http://www.mdpi.com/journal/agronomy Latest open access articles published in Agronomy at http://www.mdpi.com/journal/agronomy http://www.mdpi.com/2073-4395/3/2/462 Biochar application to agricultural soils is an interesting emerging technology with promising potential for long-term carbon storage, sustainable waste disposal, and soil fertility enhancement. Extensive information exists in the literature on the highly beneficial properties of biochar. Nevertheless, systematic application of biochar on European agricultural soils may have wide ranging policy implications as well as environmental and public health concerns. In this paper we critically review existing scientific evidence from a European policy perspective and identify research gaps for future comprehensive assessments of the policy, environmental, economic, and health implications of the systematic use of biochar in European agricultural soils. Agronomy 2013-05-22 3 2 Review 10.3390/agronomy3020462 462 473 2073-4395 2013-05-22 doi: 10.3390/agronomy3020462 Luca Montanarella Emanuele Lugato http://www.mdpi.com/2073-4395/3/2/433 Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. However, abiotic and biotic stress limits bean yields to <600 kg ha−1 in low-income countries. Current low yields result in food insecurity, while demands for increased yields to match the rate of population growth combined with the threat of climate change are significant. Novel and significant advances in genetic improvement using untapped genetic diversity available in crop wild relatives and closely related species must be further explored. A meeting was organized by the Global Crop Diversity Trust to consider strategies for common bean improvement. This review resulted from that meeting and considers our current understanding of the genetic resources available for common bean improvement and the progress that has been achieved thus far through introgression of genetic diversity from wild relatives of common bean, and from closely related species, including: P. acutifolius, P. coccineus, P. costaricensis and P. dumosus. Newly developed genomic tools and their potential applications are presented. A broad outline of research for use of these genetic resources for common bean improvement in a ten-year multi-disciplinary effort is presented. Agronomy 2013-05-10 3 2 Review 10.3390/agronomy3020433 433 461 2073-4395 2013-05-10 doi: 10.3390/agronomy3020433 Timothy Porch James Beaver Daniel Debouck Scott Jackson James Kelly Hannes Dempewolf http://www.mdpi.com/2073-4395/3/2/419 Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural production for an expanding population, but to achieve this under more adverse environmental conditions. It is now possible to systematically explore the genetic variation in historic local landraces by using GPS locators and world climate maps to describe the natural selection for local adaptation, and to identify candidate germplasm for tolerances to extreme stresses. The physiological and biochemical components of these expressions can be genomically investigated with candidate gene approaches and next generation sequencing. Wild relatives of crops have largely untapped genetic variation for abiotic and biotic stress tolerances, and could greatly expand the available domesticated gene pools to assist crops to survive in the predicted extremes of climate change, a survivalomics strategy. Genomic strategies can assist in the introgression of these valuable traits into the domesticated crop gene pools, where they can be better evaluated for crop improvement. The challenge is to increase agricultural productivity despite climate change. This calls for the integration of many disciplines from eco-geographical analyses of genetic resources to new advances in genomics, agronomy and farm management, underpinned by an understanding of how crop adaptation to climate is affected by genotype × environment interaction. Agronomy 2013-05-10 3 2 Review 10.3390/agronomy3020419 419 432 2073-4395 2013-05-10 doi: 10.3390/agronomy3020419 Robert Redden http://www.mdpi.com/2073-4395/3/2/404 The effect of rice-husk char (potentially biochar) application on the growth of transplanted lettuce (Lactuca sativa) and Chinese cabbage (Brassica chinensis) was assessed in a pot experiment over a three crop (lettuce-cabbage-lettuce) cycle in Cambodia. The biochar was the by-product of a rice-husk gasification unit and consisted of 28.7% carbon (C) by mass. Biochar application rates to potting medium of 25, 50 and 150 g kg−1 were used with and without locally available fertilizers (a mixture of compost, liquid compost and lake sediment). The rice-husk biochar used was slightly alkaline (pH 7.79), increased the pH of the soil, and contained elevated levels of some trace metals and exchangeable cations (K, Ca and Mg) in comparison to the soil. The biochar treatments were found to increase the final biomass, root biomass, plant height and number of leaves in all the cropping cycles in comparison to no biochar treatments. The greatest biomass increase due to biochar additions (903%) was found in the soils without fertilization, rather than fertilized soils (483% with the same biochar application as in the “without fertilization” case). Over the cropping cycles the impact was reduced; a 363% increase in biomass was observed in the third lettuce cycle. Agronomy 2013-05-07 3 2 Article 10.3390/agronomy3020404 404 418 2073-4395 2013-05-07 doi: 10.3390/agronomy3020404 Sarah Carter Simon Shackley Saran Sohi Tan Suy Stephan Haefele http://www.mdpi.com/2073-4395/3/2/391 Malnutrition has affected almost 31% of pre-school children. This paper provides the information of nutritional values (leaf protein, 15 amino acids, biomass and leaf dry matter) of grain, vegetable and weedy types of amaranths (n = 76 accessions); particularly those novel materials originated from the highland areas of Sumatra-Takengon. The highest values of leaf protein and total amino acids were found in many weedy species (A. viridis, A. blitum L. and A. dubius). The ranges of leaf protein and total amino acids in most of weedy types were 12–29 g 100 g−1 DM and 84–93 g 100 g−1 DW protein, respectively. The leaves of amaranths were found to be a good source for lysine which is the limiting essential amino acids in most of cereal plants. Their values were in the range of 6 g 100 g−1 DW protein which are close to that of good protein quality according to FAO/WHO’s standard. The leaves of underutilized weedy species of A. dubius, A. blitum, A. viridis and the dual purpose types of A. caudatus L., A. cruentus L. deserve to be further exploited as a low cost solution for solving malnutrition problems, especially in Indonesia. Agronomy 2013-05-03 3 2 Article 10.3390/agronomy3020391 391 403 2073-4395 2013-05-03 doi: 10.3390/agronomy3020391 Rita Andini Shigeki Yoshida Ryo Ohsawa http://www.mdpi.com/2073-4395/3/2/376 Waterlogging can reduce crop yield by 20%–50% or more, and lack of efficient selection methods is an obstacle in plant breeding. The methods currently used are mainly indices based on germination ability in Petri dishes and leaf chlorosis in plants grown in waterlogged soils. Cultivation in oxygen-depleted nutrient solution is the ultimate waterlogging system. Therefore methods based on root growth inhibition and on fluorescence in plant material hydroponically grown in oxygen-depleted solution were evaluated against data on biomass accumulation in waterlogged soils. Both traits were correlated with waterlogging tolerance in soil, but since it was easier to measure fluorescence, this method was further evaluated. A selection of F2 plants with high and low fluorescence revealed a small but significant screening effect in F3 plants. A test of 175 Nordic cultivars showed large variations in chlorophyll fluorescence in leaves from oxygen-stressed seedlings, indicating that adaptation to waterlogging has gradually improved over the past 40–50 years with the introduction of new cultivars onto the market. However, precipitation also increased during the period and new cultivars may have inadvertently been adapted to this while breeding barley for grain yield. The results suggest that the hydroponic method can be used for screening barley populations, breeding lines or phenotyping of populations in developing markers for quantitative trait loci. Agronomy 2013-04-25 3 2 Article 10.3390/agronomy3020376 376 390 2073-4395 2013-04-25 doi: 10.3390/agronomy3020376 Nils-Ove Bertholdsson http://www.mdpi.com/2073-4395/3/2/349 The presence of biochar in soils through natural processes (forest fires, bush burning) or through application to soil (agriculture, carbon storage, remediation, waste management) has received a significant amount of scientific and regulatory attention. Biochar alters soil properties, encourages microbial activity and enhances sorption of inorganic and organic compounds, but this strongly depends on the feedstock and production process of biochar. This