metallome. Those of pea seeds and basidiospores were controlled accordingly. Soil concentration spans of 9–109× in CuFeMnNiZn shrank thereby to 1.3–2× in seeds to reveal the plateau of the cultivar’s desired target metallome. This was brought about by adaptations of the seed:soil transfer factors which increased proportionally in lower-concentrated soils. The plants thereby distinguished chemically similar elements (As/P; Cd/Zn) and incorporated even non-essential ones actively. It is presumed that high- and low-concentrated soils may impair the mineral concentrations of phloems as the donors of seed minerals. In an analytical and strategic top performance, essential and non-essential phloem constituents are identified and individually transferred to the propagules in precisely delimited quantities. Full article

Lentil plays a major role in the food and nutritional security of low income Ethiopian families because of the high protein content of their seed; however, their productivity typically is low largely due to soil fertility limitations. Field and pot experiments were conducted during the 2011 cropping season to determine the effectiveness of Rhizobium strains on two cultivars of lentil in Southern Ethiopia. Six rhizobial inoculant treatments (four indigenous and two commercial inoculants), a nitrogen (N) fertilizer treatment (50 kg·urea·ha⁻¹) and an absolute control (non-inoculated non-fertilized) were used. Inoculated plants produced significantly higher nodule number, nodule dry weight, grain yield and yield components than non-inoculated non-fertilized plants. Inoculation of field grown lentil with rhizobia strain Lt29 and Lt5 enhanced seed yield by 59% and 44%, respectively. Whereas urea fertilization enhanced yields by 40%. Similarly, grain yields were increased during the pot experiment by 92% and 67% over the control treatments by inoculation with Lt29 and Lt5, respectively. The highest levels of N fixation were achieved in plants inoculated with Lt29 (65.7% Ndfa). Both field and pot investigations indicate that inoculation of lentil with native rhizobial strains replace the need for inorganic N fertilization to optimize lentil yields. Full article

The bioenergy industry produces a wide range of byproducts varying in their chemical composition depending on type of technology employed. In particular, pyrolysis and transesterification conversion processes generate C-rich byproducts of biochar (BC) and glycerol (GL), respectively, which can be added to soil. These two byproducts vary in their carbon availability, and comparing their effects when added to agricultural soil deserves attention. This study investigated the immediate and residual effects of a single application of BC and GL to a cultivated Brown Chernozem soil from the semi-arid region of southwestern Saskatchewan, Canada. In the first season following addition of amendments, BC and GL alone had no significant impact on all measured parameters. However, when combined with 50 kg urea N·ha⁻¹ (BC + UR), the yields obtained were similar to those with 100 kg urea N·ha⁻¹ alone. The GL with urea N (GL + UR) treatment had reduced crop yield and N uptake compared to urea alone in the year of application attributed to N immobilization, but had a positive residual effect in the second year due to remineralization. Both GL and GL + UR treatments enhanced dehydrogenase activity compared to other treatments whereas BC + UR tended to decrease microbial biomass C. The crop and soil response to application of biochar was less than observed in previous studies conducted elsewhere. Direct and residual effects of glycerol addition on the crop were more evident. An application rate greater than 2.8 t·ha⁻¹ and 3.5 t·ha⁻¹ for BC and GL, respectively, may be required to induce larger responses. Full article