review considers biochar sources, the production process and result of pyrolysis, interactions of biochar with soil, and associated biota. Furthermore, the paper focuses on the interactions between biochar and common anthropogenic organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), pesticides, and dioxins, which are often deposited in the soil environment. It then considers the feasibility of applying biochar in remediation technologies in addition to other perspective areas yet to be explored. Agronomy 2013-04-23 3 2 Review 10.3390/agronomy3020349 349 375 2073-4395 2013-04-23 doi: 10.3390/agronomy3020349 Uchenna Ogbonnaya Kirk Semple http://www.mdpi.com/2073-4395/3/2/340 A study was conducted for three seasons in northwest Kansas, USA to evaluate acetolactate synthase (ALS)-inhibiting herbicides for downy brome (Bromus tectorum L.) and winter annual broadleaf weed control in winter wheat. Herbicides included pyroxsulam at 18.4 g ai ha−1, propoxycarbazone-Na at 44 g ai ha−1, premixed propoxycarbazone-Na & mesosulfuron-methyl at 27 g ai ha−1, and sulfosulfuron at 35 g ai ha−1. The herbicides were applied postemergence in fall and spring seasons. Averaged over time of application, no herbicide controlled downy brome more than 78% in any year. When downy brome densities were high, control was less than 60%. Pyroxsulam controlled downy brome greater than or similar to other herbicides tested. Flixweed (Descurainia sophia L.), blue mustard [Chorispora tenella (Pallas) DC.], and henbit (Lamium amplexicaule L.) control did not differ among herbicide treatments. All herbicides tested controlled flixweed and blue mustard at least 87% and 94%, respectively. However, none of the herbicides controlled henbit more than 73%. Fall herbicide applications improved weed control compared to early spring applications; improvement ranged from 3% to 31% depending on the weed species. Henbit control was greatly decreased by delaying herbicide applications until spring compared to fall applications (49% vs. 80% control). Herbicide injury was observed in only two instances. The injury was ≤13% with no difference between herbicides and the injury did not impact final plant height or grain yield. Agronomy 2013-04-18 3 2 Article 10.3390/agronomy3020340 340 348 2073-4395 2013-04-18 doi: 10.3390/agronomy3020340 Seshadri Reddy Phillip Stahlman Patrick Geier http://www.mdpi.com/2073-4395/3/2/313 Biochar, a co-product of a controlled pyrolysis process, can be used as a tool for sequestering C in soil to offset greenhouse gas (GHG) emissions, and as a soil amendment. Whereas the impacts of biochar application on soil chemical properties are widely known, the research information on soil physical properties is scarce. The objectives of this review are to (i) synthesize available data on soil physical properties and GHG emissions, (ii) offer possible mechanisms related to the biochar-amended soil processes, and (iii) identify researchable priorities. Application rates of 1%–2% (w/w) of biochar can significantly improve soil physical quality in terms of bulk density (BD), and water holding capacity (WHC). However, little data are available on surface area (SA), aggregation stability, and penetration resistance (PR) of biochar-amended soil. While biochar amendment can initially accentuate the flux of carbon dioxide (CO2), the emission of GHGs may be suppressed over time. A 2-phase complexation hypothesis is proposed regarding the mechanisms of the interaction between soil and biochar. Agronomy 2013-04-18 3 2 Review 10.3390/agronomy3020313 313 339 2073-4395 2013-04-18 doi: 10.3390/agronomy3020313 Atanu Mukherjee Rattan Lal http://www.mdpi.com/2073-4395/3/2/294 Biochar can potentially increase soil fertility and sequester carbon by incorporating nutrients and stable black carbon into the soil; however its effect on soil nitrogen (N) and carbon (C) processes is not well understood. A defined methodology to characterize biochar is necessary to predict how specific biochars will affect C and N mineralization. We amended a Tifton soil (Fine-loamy, siliceous, thermic Plinthic Kandiudults) with peanut hull (Arachis hypogaea; PH; 2.1% N) and pine chip (Pinus taeda; PC: 0.4% N) biochar at application rates of 1% and 2% (w/w) and performed a 136-day mineralization study. A companion 24-day mineralization study amended Tifton soil with PH and PC biochar at 2% and their respective feedstocks at equal C rates. Soil C mineralization rates were monitored periodically throughout each study and total N mineralization rates were also measured. In addition, we characterized each biochar using thermogravimetric analysis with mass spectrometer (TGA-MS), proximate analysis, Fourier transform infrared spectroscopy (FTIR), and total mineral analysis to identify biochar characteristics that might correlate with mineralization properties. Limited C (<2%) mineralized from both biochars, but mineralization rates of soil amended with PH biochar were higher than PC biochar. Carbon mineralization correlated well with estimated aliphatic content determined by TGA-MS but not with volatile content indicated by proximate analysis. Nitrogen was not mineralized from either biochar, indicating that plant-based biochar should not be considered a source of N for plant growth. The N in biochar may be contained in the stable aromatic structure of the biochar, as indicated by TGA-MS, and not available to soil microbes. Agronomy 2013-04-16 3 2 Article 10.3390/agronomy3020294 294 312 2073-4395 2013-04-16 doi: 10.3390/agronomy3020294 Keith Harris Julia Gaskin Miguel Cabrera William Miller K.C. Das http://www.mdpi.com/2073-4395/3/2/275 Interest in biochar stems from its potential agronomic benefits and carbon sequestration ability. Biochar application alters soil nitrogen (N) dynamics. This review establishes emerging trends and gaps in biochar-N research. Biochar adsorption of NO3−, up to 0.6 mg g−1 biochar, occurs at pyrolysis temperatures >600 °C with amounts adsorbed dependent on feedstock and NO3− concentration. Biochar NH4+ adsorption depends on feedstock, but no pyrolysis temperature trend is apparent. Long-term practical effectiveness of inorganic-N adsorption, as a NO3− leaching mitigation option, requires further study. Biochar adsorption of ammonia (NH3) decreases NH3 and NO3− losses during composting and after manure applications, and offers a mechanism for developing slow release fertilisers. Reductions in NH3 loss vary with N source and biochar characteristics. Manure derived biochars have a role as N fertilizers. Increasing pyrolysis temperatures, during biochar manufacture from manures and biosolids, results in biochars with decreasing hydrolysable organic N and increasing aromatic and heterocyclic structures. The short- and long-term implications of biochar on N immobilisation and mineralization are specific to individual soil-biochar combinations and further systematic studies are required to predict agronomic and N cycling responses. Most nitrous oxide (N2O) studies measuring nitrous oxide (N2O) were short-term in nature and found emission reductions, but long-term studies are lacking, as is mechanistic understanding of reductions. Stable N isotopes have a role in elucidating biochar-N-soil dynamics. There remains a dearth of information regarding effects of biochar and soil biota on N cycling. Biochar has potential within agroecosystems to be an N input, and a mitigation agent for environmentally detrimental N losses. Future research needs to systematically understand biochar-N interactions over the long term. Agronomy 2013-04-16 3 2 Review 10.3390/agronomy3020275 275 293 2073-4395 2013-04-16 doi: 10.3390/agronomy3020275 Tim Clough Leo Condron Claudia Kammann Christoph Müller http://www.mdpi.com/2073-4395/3/2/256 Biochar addition to agricultural soils can improve soil fertility, with the added bonus of climate change mitigation through carbon sequestration. Conservation farming (CF) is precision farming, often combining minimum tillage, crop rotation and residue retention. In the present farmer-led field trials carried out in Zambia, the use of a low dosage biochar combined with CF minimum tillage was tested as a way to increase crop yields. Using CF minimum tillage allows the biochar to be applied to the area where most of the plant roots are present and mirrors the fertilizer application in CF practices. The CF practice used comprised manually hoe-dug planting 10-L sized basins, where 10%–12% of the land was tilled. Pilot trials were performed with maize cob biochar and wood biochar on five soils with variable physical/chemical characteristics. At a dosage as low as 4 tons/ha, both biochars had a strong positive effect on maize yields in the coarse white aeolian sand of Kaoma, West-Zambia, with yields of 444% ± 114% (p = 0.06) and 352% ± 139% (p = 0.1) of the fertilized reference plots for maize and wood biochar, respectively. Thus for sandy acidic soils, CF and biochar amendment can be a promising combination for increasing harvest yield. Moderate but non-significant effects on yields were observed for maize and wood biochar in a red sandy clay loam ultisol east of Lusaka, central Zambia (University of Zambia, UNZA, site) with growth of 142% ± 42% (p > 0.2) and 131% ± 62% (p > 0.2) of fertilized reference plots, respectively. For three other soils (acidic and neutral clay loams and silty clay with variable cation exchange capacity, CEC), no significant effects on maize yields were observed (p > 0.2). In laboratory trials, 5% of the two biochars were added to the soil samples in order to study the effect of the biochar on physical and chemical soil characteristics. The large increase in crop yield in Kaoma soil was tentatively explained by a combination of an increased base saturation (from <50% to 60%–100%) and cation exchange capacity (CEC; from 2–3 to 5–9 cmol/kg) and increased plant-available water (from 17% to 21%) as well as water vapor uptake (70 mg/g on maize cob biochar at 50% relative humidity). Agronomy 2013-04-11 3 2 Article 10.3390/agronomy3020256 256 274 2073-4395 2013-04-11 doi: 10.3390/agronomy3020256 Gerard Cornelissen Vegard Martinsen Victor Shitumbanuma Vanja Alling Gijs Breedveld David Rutherford Magnus Sparrevik Sarah Hale Alfred Obia Jan Mulder http://www.mdpi.com/2073-4395/3/1/248 Eggplant is a popular vegetable consumed all over the world. Cover cropping is an efficient way of recycling nutrients and reducing inorganic fertilizer requirements to maintain the sustainability of the soil without affecting productivity and profitability. Eggplants (Solanum melongena) (Japanese varieties Hansel and Kamo) were grown in a Piedmont soil with two main treatments, cover crop (CC) and no cover crop (NC), and four sub-fertilizer treatments (T1: 0-0-0, T2: 56-28-112, T3: 84-56-168, and T4: 168-112-224 N-P-K kg/ha), using four replications. The Hansel variety eggplant yield was significantly higher than the Kamo variety. Eggplant yields from CC treatments for both varieties were significantly higher (p < 0.001) than the yields from NC treatments. No significant difference was observed in the yields between T1 and T2 treatments, but the yields from T3 were significantly higher than T1 and T2 and yields from T4 were significantly higher than T3 yields. N released through mineralization of cover crop mixture ranged from 13.33 g/kg at the beginning of the growing season and increased to 18.32 g/kg at the end of the growing season. These results suggest that Japanese eggplants can be successfully grown in the Piedmont area of North Carolina in rotation with cover crops for higher yields. Agronomy 2013-03-22 3 1 Article 10.3390/agronomy3010248 248 255 2073-4395 2013-03-22 doi: 10.3390/agronomy3010248 Ramesh Ravella Muchha Reddy Kurt Taylor Ahmed Elobeid http://www.mdpi.com/2073-4395/3/1/232 Adding mulch biomass prior to crop seeding may improve production of tropical soil. We evaluated the response of four bean (Phaseolus vulgaris L.) genotypes to the addition of mulch biomass from Tithonia diversifolia (Hemsl.) Gray and Cajanus cajan L. Millsp. The addition of mulch did not result in significant differences (p < 0.05) in soil characteristics when compared to a control (no mulch addition) except for soil potassium (K), which was significantly greater (p < 0.05) in the T. diversifolia mulch biomass treatment. Bean yield and shoot biomass were significantly greater (p < 0.05) in the mulch biomass treatments compared to the control (no biomass added). In these treatments, Phosphorus (P)-efficient bean genotypes had a significantly greater (p < 0.05) yield and shoot biomass. Bean shoot nutrient concentrations were significantly different (p < 0.05) between mulch biomass treatments and between bean genotypes (P, K and magnesium (Mg) only). Phosphorus utilization and uptake efficiencies were significantly different (p < 0.05) between mulch biomass treatments and between bean genotypes. Bean root biomass was not significantly different (p < 0.05) between mulch biomass treatments, but was significantly different (p < 0.05) between bean genotypes. The number of root nodules was significantly greater (p < 0.05) in the T. diversifolia mulch biomass treatment and was significantly different between bean genotypes. Agronomy 2013-03-21 3 1 Article 10.3390/agronomy3010232 232 247 2073-4395 2013-03-21 doi: 10.3390/agronomy3010232 Pedro Jorge-Mustonen Maren Oelbermann Donald Kass http://www.mdpi.com/2073-4395/3/1/200 The options for increasing food production by at least 70% over the next four decades so as to keep pace with a rapidly increasing human population are bedeviled by erratic climatic conditions, depleted arable lands, dwindling water resources and by the significant environmental and health costs for increasing the use of agrochemicals. Enhanced productivities through “smart” crop varieties that yield more with fewer inputs is a viable option. However, the genetic similarities amongst crop varieties—which render entire cropping systems vulnerable to the same stresses—coupled with unvarying parental materials limit the possibilities for uncovering novel alleles of genes and, hence, assembling new gene combinations to break yield plateaux and enhance resilience. Induced mutation unmasks novel alleles that are harnessed to breed superior crop varieties. The historical antecedents, theoretical and practical considerations, and the successes of induced mutations in crop improvement are reviewed along with how induced mutagenesis underpins plant functional genomics. The roles of cell and molecular biology techniques in enhancing the efficiencies for the induction, detection and deployment of mutation events are also reviewed. Also, the integration of phenomics into induced mutagenesis and the use of pre-breeding for facilitating the incorporation of mutants into crop improvement are advocated. Agronomy 2013-03-05 3 1 Review 10.3390/agronomy3010200 200 231 2073-4395 2013-03-05 doi: 10.3390/agronomy3010200 Chikelu Mba http://www.mdpi.com/2073-4395/3/1/181 Cole crops (Brassica vegetables) can pose a significant risk for N losses during the post-harvest period due to substantial amounts of readily mineralizable N in crop residues. Amending the soil with organic C has the potential to immobilize N and thereby reduce the risk for N losses. Four field trials were conducted to determine the effects of organic C amendments (OCA) on N dynamics and spring wheat (Triticum durum L.) harvest parameters proceeding early- and late-broccoli (Brassica olecerea var italica L.) systems in 2009 and 2010. The experimental controls represented the traditional grower practice of incorporated broccoli crop residue (CR-control) and the pre-plant application of N fertilizer (CRN-control) to subsequent spring wheat. Alternative practices were compared to the controls, which included broccoli crop residue removal (CR-removal), an oat (Avena sativa L.) cover crop (CC-oat), and three different OCA of wheat straw (OCA-straw), yard waste (OCA-yard), or used cooking oil (OCA-oil). The treatments, which demonstrated reduced autumn soil mineral N (SMN) concentrations after broccoli harvest, relative to the CR-control, were CR-removal, OCA-straw, and OCA-oil. Although CR-removal and OCA-straw indicated a reduced potential for autumn soil N losses in the early-broccoli system, these practices are not recommended for growers because subsequent spring wheat yield and profit margins were reduced compared to the CR- and CRN-controls. The OCA-oil reduced autumn SMN concentrations by 53 to 112 kg N ha−1 relative to the CR-control after both early- and late-broccoli harvest, suggesting a larger potential for reduced autumn soil N losses, compared to all other treatments. No detrimental effects resulted from the OCA-oil treatment on the subsequent spring yield or grain N. The OCA-oil reduced spring wheat profit margins relative to the CR-control, like the OCA-straw and CR-removal treatments, however profit margins were similar between the OCA-oil and the CRN-control. Therefore, in areas with a high risk of environmental N contamination, growers should consider the OCA-oil practice after cole crop harvest to minimize the risk of N losses. Agronomy 2013-02-18 3 1 Article 10.3390/agronomy3010181 181 199 2073-4395 2013-02-18 doi: 10.3390/agronomy3010181 Katelyn Congreves Richard Vyn Laura Van Eerd http://www.mdpi.com/2073-4395/3/1/148 In light of the environmental challenges ahead, resilience of the most abundant field crop production systems must be improved to guarantee yield stability with more efficient use of nitrogen inputs, soil and water resources. Along with genetic and agronomic innovations, diversification of northern agro-ecosystems using inter-seeded legumes provides further opportunities to improve land management practices that sustain crop yields and their resilience to biotic and abiotic stresses. Benefits of legume cover crops have been known for decades and red clover (Trifolium