The aim of this study was to investigate the role of ASN3-encoded asparagine synthetase (AS, EC 6.3.5.4) during vegetative growth, seed development and germination of Arabidopsis thaliana. Phenotypic analysis of knockout (asn3-1) and knockdown (asn3-2) T-DNA insertion mutants for the ASN3 gene (At5g10240) demonstrated wild-type contents of asparagine synthetase protein, chlorophyll and ammonium in green leaves at 35 days after sowing. In situ hybridization localized ASN3 mRNA to phloem companion cells of vasculature. Young siliques of the asn3-1 knockout line showed a decrease in asparagine but an increase in glutamate. The seeds of asn3-1 and asn3-2 displayed a wild-type nitrogen status expressed as total nitrogen content, indicating that the repression of ASN3 expression had only a limited effect on mature seeds. An analysis of amino acid labeling of seeds imbibed with (¹⁵N) ammonium for 24 h revealed that asn3-1 seeds contained 20% less total asparagine while ¹⁵N-labeled asparagine ((2-¹⁵N)asparagine, (4-¹⁵N)asparagine and (2,4-¹⁵N)asparagine) increased by 12% compared to wild-type seeds. The data indicate a fine regulation of asparagine synthesis and hydrolysis in Arabidopsis seeds. Full article

In the Sahel zone of West Africa that extends from Senegal to Chad, temperatures can vary from less than 15 °C to 25 °C from November to February. These low temperatures affect the growth, development and yield of rice plants, and therefore constitute a major constraint to rice production in the Sahel. In order to identify rice varieties tolerant to cold stress at different developmental stages, a diverse set of 224 rice germplasm was evaluated for yield and yield-related traits in Ndiaye, Senegal, using three different sowing dates. The first sowing date (October 2010), was chosen so as to expose the rice plants to cold stress at the reproductive stage while the rice crop planted at the second sowing date (January 2011) experienced cold stress at the vegetative stage. The third sowing date (July 2011) was the normal planting date for irrigated rice in the Sahel and it served as the control date when the crop does not experience any cold stress throughout its growth cycle. Among the data collected, significant genetic variation was detected and genotype-by-environment interaction was also significant for the traits. At the vegetative stage, cold stress reduced tillering and plant vigor and delayed flowering but increased yield, whereas at the reproductive stage, aside from delaying flowering, cold stress also inhibited panicle exsertion and reduced panicle length, spikelet fertility, grain filling and strongly reduced yields. Principal Component Analysis and correlation analysis using agro-morphological traits helped to identify genotypes that were tolerant to cold stress at either the vegetative or the reproductive stage and the traits associated with high yield under cold stress at each of these stages. Our results can be used to develop cold tolerant rice varieties adapted to double cropping in the Sahelian zone of West Africa. Full article

Sugarcane, Saccharum spp., in the United States is attacked by a number of different arthropod pests. The most serious among those pests are two stalk boring moths in the Family Crambidae: the sugarcane borer, Diatraea saccharalis (F.), and the Mexican rice borer, Eoreuma loftini (Dyar). The two species are affected by abiotic and biotic environmental stress factors. Water deficit and excessive soil nitrogen alter physical and physiochemical aspects of the sugarcane plant that make the crop increasingly vulnerable to E. loftini. Weed growth can be competitive with sugarcane but it also supports enhanced abundances and diversity of natural enemies that can suppress infestations of D. saccharalis. In an instance where the stalk borer is considered a stress factor, proximity of vulnerable crops to sugarcane can influence levels of E. loftini infestation of sugarcane. The adverse effects of each stress factor, in terms of stalk borer attack, can be reduced by adopting appropriate cultural practices, such as adequate irrigation, judicious use of nitrogen fertilizer, using noncompetitive weed growth, and not planting vulnerable crops near sugarcane fields. Understanding the relationships between stress factors and crop pests can provide valuable insights for plant breeders and tools for incorporation into integrated pest management strategies. Full article