pratense) is one of the most common and beneficial when frost-seeded under winter wheat in advance of maize in a rotation. However, its use has been declining mostly due to the use of synthetic fertilizers and herbicides, concerns over competition with the main crop and the inability to fully capture red clover benefits due to difficulties in the persistence of uniform stands. In this manuscript, we first review the environmental, agronomic, rotational and economical benefits associated with inter-seeded red clover. Red clover adaptation to a wide array of common wheat-based rotations, its potential to mitigate the effects of land degradation in a changing climate and its integration into sustainable food production systems are discussed. We then identify areas of research with significant potential to impact cropping system profitability and sustainability. Agronomy 2013-02-08 3 1 Review 10.3390/agronomy3010148 148 180 2073-4395 2013-02-08 doi: 10.3390/agronomy3010148 Amélie Gaudin Sabrina Westra Cora Loucks Ken Janovicek Ralph Martin William Deen http://www.mdpi.com/2073-4395/3/1/135 To identify and develop drought tolerant maize (Zea mays L.), high-throughput and cost-effective screening methods are needed. In dicot crops, measuring survival and recovery of seedlings has been successful in predicting drought tolerance but has not been reported in C4 grasses such as maize. Seedlings of sixty-two diverse maize inbred lines and their hybrid testcross progeny were evaluated for germination, survival and recovery after a series of drought cycles. Genotypic differences among inbred lines and hybrid testcrosses were best explained approximately 13 and 18 days after planting, respectively. Genotypic effects were significant and explained over 6% of experimental variance. Specifically three inbred lines had significant survival, and 14 hybrids had significant recovery. However, no significant correlation was observed between hybrids and inbreds (R2 = 0.03), indicating seedling stress response is more useful as a secondary screening parameter in hybrids than in inbred lines per se. Field yield data under full and limited irrigation indicated that seedling drought mechanisms were independent of drought responses at flowering in this study. Agronomy 2013-02-07 3 1 Article 10.3390/agronomy3010135 135 147 2073-4395 2013-02-07 doi: 10.3390/agronomy3010135 Meghyn Meeks Seth Murray Steve Hague Dirk Hays http://www.mdpi.com/2073-4395/3/1/117 Soybean (Glycine max) cultivars adapted to high latitudes have a weakened or absent sensitivity to photoperiod. The purposes of this study were to determine the molecular basis for photoperiod insensitivity in various soybean accessions, focusing on the sequence diversity of the E4 (GmphyA2) gene, which encodes a phytochrome A (phyA) protein, and its homoeolog (GmphyA1), and to disclose the evolutionary consequences of two phyA homoeologs after gene duplication. We detected four new single-base deletions in the exons of E4, all of which result in prematurely truncated proteins. A survey of 191 cultivated accessions sourced from various regions of East Asia with allele-specific molecular markers reliably determined that the accessions with dysfunctional alleles were limited to small geographical regions, suggesting the alleles’ recent and independent origins from functional E4 alleles. Comparison of nucleotide diversity values revealed lower nucleotide diversity at non-synonymous sites in GmphyA1 than in E4, although both have accumulated mutations at almost the same rate in synonymous and non-coding regions. Natural mutations have repeatedly generated loss-of-function alleles at the E4 locus, and these have accumulated in local populations. The E4 locus is a key player in the adaptation of soybean to high-latitude environments under diverse cropping systems. Agronomy 2013-02-04 3 1 Article 10.3390/agronomy3010117 117 134 2073-4395 2013-02-04 doi: 10.3390/agronomy3010117 Yasutaka Tsubokura Hisakazu Matsumura Meilan Xu Baohui Liu Hiroko Nakashima Toyoaki Anai Fanjiang Kong Xiaohui Yuan Hiroyuki Kanamori Yuichi Katayose Ryoji Takahashi Kyuya Harada Jun Abe http://www.mdpi.com/2073-4395/3/1/86 Phosphorus underpins the world’s food systems by ensuring soil fertility, maximising crop yields, supporting farmer livelihoods and ultimately food security. Yet increasing concerns around long-term availability and accessibility of the world’s main source of phosphorus—phosphate rock, means there is a need to investigate sustainable measures to buffer the world’s food systems against the long and short-term impacts of global phosphorus scarcity. While the timeline of phosphorus scarcity is contested, there is consensus that more efficient use and recycling of phosphorus is required. While the agricultural sector will be crucial in achieving this, sustainable phosphorus measures in sectors upstream and downstream of agriculture from mine to fork will also need to be addressed. This paper presents a comprehensive classification of all potential phosphorus supply- and demand-side measures to meet long-term phosphorus needs for food production. Examples range from increasing efficiency in the agricultural and mining sector, to technologies for recovering phosphorus from urine and food waste. Such measures are often undertaken in isolation from one another rather than linked in an integrated strategy. This integrated approach will enable scientists and policy-makers to take a systematic approach when identifying potential sustainable phosphorus measures. If a systematic approach is not taken, there is a risk of inappropriate investment in research and implementation of technologies and that will not ultimately ensure sufficient access to phosphorus to produce food in the future. The paper concludes by introducing a framework to assess and compare sustainable phosphorus measures and to determine the least cost options in a given context. Agronomy 2013-01-31 3 1 Article 10.3390/agronomy3010086 86 116 2073-4395 2013-01-31 doi: 10.3390/agronomy3010086 Dana Cordell Stuart White http://www.mdpi.com/2073-4395/3/1/59 There is increasing concern about the sustainability and environmental impacts of mineral fertilizer use in agriculture. Increased recycling of nutrients via the use of animal and green manures and fertilizers made from domestic organic waste may reduce reliance on mineral fertilizers. However, the relative availability of nutrients (especially nitrogen) is lower in organic compared to mineral fertilizers, which can result in significantly lower yields in nutrient demanding crops such as potato. It is therefore important to gain a better understanding of the factors affecting nutrient use efficiency (yield per unit fertilizer input) from organic fertilizers. Here we show that (a) previous crop management (organic vs. conventional fertilization and crop protection regimes), (b) organic fertilizer type and rate (composted cattle manure vs. composted chicken manure pellets) and (c) watering regimes (optimized and restricted) significantly affected leaf chlorophyll content, potato tuber N-concentration, proteome and yield. Protein inference by gel matching indicated several functional groups significantly affected by previous crop management and organic fertilizer type and rate, including stress/defense response, glycolysis and protein destination and storage. These results indicate genomic pathways controlling crop responses (nutrient use efficiency and yield) according to contrasting types and rates of organic fertilizers that can be linked to the respective encoding genes. Agronomy 2013-01-15 3 1 Article 10.3390/agronomy3010059 59 85 2073-4395 2013-01-15 doi: 10.3390/agronomy3010059 Catherine Tétard-Jones Martin Edwards Leonidas Rempelos Angharad Gatehouse Mick Eyre Stephen Wilcockson Carlo Leifert http://www.mdpi.com/2073-4395/3/1/43 Appropriate organic amendment management is essential in potato production to increase soil productivity and potato (Solanum tuberosum L.) quality. The objectives of this two-year field study (2004–2005) were to evaluate the effects of organic amendment applications with or without mineral N fertilizer addition on potato yield, N uptake, N use efficiency (NUE), and on disease incidence. The experimental design was a split-plot, which included nine treatments with four different organic amendments applied in fall 2003 or in spring 2004 at a rate of 40 Mg ha−1 (wet basis) and an unamended control in main plots, and N fertilizer rates (0 and 90 kg N ha−1) in sub-plots. Organic amendments consisted of fresh cattle manure (FCM), composted cattle manure (CCM), paper mill sludge with C/N ratio <15 (PMS1) and paper mill sludge with C/N >15 (PMS2) applied alone (0 kg N ha−1) or supplemented with mineral fertilizer at a rate 90 kg N ha−1. The N fertilizer rate in the unamended control consisted of 0 and 150 kg N ha−1. No organic amendments were applied in 2005 to evaluate residual effects. Fall and spring applications of FCM, CCM and PMS alone significantly increased N uptake and potato marketable yields by 2.5 to 16.4 Mg ha−1, compared to the unfertilized control. Combining organic amendments with N fertilizer at 90 kg N ha−1 increased potato yields, N uptake, and specific gravity, which were comparable to those obtained in mineral N fertilizer treatments (150 kg N ha−1). Residual effects of organic amendments alone had no significant effects on potato yields or on N uptake compared to the unfertilized control. Potato NUE for FCM, CCM and PMS ranged from 6% to 25% in the first year and from 2% to 8% in the residual year. The NUE values were higher for PMS with lower C/N ratio compared to FCM and CCM. This study did not show any difference between organic amendment applied in spring or fall on potato yield and quality. It was also demonstrated that mineral N fertilizer needed to be combined with organic amendments to sustain potato yield and N nutrition. This study showed that appropriate organic amendment management could increase potato yield and quality and reduce N fertilizer requirement. Agronomy 2013-01-15 3 1 Article 10.3390/agronomy3010043 43 58 2073-4395 2013-01-15 doi: 10.3390/agronomy3010043 Adrien N'Dayegamiye Judith Nyiraneza Marcel Giroux Michèle Grenier Anne Drapeau http://www.mdpi.com/2073-4395/3/1/28 A three year field experiment was conducted to evaluate the role of soil inversion, cover crops and spring tillage methods for Palmer amaranth between-row (BR) and within-row (WR) management in glufosinate-resistant cotton. Main plots were two soil inversion treatments: fall inversion tillage (IT) and non-inversion tillage (NIT). Subplots were three cover treatments: crimson clover, cereal rye or none (i.e., winter fallow); and the sub subplots were four secondary spring tillage methods: disking followed by (fb) cultivator (DCU), disking fb chisel plow (DCH), disking fb disking (DD) and no tillage (NT). Averaged over years and soil inversion, the crimson clover produced maximum cover biomass (4390 kg ha−1) fb cereal rye (3698 kg ha−1) and winter fallow (777 kg ha−1). Two weeks after planting (WAP) and before the postemergence (POST) application, Palmer amaranth WR and BR density were two- and four-times less, respectively, in IT than NIT. Further, Palmer amaranth WR and BR density were reduced two-fold following crimson clover and cereal rye than following winter fallow at 2 WAP. Without IT, early season Palmer amaranth densities were 40% less following DCU, DCH and DD, when compared with IT. Following IT, no spring tillage method improved Palmer amaranth control. The timely application of glufosinate + S-metolachlor POST tank mixture greatly improved Palmer amaranth control in both IT and NIT systems. The highest cotton yields were obtained with DD following cereal rye (2251 kg ha−1), DD following crimson clover (2213 kg ha−1) and DD following winter fallow (2153 kg ha−1). On average, IT cotton yields (2133 kg ha−1) were 21% higher than NIT (1766 kg ha−1). Therefore, from an integrated weed management standpoint, an occasional fall IT could greatly reduce Palmer amaranth emergence on farms highly infested with glyphosate-resistant Palmer amaranth. In addition, a cereal rye or crimson clover cover crop can effectively reduce early season Palmer amaranth emergence in both IT and NIT systems. For effective and season-long control of Palmer amaranth, one or more POST applications of glufosinate + residual herbicide as tank mixture may be needed in a glufosinate-based cotton production system. Agronomy 2013-01-15 3 1 Article 10.3390/agronomy3010028 28 42 2073-4395 2013-01-15 doi: 10.3390/agronomy3010028 Jatinder Aulakh Andrew Price Stephen Enloe Glenn Wehtje Michael Patterson http://www.mdpi.com/2073-4395/3/1/13 In this work, we evaluate the role of agronomic factors in the selection for herbicide resistance in Apera spica-venti L. Beauv. (silky windgrass). During a period of three years, populations were collected in more than 250 conventional fields across Europe and tested for resistance in the greenhouse. After recording the field history of locations, a geo-referenced database has been developed to map the distribution of herbicide-resistant A. spica-venti populations in Europe. A Logistic Regression Model was used to assess whether and to what extent agricultural and biological factors (crop rotation, soil tillage, sowing date, soil texture and weed density) affect the probability of resistance selection apart from the selection pressure due to herbicide application. Our results revealed that rotation management and soil tillage are the factors that have the greatest influence on the model. In addition, first order interactions between these two variables were highly significant. Under conventional tillage, a percentage of winter crops in the rotation exceeding 75% resulted in a 1280-times higher risk of resistance selection compared to rotations with less than 50% of winter crops. Under conservation tillage, the adoption of >75% of winter crops increased the risk of resistance 13-times compared to rotations with less than 50% of winter crops. Finally, early sowing and high weed density significantly increased the risk of resistance compared to the reference categories (later sowing and low weed density, respectively). Soil texture had no significant influence. The developed model can find application in management programs aimed at preventing the evolution and spread of herbicide resistance in weed populations. Agronomy 2013-01-04 3 1 Article 10.3390/agronomy3010013 13 27 2073-4395 2013-01-04 doi: 10.3390/agronomy3010013 Dario Massa Yasmin Kaiser Dionisio Andújar-Sánchez Rocío Carmona-Alférez Jörg Mehrtens Roland Gerhards http://www.mdpi.com/2073-4395/3/1/1 High seed cost accompanied by poor germination and seedling performance renders cabbage nursery and field production enterprises unsustainable to many small-scale growers in tropical and sub-tropical countries. In most nurseries, adverse ecological conditions and pest damage are among the major factors responsible for poor seedling performance. The objective of this study was to test the potential use of eco-friendly net (EFN) covers as a low cost technology for sustainable cabbage seedling production. The study was a two-season experiment conducted using a randomized complete block design with five replications and two treatments. Treatments were: the standard open field transplant production (control) and transplant production under 0.4 mm mesh polyethylene net covering. EFN covering increased both temperature and relative humidity, enhanced seedling growth and reduced insect pest damage. Seed germination and seedling emergence were under the net covering earlier. Higher seed germination and seedling survival were recorded under the EFN treatment, indicating a potential for reducing the seed requirement per unit area of cabbage production. Seedlings grown under the nets had higher stomatal conductance and leaf chlorophyll content; furthermore, they grew taller, with more leaves within a shorter period of time compared to the control seedlings. The use of EFN in cabbage nurseries offers a sustainable technology for enhancing seedling performance by reducing pest infestation, thereby lowering production cost and improving the grower’s income. Agronomy 2012-12-24 3 1 Article 10.3390/agronomy3010001 1 12 2073-4395 2012-12-24 doi: 10.3390/agronomy3010001 Everlyne Muleke Mwanarusi Saidi Francis Itulya Thibaud Martin Mathieu Ngouajio http://www.mdpi.com/2073-4395/2/4/371 The introduction in Italy of Clearfield® rice cultivars carrying imidazolinone-resistant traits provides an efficient option to control red rice, a conspecific weed of cultivated rice. However, despite the promulgation of specific guidelines for Clearfield® technology management, imazamox red rice survivors have been reported by farmers. Forty-two fields were monitored in 2010 and 2011 throughout the Piedmont and Lombardy regions and field cases were recorded of herbicides use and agronomic practices. Whole-plant sensitivity to imazamox was assessed and the resistance mechanism was determined by molecular analysis. Twenty-six red rice populations out of 42 were imazamox-resistant and plants of all the resistant populations possess a Ser to Asn substitution at locus 653 of the ALS gene determining the target-site resistance. Farmers frequently grow Clearfield® varieties for more than two consecutive years so increasing the selection pressure exerted by imazamox and favoring the evolution of resistant red rice. To maintain the sustainability of this new technology, a proper management based on crop rotation, utilization of certified seeds and strict control of red rice escapes has to be implemented. More generally, all stakeholders must increase their awareness that the selection pressure exerted by ALS inhibitors in rice cropping system should be reduced. Agronomy 2012-12-19 2 4 Article 10.3390/agronomy2040371 371 383 2073-4395 2012-12-19 