Enhanced efficiency nitrogen (N) fertilizers (EEFs) may improve crop recovery of fertilizer-N, but there is evidence that some EEFs cause a lag in crop growth compared to growth with standard urea. Biomass and mineral nutrient accumulation was investigated in rice fertilized with urea, urea-3,4-dimethylpyrazole phosphate (DMPP) and polymer-coated urea (PCU) to determine whether any delays in biomass production alter the accumulation patterns, and subsequent grain concentrations, of key mineral nutrients. Plant growth and mineral accumulation and partitioning to grains did not differ significantly between plants fertilized with urea or urea-DMPP. In contrast, biomass accumulation and the accumulation of phosphorus, potassium, calcium, magnesium, copper, zinc and manganese were delayed during the early growth phase of plants fertilized with PCU. However, plants in the PCU treatment ultimately compensated for this by increasing growth and nutrient uptake during the latter vegetative stages so that no differences in biomass or nutrient accumulation generally existed among N fertilizer treatments at anthesis. Delayed biomass accumulation in rice fertilized with PCU does not appear to reduce the total accumulation of mineral nutrients, nor to have any impact on grain mineral nutrition when biomass and grain yields are equal to those of rice grown with urea or urea-DMPP. Full article

Crop system models are generally parametrized with daily air temperatures recorded at 1.5 or 2 m height. These data are not able to represent temperatures at the canopy level, which control crop growth, and the impact of heat stress on crop yield, which are modified by canopy characteristics and plant physiological processes Since such data are often not available and current simulation approaches are complex and/or based on unrealistic assumptions, new methods for integrating canopy temperatures in the framework of crop system models are needed. Based on a forward stepwise-based model selection procedure and quantile regression analyses, we developed empirical regression models to predict winter wheat canopy temperatures obtained from thermal infrared observations performed during four growing seasons for three irrigation levels. We used daily meteorological variables and the daily output data of a crop system model as covariates. The standard cross validation revealed a root mean square error (RMSE) of ~0.8 °C, 1.5–2 °C and 0.8–1.2 °C for estimating mean, maximum and minimum canopy temperature, respectively. Canopy temperature of both water-deficit and fully irrigated wheat plots significantly differed from air temperature. We suggest using locally calibrated empirical regression models of canopy temperature as a simple approach for including potentially amplifying or mitigating microclimatic effects on plant response to temperature stress in crop system models. Full article

Soil and water pollution by metals and other toxic chemicals is difficult to measure and control, and, as such, presents an ongoing global threat to sustainable agriculture and human health. Efforts to remove contaminants by plant-mediated pathways, or “phytoremediation”, though widely studied, have failed to yield consistent, predictable removal of biological and chemical contaminants. Emerging research has revealed that one major limitation to using plants to clean up the environment is that plants are programmed to protect themselves: Like white blood cells in animals, border cells released from plant root tips carry out an extracellular trapping process to neutralize threats and prevent injury to the host. Variability in border cell trapping has been found to be correlated with variation in sensitivity of roots to aluminum, and removal of border cell results in increased Al uptake into the root tip. Studies now have implicated border cells in responses of diverse plant roots to a range of heavy metals, including arsenic, copper, cadmium, lead, mercury, iron, and zinc. A better understanding of border cell extracellular traps and their role in preventing toxin uptake may facilitate efforts to use plants as a nondestructive approach to neutralize environmental threats. Full article

Stripe rust (caused by Puccinia striiformis f. sp. tritici) of wheat (Triticum aestivum) is a devastating disease in temperate regions when susceptible varieties are grown and environmental conditions sustain high disease pressures. With frequent and severe outbreaks, disease resistance is a key tool for controlling stripe rust on wheat. The goal of this research was to identify quantitative trait loci (QTL) involved in stripe rust resistance from the important US Pacific Northwest soft white winter wheat varieties “Eltan” and “Finch”. An F_2:5 recombinant inbred line (RIL) mapping population of 151 individuals derived from the Finch × Eltan cross was developed through single seed descent. A linkage map comprising 683 unique single nucleotide polymorphism (SNP) loci and 70 SSR markers were used to develop 22 linkage groups consisting of 16 of the 21 chromosomes. Stripe rust data were collected on the RILs during the summers of 2012 to 2014. QTL analysis identified two genomic regions on chromosomes 4A (QYrel.wak-4A) and 6B (QYrfi.wak-6B) associated with resistance from Eltan and Finch, respectively. The results of the QTL analysis showed that QYrel.wak-4A and QYrfi.wak-6B reduced infection type and disease severity. Based upon both molecular and phenotypic differences, QYrel.wak-4A is a novel QTL for adult plant resistance (APR) to stripe rust. Full article