doi: 10.3390/agronomy2040371 Laura Scarabel Cesare Cenghialta Dario Manuello Maurizio Sattin http://www.mdpi.com/2073-4395/2/4/358 Greenhouse and field studies were conducted in 2007 and 2008 to investigate possible multiple-resistance of horseweed to paraquat and glyphosate, and to evaluate the effect of the addition of metribuzin to paraquat on control of paraquat-resistant horseweed. Results indicated that the GR50 (herbicide dose required to cause a 50% reduction in plant growth) value for the susceptible population S102 was 0.066 kg ae/ha glyphosate, and for the resistant population MDOT was 0.78 kg/ha glyphosate. The level of glyphosate resistance for MDOT was 12-fold compared with S102. The GR50 value for the susceptible population S102 was 0.078 kg ai/ha paraquat, and for the resistant population MDOT was 0.67 kg/ha paraquat. The level of paraquat resistance for MDOT was 9-fold compared to S102, suggesting multiple-resistance to glyphosate and paraquat in the MDOT population. In field studies the addition of metribuzin to paraquat improved horseweed control. Agronomy 2012-12-19 2 4 Article 10.3390/agronomy2040358 358 370 2073-4395 2012-12-19 doi: 10.3390/agronomy2040358 Thomas Eubank Vijay Nandula Daniel Poston David Shaw http://www.mdpi.com/2073-4395/2/4/321 Through the development of superior plant varieties that benefit from high agrochemical inputs and irrigation, the agricultural Green Revolution has doubled crop yields, yet introduced unintended impacts on environment. An expected 50% growth in world population during the 21st century demands novel integration of advanced technologies and low-input production systems based on soil and plant biology, targeting precision delivery of inputs synchronized with growth stages of crop plants. Further, successful systems will integrate subsurface water, air and nutrient delivery, real-time soil parameter data and computer-based decision-making to mitigate plant stress and actively manipulate microbial rhizosphere communities that stimulate productivity. Such an approach will ensure food security and mitigate impacts of climate change. Agronomy 2012-12-18 2 4 Review 10.3390/agronomy2040321 321 357 2073-4395 2012-12-18 doi: 10.3390/agronomy2040321 Jonathan Weekley Joseph Gabbard Jerzy Nowak http://www.mdpi.com/2073-4395/2/4/312 Establishing bare-root transplants in Florida, United States, is an inefficient water-consuming activity. Between 3500 and 5500 m3/ha are applied with sprinkler irrigation to lower temperatures around the transplant crown and aid early root development, but more than 97% of the water volume runs off the polyethylene-covered beds. Research has been conducted to evaluate the feasibility of producing containerized (plug) short-day cultivar transplants under Florida conditions, the effect of continuous and intermittent low-volume sprinklers on transplant establishment and the use of kaolin clay to reduce stress on young transplants. Research results demonstrated that growers may have alternatives to reduce water use and pumping costs during strawberry transplant establishment by the following: (a) plug transplants can be produced from mother plants from Florida’s subtropical weather without chilling conditioning and still be competitive in the winter market; (b) using continuous and intermittent low-volume sprinkler irrigation saves between 16% and 33% of the water volumes for strawberry establishment; and (c) using kaolin clay showed to be a low-cost (US$63/ha plus application costs) investment to reduce irrigation volumes by at least 30%. Agronomy 2012-12-06 2 4 Communication 10.3390/agronomy2040312 312 320 2073-4395 2012-12-06 doi: 10.3390/agronomy2040312 Bielinski Santos Craig Stanley Alicia Whidden Teresa Salame-Donoso Vance Whitaker Ixchel Hernandez-Ochoa Pei-Wen Huang Emmanuel Torres-Quezada http://www.mdpi.com/2073-4395/2/4/295 A three year field experiment was conducted to evaluate the role of soil-inversion, cover crops and herbicide regimes for Palmer amaranth between-row (BR) and within-row (WR) management in glufosinate-resistant cotton. The main plots were two soil-inversion treatments: fall inversion tillage (IT) and non-inversion tillage (NIT). The subplots were three cover crop treatments: crimson clover, cereal rye and winter fallow; and sub subplots were four herbicide regimes: preemergence (PRE) alone, postemergence (POST) alone, PRE + POST and a no herbicide check (None). The PRE herbicide regime consisted of a single application of pendimethalin at 0.84 kg ae ha−1 plus fomesafen at 0.28 kg ai ha−1. The POST herbicide regime consisted of a single application of glufosinate at 0.60 kg ai ha−1 plus S-metolachlor at 0.54 kg ai ha−1 and the PRE + POST regime combined the prior two components. At 2 weeks after planting (WAP) cotton, Palmer amaranth densities, both BR and WR, were reduced ≥90% following all cover crop treatments in the IT. In the NIT, crimson clover reduced Palmer amaranth densities >65% and 50% compared to winter fallow and cereal rye covers, respectively. At 6 WAP, the PRE and PRE + POST herbicide regimes in both IT and NIT reduced BR and WR Palmer amaranth densities >96% over the three years. Additionally, the BR density was reduced ≥59% in no-herbicide (None) following either cereal rye or crimson clover when compared to no-herbicide in the winter fallow. In IT, PRE, POST and PRE + POST herbicide regimes controlled Palmer amaranth >95% 6 WAP. In NIT, Palmer amaranth was controlled ≥79% in PRE and ≥95% in PRE + POST herbicide regimes over three years. POST herbicide regime following NIT was not very consistent. Averaged across three years, Palmer amaranth controlled ≥94% in PRE and PRE + POST herbicide regimes regardless of cover crop. Herbicide regime effect on cotton yield was highly significant; the maximum cotton yield was produced by the PRE + POST herbicide regime. Averaged over three years, the PRE, POST and PRE + POST cotton yields were about three times higher than no herbicide regime. In a conservation tillage production system, a PRE + glufosinate POST herbicide based regime coupled with a cereal rye cover crop may effectively control Palmer amaranth and maximize cotton yields. Agronomy 2012-11-05 2 4 Article 10.3390/agronomy2040295 295 311 2073-4395 2012-11-05 doi: 10.3390/agronomy2040295 Jatinder Aulakh Andrew Price Stephen Enloe Edzard Santen Glenn Wehtje Michael Patterson http://www.mdpi.com/2073-4395/2/4/284 Controlling black-grass in winter wheat production in northern Europe is an increasing problem because of more frequent winter crops and development of herbicide resistance in weeds. Alternative weed management strategies are needed, e.g., use of more competitive cultivars. Factors that increase cultivar competitiveness include early vigor and straw length, but also allelopathy. Therefore, the allelopathic properties of wheat cultivars included in the Swedish national list or in the release pipeline were investigated using a bioassay with herbicide-resistant and herbicide-sensitive black-grass as receiver plants. Wheat-rye translocation lines were also included in this screening to identify possible sources of high allelopathic activity. The bioassay results were followed up in two-year field trials. The results revealed large variations in allelopathic activity between cultivars. Most cultivars showed interference with both herbicide-sensitive and herbicide-resistant black-grass, although the allelopathic effect was lower on the herbicide-resistant biotype. Cultivars with high allelopathic activity gave only half the black-grass biomass of low allelopathic cultivars. Dinaro, a triticale (wheat-rye hybrid) cultivar and the new wheat cultivar Nimbus showed the highest allelopathy and inhibition of black-grass growth. Only a few wheat lines with rye chromatin, all or part of a rye chromosome, showed high allelopathy. Use of cultivars with high allelopathic activity can thus be important in integrated weed management of black-grass. Agronomy 2012-10-18 2 4 Article 10.3390/agronomy2040284 284 294 2073-4395 2012-10-18 doi: 10.3390/agronomy2040284 Nils-Ove Bertholdsson http://www.mdpi.com/2073-4395/2/4/240 The Green Revolution has enabled Asian countries to boost their crop production enormously. However, Africa has not benefitted from this agricultural revolution since it did not consider local, but important crops grown in the continent. In addition to their versatile adaptation to extreme environmental conditions, African indigenous crops provide income for subsistence farmers and serve as staple food for the vast majority of low-income consumers. These crops, which are composed of cereals, legumes, vegetables and root crops, are commonly known as underutilized or orphan crops. Recently, some of these under-researched crops have received the attention of the national and international research community, and modern improvement techniques including diverse genetic and genomic tools have been applied in order to boost their productivity. The major bottlenecks affecting the productivity of these crops are unimproved genetic traits such as low yield and poor nutritional status and environmental factors such as drought, weeds and pests. Hence, an agricultural revolution is needed to increase food production of these under-researched crops in order to feed the ever-increasing population in Africa. Here, we present both the benefits and drawbacks of major African crops, the efforts being made to improve them, and suggestions for some future directions. Agronomy 2012-10-16 2 4 Review 10.3390/agronomy2040240 240 283 2073-4395 2012-10-16 doi: 10.3390/agronomy2040240 Zerihun Tadele Kebebew Assefa http://www.mdpi.com/2073-4395/2/3/222 The 40 million hectare southern Australian winter cropping region suffers from widespread infestation by Lolium rigidum (commonly known as annual or rigid ryegrass), a Mediterranean species initially introduced as a pasture plant. Along with its high competitiveness within crops, rapid adaptability and widespread resistance to herbicides, the dormancy of its seeds means that L. rigidum is the primary weed in southern Australian agriculture. With the individuals within a L. rigidum population exhibiting varying levels of seed dormancy, germination can be staggered across the crop-growing season, making complete weed removal virtually impossible, and ensuring that the weed seed bank is constantly replenished. By understanding the processes involved in induction and release of dormancy in L. rigidum seeds, it may be possible to develop strategies to more effectively manage this pest without further stretching herbicide resources. This review examines L. rigidum seed dormancy and germination from a weed-management perspective and explains how the seed bank can be depleted by control strategies encompassing all stages in the lifecycle of a seed, from development to germination. Agronomy 2012-09-24 2 3 Article 10.3390/agronomy2030222 222 239 2073-4395 2012-09-24 doi: 10.3390/agronomy2030222 Danica E. Goggin Stephen B. Powles Kathryn J. Steadman http://www.mdpi.com/2073-4395/2/3/199 The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early maturity helps in escaping terminal drought and heat stresses and the adaptation of chickpea to short-season environments. Ascochyta blight continues to be a major challenge to chickpea productivity in areas where chickpea is exposed to cool and wet conditions. Limited variability for pod borer resistance has been a major bottleneck in the development of pod borer resistant cultivars. The use of genomics technologies in chickpea breeding programs has been limited, since available genomic resources were not adequate and limited polymorphism was observed in the cultivated chickpea for the available molecular markers. Remarkable progress has been made in the development of genetic and genomic resources in recent years and integration of genomic technologies in chickpea breeding has now started. Marker-assisted breeding is currently being used for improving drought tolerance and combining resistance to diseases. The integration of genomic technologies is expected to improve the precision and efficiency of chickpea breeding in the development of improved cultivars with enhanced resistance to abiotic and biotic stresses, better adaptation to existing and evolving agro-ecologies and traits preferred by farmers, industries and consumers. Agronomy 2012-08-23 2 3 Review 10.3390/agronomy2030199 199 221 2073-4395 2012-08-23 doi: 10.3390/agronomy2030199 Pooran M. Gaur Aravind K. Jukanti Rajeev K. Varshney http://www.mdpi.com/2073-4395/2/3/187 Problems arising from conventional tillage (CT) systems (such as soil erosion, decrease of organic matter, environmental damage etc.) have led many farmers to the adoption of no-till (NT) systems that are more effective in improving soil physical, chemical and microbial properties. Results from this study clearly indicated that NT, mulch tillage (MT), and winter rye cover cropping systems increased the activity of phosphatase, β-glucosidase and arylsulfatase at a 0–10 cm soil depth but decreased the activity of these enzymes at 10–20 cm. The increase in enzyme activity was a good indicator of intensive soil microbial activity in different soil management practices. Poultry litter (PL) application under NT, MT, and rye cropping system could be considered as effective management practices due to the improvement in carbon (C) content and the biochemical quality at the soil surface. The activities of the studied enzymes were highly correlated with soil total nitrogen (STN) soil organic carbon (SOC) at the 0–10 cm soil depth, except for acid phosphatase where no correlation was observed. This study revealed that agricultural practices such as tillage, PL, and cover crop cropping system have a noticeable positive effect on soil biochemical activities under cotton production. Agronomy 2012-07-25 2 3 Article 10.3390/agronomy2030187 187 198 2073-4395 2012-07-25 doi: 10.3390/agronomy2030187 Regine Mankolo Chandra Reddy Zachary Senwo Ermson Nyakatawa Seshadri Sajjala http://www.mdpi.com/2073-4395/2/3/167 A laboratory microcosm incubation was conducted to study the influence of mixed cowpea-maize residues on N2O emission and N mineralization in a tropical acrisol. The soils were incorporated with different ratios of cowpea:maize mixtures on weight basis: 100:0, 75:25, 50:50, 25:75 and 0:100, and a control treatment in which there was no residue incorporation. The results show that N2O and CO2 emissions were higher in the sole cowpea treatment (100:0) than the sole maize treatment (0:100) and the control. However, cowpea-maize residue mixtures increased the proportion of N lost as N2O compared to the sole treatments. This interactive effect was highest in the 75:25 treatment. The 50:50 treatment showed moderate N2O emission compared to the 100:0, 75:25 and 25:75 treatments but with corresponding steady N mineralization and appreciable mineral N concentration. It is concluded that mixing cowpea-maize residues might increase the proportion of N lost as N2O in a tropical acrisol. However, compared to the other residue mixture treatments, mixing cowpea-maize residues in equal proportions on weight basis might offer a path to reducing N2O emissions while maintaining a steady N mineralization without risking good N supply in acrisols. The study therefore offers potential for mitigating greenhouse gas emissions while maintaining soil fertility in tropical acrisols. However, further studies under both laboratory and field conditions will be required to verify and validate this claim. Agronomy 2012-07-10 2 3 Article 10.3390/agronomy2030167 167 186 2073-4395 2012-07-10 doi: 10.3390/agronomy2030167 Kwame A. Frimpong David O. Yawson Kofi Agyarko Elizabeth M. Baggs http://www.mdpi.com/2073-4395/2/3/132 Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly suitable for faba bean. However, traditional breeding methods such as recurrent mass selection have been established in faba bean and used successfully in breeding for resistance to diseases. Molecular breeding strategies that integrate the latest innovations in genetics and genomics with traditional breeding strategies have many potential applications for future faba bean cultivar development. Hence, considerable efforts have been undertaken in identifying molecular markers, enriching genetic and genomic resources using high-throughput sequencing technologies and improving genetic transformation techniques in faba bean. However, the impact of research on practical faba bean breeding and cultivar release to farmers has been limited due to disconnects between research and breeding objectives and the high costs of research and implementation. The situation with faba bean is similar to other small crops and highlights the need for coordinated, collaborative research programs that interact closely with commercially focused breeding programs to ensure that technologies are implemented effectively. Agronomy 2012-07-04 2 3 Review 10.3390/agronomy2030132 132 166 2073-4395 2012-07-04 doi: 10.3390/agronomy2030132 Annathurai Gnanasambandam Jeff Paull Ana Torres Sukhjiwan Kaur Tony Leonforte Haobing Li Xuxiao Zong Tao Yang Michael Materne http://www.mdpi.com/2073-4395/2/2/116 Clovers (genus Trifolium) are a large and widespread genus of legumes. A number of clovers are of agricultural importance as forage crops in grassland agriculture, particularly temperate areas. White clover (Trifolium repens L.) is used in grazed pasture and red clover (T. pratense L.) is widely cut and conserved as a winter feed. For the diploid red clover, genetic and genomic tools and resources have developed rapidly over the last five years including genetic and physical maps, BAC (bacterial artificial chromosome) end sequence and transcriptome sequence information. This has paved the way for the use of genome wide selection and high throughput phenotyping in germplasm development. For the allotetraploid