Field experiments at Oakes, ND, USA in 2010 and Carrington, ND, USA in 2011 were conducted to evaluate the potential for cover crops grown in the Northern Great Plains, USA in order to reduce weed emergence and density in irrigated potatoes. Treatments included five cover crop treatments and three cover crop termination treatments. Termination of cover crops was done with glyphosate, disk-till, and roto-till. Cover crop biomass accumulation was greatest for rye/canola and triticale at Oakes, and hairy vetch and hairy vetch/rye at Carrington. Cover crop and termination affected weed control 14, 29, and 51 days after planting (DAP) at Oakes. Weed control at Carrington was at least 90% for all cover crop and termination treatments at all three evaluation timings. Marketable yield at Oakes was greater when roto-till was used to terminate the cover crops compared with disk-till or herbicide, which is beneficial for organic systems where herbicides are not used. Marketable yield at Carrington was not affected by cover crop or termination treatments. Results suggest that cover crops can successfully be integrated into irrigated potato production for weed control with yields equal to no cover crop, and with attention to potential mechanical difficulties. Full article

Genotypic variation in N efficiency defined as high grain yield under limited nitrogen (N) supply of winter oilseed-rape line-cultivars has been predominantly attributed to N uptake efficiency (NUPT) through maintained N uptake during reproductive growth related to functional stay-green. For investigating the role of stay-green, N retranslocation and N uptake during the reproductive phase for grain yield formation, two line cultivars differing in N starvation-induced leaf senescence were grown in a field experiment without mineral N (N0) and with 160 kg N·ha⁻¹ (N160). Through frequent harvests from full flowering until maturity N uptake, N utilization and apparent N remobilization from vegetative plant parts to the pods could be calculated. NUPT proved being more important than N utilization efficiency (NUE) for grain yield formation under N-limiting (N0) conditions. For cultivar differences in N efficiency, particularly N uptake during flowering (NUPT) and biomass allocation efficiency (HI) to the grains, were decisive. Both crop traits were related to delayed senescence of the older leaves. Remobilization of N particularly from stems and leaves was more important for pod N accumulation than N uptake after full flowering. Pod walls (high N concentrations) and stems (high biomass) mainly contributed to the crop-residue N at maturity. Decreasing the crop-inherent high N budget surplus of winter oilseed-rape requires increasing the low N remobilization efficiency particularly of pod-wall N to the grains. Addressing this conclusion, multi-year and -location field experiments with an extended range of cultivars including hybrids are desirable. Full article

Since silage maize is the main crop grown for biogas production (biomass crop) in Germany; its increasing cultivation is critically discussed in terms of social and agronomical aspects. To investigate if sugar beet is suitable as an alternative biomass crop to silage maize; three-year field trials with both biomass crops in rotations with winter wheat (food crop) and continuous cultivation were conducted at three highly productive sites. Dry matter (DM) yield per hectare was measured via field trials whereas methane yield per hectare was estimated via a calculation. Higher annual DM yield was achieved by silage maize (19.5–27.4 t∙ha⁻¹∙a⁻¹) compared to sugar beet root (10.7–23.0 t∙ha⁻¹∙a⁻¹). Dry matter yield was found to be the main driver for the estimated methane yield. Thus; higher estimated methane yield was produced by silage maize (6458–9388 Nm³∙ha⁻¹) with overlaps to sugar beet root (3729–7964 Nm³∙ha⁻¹). We; therefore; classify sugar beet as a suitable alternative biomass crop to silage maize; especially when cultivated in crop rotations with winter wheat. Additionally; we found that the evaluation of entire crop rotations compared to single crops is a more precise approach since it includes rotational effects. Full article