white clover progress has been slower although marker assisted selection is in use and relatively robust genetic maps and QTL (quantitative trait locus) information now exist. For both species the sequencing of the model legume Medicago truncatula gene space is an important development to aid genomic, biological and evolutionary studies. The first genetic maps of another species, subterranean clover (Trifolium subterraneum L.) have also been published and its comparative genomics with red clover and M. truncatula conducted. Next generation sequencing brings the potential to revolutionize clover genomics, but international consortia and effective use of germplasm, novel population structures and phenomics will be required to carry out effective translation into breeding. Another avenue for clover genomic and genetic improvement is interspecific hybridization. This approach has considerable potential with regard to crop improvement but also opens windows of opportunity for studies of biological and evolutionary processes. Agronomy 2012-05-09 2 2 Review 10.3390/agronomy2020116 116 131 2073-4395 2012-05-09 doi: 10.3390/agronomy2020116 Adriana Ravagnani Michael T. Abberton Leif Skøt http://www.mdpi.com/2073-4395/2/2/74 Pea (Pisum sativum L.) was the original model organism used in Mendel’s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS) programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput ‘omics’ methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems. Agronomy 2012-04-04 2 2 Review 10.3390/agronomy2020074 74 115 2073-4395 2012-04-04 doi: 10.3390/agronomy2020074 Petr Smýkal Gregoire Aubert Judith Burstin Clarice J. Coyne Noel T. H. Ellis Andrew J. Flavell Rebecca Ford Miroslav Hýbl Jiří Macas Pavel Neumann Kevin E. McPhee Robert J. Redden Diego Rubiales Jim L. Weller Tom D. Warkentin http://www.mdpi.com/2073-4395/2/1/62 Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range from large generic databases which hold specific data types for a broad range of species, to carefully integrated and curated databases which act as a resource for the improvement of specific crops. In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome databases. Agronomy 2012-03-20 2 1 Review 10.3390/agronomy2010062 62 73 2073-4395 2012-03-20 doi: 10.3390/agronomy2010062 Kaitao Lai Michał T. Lorenc David Edwards http://www.mdpi.com/2073-4395/2/1/40 Alfalfa (Medicago sativa L.), a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL) related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP) in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1) diversity selection and paternity testing, (2) introgression of QTL and (3) genomic selection. Agronomy 2012-03-15 2 1 Review 10.3390/agronomy2010040 40 61 2073-4395 2012-03-15 doi: 10.3390/agronomy2010040 Xuehui Li E. Charles Brummer http://www.mdpi.com/2073-4395/2/1/28 Aflatoxin contamination of maize grain threatens human food and animal feed safety. Breeding for reduced grain aflatoxin accumulation is one of the best strategies presently available to lower grain aflatoxin accumulation. Previously identified sources of germplasm with reduced grain aflatoxin accumulation are excessively tall and late maturing. The objective of this research was to screen germplasm and identify potential sources of aflatoxin resistance. KO679Y and CUBA117:S15-101-001-B-B-B-B inbreds were evaluated for aflatoxin accumulation alongside resistant and susceptible checks with both performing well. These two lines were also evaluated in various crosses. KO679Y performed especially well in crosses with Mp494 and Mp717, resulting in low ear rot and very low aflatoxin levels, but not well in other crosses. A breeding cross including CUBA117:S15-101-001-B-B-B-B as a parent accumulated low levels of aflatoxin both years it was evaluated. Lines resulting from these crosses are being advanced for further evaluation and improvement. KO679Y and CUBA117:S15-101-001-B-B-B-B may prove useful for breeders seeking germplasm sources for ear rot and mycotoxin reduction, especially KO679Y which matures a week earlier and is approximately 25% shorter than current lines resistant to grain aflatoxin accumulation. Agronomy 2012-03-14 2 1 Article 10.3390/agronomy2010028 28 39 2073-4395 2012-03-14 doi: 10.3390/agronomy2010028 W. Brien Henry Gary L. Windham Michael H. Blanco http://www.mdpi.com/2073-4395/2/1/14 Improving understanding and prediction of the potato (Solanum tuberosum) tuber size over the growing season is important due to its effects on crop price and marketing. Several models have been proposed to describe potato growth and development, but are based on short-term data and have little use for predicting yields or in-season management decisions. This analysis uses long-term data collected from 1979 to 1993 in central Wisconsin to describe growth and development of the Russet Burbank potato variety. This paper describes average number of potato tubers per plant and tuber length as influenced by thermal time and stem number per plant over 14 years. For each plant variable, data analysis uses multivariate techniques to fit a hierarchical logistic model with parameters potentially depending on stem number per plant. Analysis finds that the average number of potato tubers and average tuber length were affected by thermal time and stem number per plant. Estimated models are biologically relevant, provide an understanding of seasonal thermal variability and stem number per plant effects on average tuber set and growth, and can be used to describe yearly variation in average potato growth and development. Increased understanding of potato growth in response to thermal time and stem number per plant can improve management recommendations and predictions of crop economic value. Agronomy 2012-03-14 2 1 Article 10.3390/agronomy2010014 14 27 2073-4395 2012-03-14 doi: 10.3390/agronomy2010014 Nicholas J. Goeser Paul D. Mitchell Paul D. Esker David Curwen Gavin Weis Alvin J. Bussan http://www.mdpi.com/2073-4395/2/1/1 The effects of five rates of nitrogen fertiliser applications on the performance of the cereal aphid Metopolophium dirhodum on winter wheat, within the range of rates recommended for UK crops, were investigated over two seasons in field-grown crops and also on plants grown in the glasshouse. Longevity was unaffected by the level of fertilisation, but aphid intrinsic rate of increase and fecundity increased with each level applied. In the second field season, when a higher upper limit was used, many of these increases were significant. A previously unreported finding for this species was that there was a significant decrease in fecundity for the highest rate of fertilisation. Results for the glasshouse-reared aphids followed a similar pattern to those in the field, and overall they underline recent reports in the literature of the negative effects of high nutrient concentrations on the performance of herbivorous insects. The underlying reasons for these are discussed. Agronomy 2012-02-09 2 1 Article 10.3390/agronomy2010001 1 13 2073-4395 2012-02-09 doi: 10.3390/agronomy2010001 Alan F. J. Gash http://www.mdpi.com/2073-4395/1/1/3 Peanut (Arachis hypogaea L.) has lagged other crops on use of molecular genetic technology for cultivar development in part due to lack of investment, but also because of low levels of molecular polymorphism among cultivated varieties. Recent advances in molecular genetic technology have allowed researchers to more precisely measure genetic polymorphism and enabled the development of low density genetic maps for A. hypogaea and the identification of molecular marker or QTL’s for several economically significant traits. Genomic research has also been used to enhance the amount of genetic diversity available for use in conventional breeding through the development of transgenic peanut, and the creation of TILLING populations and synthetic allotetraploids. Marker assisted selection (MAS) is becoming more common in peanut cultivar development programs, and several cultivar releases are anticipated in the near future. There are also plans to sequence the peanut genome in the near future which should result in the development of additional molecular tools that will greatly advance peanut cultivar development. Agronomy 2011-12-20 1 1 Article 10.3390/agronomy1010003 3 17 2073-4395 2011-12-20 doi: 10.3390/agronomy1010003 C. Corley Holbrook Peggy Ozias-Akins Ye Chu Baozhu Guo http://www.mdpi.com/2073-4395/1/1/1 Agronomy is a highly multidisciplinary area of science. It includes all aspects of science and technology related to the production and utilization of plants for food, feed, fuel, fiber and even land reclamation. In many respects, agronomy represents the integration of activities and disciplines ranging from genetics, chemistry and biotechnology to ecology, soil science and meteorology. [...] Agronomy 2011-01-21 1 1 Editorial 10.3390/agronomy1010001 1 2 2073-4395 2011-01-21 doi: 10.3390/agronomy1010001 Peter Langridge